Program : MOLEMAN2
Version : 070913
Author : Gerard J. Kleywegt, Dept. of Cell and Molecular Biology,
Uppsala University, Biomedical Centre, Box 596,
SE-751 24 Uppsala, SWEDEN
E-mail : gerard@xray.bmc.uu.se
Purpose : manipulation and analysis of PDB files
Package : X-UTIL
Reference(s) for this program:
* 1 * G.J. Kleywegt (1995). Dictionaries for Heteros. CCP4/ESF-EACBM Newsletter on Protein Crystallography 31, June 1995, pp. 45-50. [http://xray.bmc.uu.se/usf/factory_5.html]
* 2 * G.J. Kleywegt (1996). Making the most of your search model. CCP4/ESF-EACBM Newsletter on Protein Crystallography 32, June 1996, pp. 32-36. [http://xray.bmc.uu.se/usf/factory_6.html]
* 3 * G.J. Kleywegt & T.A. Jones (1996). Phi/Psi-chology: Ramachandran revisited. Structure 4, 1395-1400. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=8994966&dopt=Citation]
* 4 * G.J. Kleywegt & T.A. Jones (1997). Model-building and refinement practice. Methods in Enzymology 277, 208-230. [http://xray.bmc.uu.se/gerard/gmrp/gmrp.html]
* 5 * G.J. Kleywegt (1997). Validation of protein models from CA coordinates alone. J Mol Biol 273, 371-376. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=9344745&dopt=Citation]
* 6 * G.J. Kleywegt (1999). Experimental assessment of differences between related protein crystal structures. Acta Cryst. D55, 1878-1857. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=10531486&dopt=Citation] [http://scripts.iucr.org/cgi-bin/paper?se0283]
* 7 * G.J. Kleywegt (2000). Validation of protein crystal structures. Acta Cryst. D56, 249-265 (Topical Review). [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=10713511&dopt=Citation] [http://scripts.iucr.org/cgi-bin/paper?gr0949]
* 8 * G.J. Kleywegt (2001). Validation of protein crystal structures. In: "International Tables for Crystallography, Volume F. Crystallography of Biological Macromolecules" (Rossmann, M.G. & Arnold, E., Editors). Chapter 21.1, pp. 497-506, 526-528. Dordrecht: Kluwer Academic Publishers, The Netherlands.
* 9 * G.J. Kleywegt & T.A. Jones (2002). Homo Crystallographicus - Quo Vadis ? Structure 10, 465-472. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=11937051&dopt=Citation]
* 10 * G.J. Kleywegt, M.R. Harris, J.Y. Zou, T.C. Taylor, A. Wahlby & T.A. Jones (2004). The Uppsala Electron Density Server. Submitted.
* 11 * G.J. Kleywegt (2004). Quality control and validation. In "Crystallographic Methods", S. Doublie, Ed. Submitted.
* 12 * Kleywegt, G.J., Zou, J.Y., Kjeldgaard, M. & Jones, T.A. (2001). Around O. In: "International Tables for Crystallography, Vol. F. Crystallography of Biological Macromolecules" (Rossmann, M.G. & Arnold, E., Editors). Chapter 17.1, pp. 353-356, 366-367. Dordrecht: Kluwer Academic Publishers, The Netherlands.
951107 - 0.1 - initial programming
951108 - 0.2 - more (REad and APpend commands)
960216 - 0.3 - more (some BF and OC commands; implemented main/side;
SElections; first documentation)
960217 - 0.4 - WRite command; PDb CRystal/HEtero; PRotein MC_analysis
960222 - 0.5 - PRotein SC_analysis
960223 - 0.6 - PRotein CA_analysis; COnstant; BF BOnded; BF SMooth;
STatistics; more SElect ANd/OR options; some XYz commands
960226 - 0.7 - more XYz commands; BF/OC PRod_plus; first CHain commands
960227 - 0.8 - SPlit command; more CHain commands; more PDb commands
960301 - 0.9 - SElect NUmeric; LIst_selected; ONo RSr/FIt/COnnect/TOrsion
960303 - 0.10 - implemented macro facility; split PDb REmark command
into three separate ones (LIst, DElete, REmark); changed
some parameters from optional to required to make them
useful for macros (e.g., XYz ROtate/TRanslate); ONo
DIsulfide and ONo WAter_fit
960304 - 0.11 - ONo OOps; DIstance PLot, DIstribution, SHort, SElect;
GEometry_selected; first useful version for Uppsala
960311 - 0.12 - PDb NAme/NUmber; ONo XPlor_hydrogens; SQuence LIst/PIr;
SQuence GLyco_sites/MOtif
960405 - 0.13 - minor bug fixes; MUlti_geom
960408 - 0.14 - XYz CEntre_origin and XYz ALign_inertia_axes; first
general release
960410 - 0.15 - add END card at end of PDB file (oops ...)
960411 - 0.16 - debug generate.inp file for X-PLOR with SPlit command;
debug write CCP4 format (include cryst1 etc. cards)
960412 - 0.17 - implemented LS_plane and ONo LS_plane_odl; SQuence
COunt, EXtinction_280; added optional parameter to
the "?" command which may be the name of any command
that has sub-commands; DELETE_molecule command;
AUto SPink, BOnes
960414 - 0.18 - AUto SSe; lot of debugging in the core AUto subroutine
to fix instabilities -> the new algorithm appears to
be stable (and no longer has a random component ;-)
960415 - 0.19 - minor bug fixes
960416 - 0.20 - minor bug fixes
960513 - 0.21 - correct naming of OT1/OT2 with SPlit command; includes
automatic generation of OT2 if necessary !
960517 - 0.22 - implemented simple SYMBOL mechanism (& command)
960520 - 0.23 - check for atoms which have X~Y~Z when reading a PDB
file (and in the BOok_keep command); new PDb command
CHemical+charge to add the symbol of the chemical
element and the charge to columns 77-80 of the ATOM and
HETATM records
960521 - 1.0 - added optional "use_masses" parameter to the XYz
CEntre_origin command; this version stable and useful
enough for goverment work
960629 - 1.0.1 - several small bug fixes made while at Yale
960801 - 1.0.2 - added code to PRotein CA_analysis command to look
for sequential stretches of poor residues; this
also seems to detect some register errors !
960802 - 1.0.3 - vastly improved ONo LS_plane command
960804 - 1.0.4 - make border around atoms a parameter for ONo LS_plane
960805 - 1.1 - MUlti_geometry now correctly averages dihedrals,
i.e., using RTODEG*ATAN2(AVESIN,AVECOS)
961101 - 1.1.1 - change X-PLOR "generate" input files from SPlit command
so as to delete hydrogens and atoms with unknown coordinates
970124 - 1.1.2 - minor bug fix (SE ? would crash on Alphas)
970211 - 1.1.3 - the SQ PIr command to create a PIR file now only writes
one-letter code for residues for which at least one atom
has been selected (so you can easily avoid getting
hundreds of '?' residues for your waters etc.)
970626 - 1.2 - support initialisation macro (setenv GKMOLEMAN2 macrofile)
970701 - 1.2.1 - check for weird B-factors and occupancies while reading
a new PDB file
970714 - 1.2.2 - implemented X-PLOR polars and X-PLOR/Lattmann Euler
angles in XYz ROtate
970723 - 2.0 - implemented VRML commands
970724 - 2.1 - added VRml CEll command; SElect NUmeric can now also
select on atomic Mass, Covalent bond radius and
chemical Element number; added SElect BUtnot,
SElect BY_residue and SElect Dist_to_sel; SElect
NUmeric can now have AND, OR or BUTNOT; VRml FAt_trace
970729 - 2.1.1 - fixed bug in calculation of radius-of-gyration
970807 - 2.1.2 - allow "?" wildcards in atom names in library file
(e.g., some people call their water oxygen " O ",
others " O1 ", " OHH", etc.; use " O??" in the library
to capture all of these; similarly for metal ions)
970924 - 2.1.3 - new PDb NO_atom_numbers command to remove O-style
atom numbers (indicating chemical element type)
980420 - 2.1.4 - fixed bug in SElect DIst command (wrong parameters
were passed to the subroutine)
981009 - 2.1.5 - improved macro generated by ONo OOps_macro command
981014 - 2.1.6 - correct ONo COnnect and TOrsion datablocks even if
hydrogen atoms are present
981021 - 2.1.7 - new ECho command to echo command-line input (useful
in scripts)
981022 - 2.2 - implemented command history (# command)
981216 - 2.2.1 - added some comments to output PostScript files
990223 - 2.2.2 - doubled max nr of atoms and residues; removed
"on_off" commands from O macros generated by MOLEMAN2
990301 - 2.2.3 - echo some PDB header lines when reading a PDB file
990504 - 2.3 - ANISOU cards are now read and written
- the SElect ANd, OR and BUtnot commands can now also
be used with the attributes ALtloc (alternative
location identifier, e.g. A, B, X, " ", etc.) and
ANisou (can be either T(rue) or F(alse))
- new BFactor NO_anisou command to delete all ANISOUs
- up to 20 least-squares planes (ONo LS_plane command)
can be stored, and their mutual angles calculated
with the new ONo ANgle_ls_planes command
990823 - 2.3.1 - the STats, BFactor STats and OCcupancy STats commands
now also list the RMS values and the harmonic
averages of the B-factors and occupancies
990924 - 2.4 - new VRml CRamp_selection, SPhere, CYlinder, and LIquorice
commands; debugged some of the VRML-generating routines
990930 - 2.4.1 - in Ramachandran plots (PRot MC), D-amino acids are
now treated explicitly (their -phi and -psi are used
to assess if they're outliers or not; in the PostScript
plot they will be shown as red diamonds)
991029 - 2.4.2 - fixed bug in XYZ PErturb command (shift for B and Q
used to be equal to the shift for Z, no matter what ...)
991130 - 2.4.3 - increased max. number of atoms to 500,000 and max. number
of residues to 50,000
991213 - 2.5 - implemented YASSPA routine (invoked during book-keeping),
the results can be used in SElect NUmeric, SElect ANd,
SElect OR, and SElect BUtnot (e.g., to colour helices
and strands differently in a VRML world)
991221 - 2.6 - several bug fixes to get it to work properly with Linux/g77
000310 - 2.6.1 - minor bug fix for CHain AUto command (used to coredump on Alphas)
000313 - 2.6.2 - minor bug fix in REad command (Linux version choked on some CRYST1 cards)
000526 - 2.7 - new ONo RIngs command (requires new version of moleman2.lib
library file !) to generate ODL files to draw the rings
as semi-transparent solid planes (e.g., Tyr, Trp, etc.)
000529 - 2.7.1 - minor change
001113 - 2.7.2 - PDb FArout command to generate quick-n-dirty HELIX
and SHEET records for use with FarOut
001117 - 2.8 - new NUcleic DUarte_pyle command to make "Ramachandran-like"
plots to help analyse the conformation of RNA and DNA
001130 - 2.8.1 - new VRml CLose_file command
001229 - 2.8.2 - minor changes
010725 - 2.8.3 - new ONo CEll command
010727 - 2.8.4 - minor changes
010803 - X - added a number of pictures to this manual to illustrate the
results of some commands
010816 - 2.8.5 - minor changes
010905 - 2.8.6 - DIstance LIst command (e.g., to find atoms that are
too close to one another)
011023 - 2.8.7 - minor changes
011114 - 2.9 - PRot MC, PRot CA and Nucleic DUarte commands now delete
the PostScript file they normally produce if it contains
no residues; all these three commands now also have an
extra (optional) argument to decide whether the analysis
should be carried out for all chains in one go, for
one chain in particular, or for each chain in turn
(in the latter case, you will get one PostScript file
for each chain, so this makes it easy to inspect
Ramachandran plots on a chain-by-chain basis)
011115 - 2.9.1 - PRot MC, PRot CA and Nucleic DUarte option with "_"
as a chain argument now also work if a chain
has a blank chain ID
011123 - 2.9.2 - minor bug fix
011220 - 2.9.3 - minor change
020129 - 2.9.4 - minor changes
020221 - 2.9.5 - the STatistics command now also prints the range of
X, Y, and Z coordinates (together with the XYz ALign
command, this enables you to determine the dimensions
of your molecule)
020514 - 2.9.6 - new ONo MOlray command to generate a trace pseudo-molecule
if you want to "fly" along a protein chain in a MolRay movie
020516 - 2.9.7 - more options for ONo MOlray command
020611 - 2.9.8 - new OCcupancy PLot command
020628 - 3.0 - new DIstance CHains command to quickly find contacts
between two different chains (e.g., two monomers in
a dimer, or protein vs. DNA, or protein vs. ligand)
020718 - 3.0.1 - new XYz AXis_rotate command to rotate around the
X, Y or Z axis by a user-specified angle
020729 - 3.0.2 - optional 'how' parameter for the ONo DIsulfide
command (default = S, draw as sticks; alternative
L, draw as lines, i.e. like normal bonds) - suggested
by Marko Hyvonen. Also optional ODL object name
(in case you want more than one SS-bond object)
020819 - 3.0.3 - renamed the VRml LIst_colours command to VRml
NAmed_colours (to avoid a clash with the VRml
LIquorice command ... thanks to Kevin Battaile
for pointing this out)
020827 - 3.0.4 - ODL objects produced by same of the ONo commands
now have default names that begin with an underscore
to prevent any clashes with POV-Ray terms (such as
"plane")
020927 - 3.0.5 - new ONo INertia_axes_odl command to generate an ODL
file to draw the axes of inertia for the selected
set of atoms (following a question from Michael Merckel)
021023 - 3.0.6 - improved macro produced by ONo OOps command
021030 - 3.0.7 - (while in Toronto) further improved macro produced by ONo OOps command
021111 - 3.1 - minor bug fixes; new PDb SAnity_check command
021114 - 3.1.1 - fix: now uses insert code to delineate different residues
(in addition to residue number, type, chain name, and
seqment ID)
021121 - 3.1.2 - further improved macro produced by ONo OOps command
030221 - 3.2 - new BFactor PSeudo, BF SAve, BF REstore, BF SCale, and
BF ODb commands to replace B-values by other properties, e.g.
for colour-ramping in O or Rasmol. With BF PSeudo you can
also calculate B-values predicted using Halle's method
031204 - 3.2.1 - TER records are now written out in between ATOM records
in the same order as they were read
031209 - 3.2.2 - PRot MC command will list possible left-handed helices
031211 - - corrected documentation of XYz MAtrix and XYz RT
commands w.r.t. the order in which the RT-operator
is read (thanks to Lluís Bellsolell for pointing out
the inconsistencies)
041001 - 3.3 - replaced Kabsch' routine U3BEST by quaternion-based
routine (U3QION) to do least-squares superpositioning
041018 - 3.3.1 - added "mode" parameter to DIstance SElected command (q.v.)
041203 - 3.3.2 - implemented RContact_order command to calculate the
relative contact order (see Plaxco et al., J Mol Biol
277, 985-994, 1998)
041206 - 3.3.3 - minor changes
050317 - 3.3.4 - minor bug fix (in the COnstants LIst command; thanks to
Bryan Lepore for finding this)
050909 - 3.3.5 - PDb FArout command renamed to PDb INdonesia (although
the old command name is still recognised); also
added a brief description of this command to this manual
050916 - 3.3.6 - implemented PDb SEqres command
060329 - 3.3.7 - implemented XYz DIstort command
061122 - 3.3.8 - implemented SElect POint command
070913 - 3.3.9 - updated NUcleic DUarte command to work with new-style
PDB files of DNA (DA, DC, etc.)
From version 1.2 on, MOLEMAN2 can execute a macro at start-up (whether it is run interactively or in batch mode). This can be used to execute commands which you (almost) always want to have executed. To use this feature, set the environment variable GKMOLEMAN2 to point to a MOLEMAN2 macro file, e.g.:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- setenv GKMOLEMAN2 /home/gerard/moleman2.init ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
MOLEMAN2 is a new version of the old MOLEMAN program. It can be used for all sorts of manipulation and analysis of PDB files. It is intended primarily for practicing crystallographers who need to do hundreds of little things to their PDB files when switching between different programs, etc. Users of O, CCP4 and X-PLOR will benefit most from the functionality of this program.
The user-interface is different from that of the old MOLEMAN, and more similar
to that of MAPMAN, DATAMAN, etc. I.e., instead of question-and-answer
game you can supply any or all parameters for a command on one line.
For example, to read a PDB file, "re file.pdb" is enough. The other
two parameters of the REad command (format and option to read hydrogens)
will be set to their default values. For all commands, the first
two characters are unique, so "re" is the same as "read", etc. Optional
parameters are enclosed in [square brackets] in the list of commands.
NOTE: the DELETE_molecule command is an exception and requires the
first six characters to be typed (i.e., the word "delete"); this
is to reduce the risk of accidental deletion of your molecule !
An important difference with the old MOLEMAN is the fact that you can select subsets of atoms which will be used by many commands. In this fashion, you can use the same command ("bfactor stats") to get statistics about all atoms, all protein atoms, all main-chain atoms in segment XYZ1, etc. This makes the program much more flexible and easier to maintain (since no special-purpose options are necessary for different possible subsets of atoms).
Another important difference is that a library file is used which contains information about residues, such as their constituent main-chain and side-chain atoms, their type (protein, metal, carbohydrate, etc.), aliases (e.g., waters may be called WAT, HOH, H2O, etc.), and so on. You can use residue types in your selections so that it is very easy to get B-factor statistics for all non-hydrogen carbohydrate atoms with segment id CRB1, for instance.
MOLEMAN2 also allows you to write and execute macros for series of commands that you execute often (e.g., when going from a new X-PLOR model to a PDB file suitable for O and CCP4).
Many commands have a built-in mini-help facility which explains what the parameters to the command are or what values they may have. For instance, if you type "write ?" the program will explain what the parameters are:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: WRite file [format] [which]
file = PDB file name
format = Pdb | Xplor | Ccp4
which = ALl | NO_hydro | SElected | PAla |
PGly | PSer | CAlpha
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Parameters in [square brackets] are optional and will default to the first value listed (e.g., in this example, the default is to write ALl atoms to a Pdb-formatted file).
For parameters which can have several values, the UPPERCASE characters show how many characters define a unique value. In the example above, you can enter P, X or C for the format, but for the "which" parameter you must supply (at least) *two* characters.
You will be prompted to supply values for all parameters that you do not type on the command line, except those for which default values exist. Usually, the values suggested by the program make sense (if not, let me know).
If you need to provide a text parameter which contains spaces (such as the spacegroup symbol for the PDB CRYST1 record), enclose the whole string in "double quotes". Otherwise, one or more blanks and/or tabs are used to delimit parameter values.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > pd cr 84 84 111.8 90 90 90 8 "P 21 21 2" Unit-cell axes (A) : ( 84.000 84.000 111.800) Unit-cell angles (deg) : ( 90.000 90.000 90.000) Unit-cell volume (A3) : ( 7.889E+05) Nr of molecules in cell : ( 8) Spacegroup symbol : (P 21 21 2) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The dimensioning of the program (e.g., the maximum number of atoms, etc.) is shown at startup. If you need a bigger version. let me know.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Array dimensioning:1) Library: Max nr of residue types : ( 200) Max nr of atom types : ( 2000) Max nr of residue aliases : ( 100) Nr of defined residue classes : ( 100)
2) Molecule: Max nr of atoms : ( 100000) Max nr of residues : ( 10000) Max nr of REMARK records : ( 1000) Max nr of other records : ( 1000)
3) Program: Max buffer size : ( 524288) Max nr of atoms per residue : ( 100) Max nr of residue torsions : ( 100) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
In MOLEMAN2 you can also use macros (as in MAMA). A macro is a small text file containing MOLEMAN2 commands (but usually few parameters; these are left to the user to enter on demand) and comments. A simple macro to convert an X-PLOR PDB file into one suitable for O and CCP4 may look as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! xplor_to_ccp4.momac - gj kleywegt @ 960303 ! ! MOLEMAN2 macro to go from an X-PLOR PDB file with segment ids ! and hydrogen atoms, to a ccp4/o file with chain names and ! no hydrogens etc. ! ! Enter X-PLOR PDB file name: read ! ! Some information about the molecule(s) statistics ! ! Generate chain names from segment IDs chain from_segid auto ! ! Enter cell constants etc.: pdb crystal ! ! Enter * to delete all X-PLOR remarks: pdb delete_remark ! ! Enter a descriptive remark about the file: pdb remark ! ! Enter CCP4/O PDB file name: write ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
When executed (with the @ command), this will give the following:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > @xplor_to_ccp4.momac ... Opened macro file : (xplor_to_ccp4.momac) ... On unit : ( 61) > (!) > (! xplor_to_ccp4.momac - gj kleywegt @ 960303) > (!) > (! MOLEMAN2 macro to go from an X-PLOR PDB file with segment ids) > (! and hydrogen atoms, to a ccp4/o file with chain names and) > (! no hydrogens etc.) > (!) > (! Enter X-PLOR PDB file name:) > (read) PDB file ? (m1.pdb) hydro.pdb Reading from file : (hydro.pdb) ... > (! Some information about the molecule(s)) > (statistics) Nr of atoms : ( 5794) Nr of residues : ( 802) ... > (! Generate chain names from segment IDs) > (chain from_segid auto)RESIDUE ALA 86 AAAA New chain name : (A)
RESIDUE NAG 501 BBBB New chain name : (B) ... > (! Enter cell constants etc.:) > (pdb crystal) A axis (A) ? ( 1.00) 49.1 B axis (A) ? ( 1.00) 75.8 C axis (A) ? ( 1.00) 92.9 Alpha angle (deg) ? ( 90.00) Beta angle (deg) ? ( 90.00) 103.2 Gamma angle (deg) ? ( 90.00) Nr of molecules in cell ? ( 1) 4 Spacegroup symbol ? (P 1) P 21 ... > (! Enter * to delete all X-PLOR remarks:) > (pdb delete_remark) Which ? (-1) * Delete all REMARK records > (!) > (! Enter a descriptive remark about the file:) > (pdb remark) Text ? (???) Model M3 @ 960303 R=0.231 Rfree=0.273 Add REMARK record : (Model M3 @ 960303 R=0.231 Rfree=0.273) 1: REMARK Model M3 @ 960303 R=0.231 Rfree=0.273 > (!) > (! Enter CCP4/O PDB file name:) > (write) PDB file ? (hydro.pdb) m3.pdb Output PDB file : (m3.pdb) Format : (Pdb) Atoms : (ALl) ... ... End of macro file ... Control returned to terminal ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Generally useful macros will be made available via the public domain OMAC directory (/nfs/public/omac in Uppsala; pub/gerard/omac for downloading from other sites).
Note that macros may be nested (the level depends on how many files may be open at the same time on your paticular type of machine). For instance, a macro which converts a new X-PLOR model into a PDB for O/CCP4, and does some quality analysis, and lists B-factor statistics may look as simple as this (assuming your directory contains a soft link called "omac" to your local OMAC directory):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! ! new_model.momac - gj kleywegt @ 960303 ! ! MOLEMAN2 macro to generate an O/CCP4 PDB file from an X-PLOR PDB ! file; analyse main-chain, side-chain and CA-geometry, and list ! B-factor statistics ! @omac/xplor_to_ccp4.momac @omac/prot_qual.momac @omac/bfac_stats.momac ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
A number of features and options from the old MOLEMAN have been dropped (but many more have been improved ;-). If you need any of these, use the old MOLEMAN program. Dropped features include:
- Balasubramanian plots
- HPGL and O2D files for Ramachadran plots
- occupancy plots (if someone really needs them, let me know)
- averaging temperature factors over different chains
- BAD files (i.e., internal coordinates, Bond-distances, Angles,
Dihedrals)
- flag-colour datablocks (e.g., to colour your molecule according
to the Dutch or Swedish flag)
Note that MOLEMAN2 versions below 1.0 are still development versions, so not all the functionality may have been implemented yet !
The following list shows the old MOLEMAN commands and their counterparts in the new MOLEMAN2 (up-to-date at 960304):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- READ_pdb_file = REad NO_H_read = REad ALWYn_format_read = REad APPEnd_pdb_file = APpend WRITe_pdb_file = WRite DUMP_pdb_file = WRite SPLIt_pdb_file = SPlit EXPOrt_bad_file = NOT SUPPORTED IMPOrt_bad_file = NOT SUPPORTED SAME_export = NOT SUPPORTED HELIx_generate = AUto SPink/BOnes/SSe STRAnd_generate = AUto SPink/BOnes/SSe QUIT = QUitREMArk_etc_cards = PDb REmark/LIst_remark/DElete_remark CRYStal_PDB_card = PDb CRystal SSBOnd_records = PDb SSbond PIR_sequence_file = SQuence PIr GLYCo_sites = SQuence GLyco_sites EXTInction_280 = SQuence EXtinction_280 TALLy_residues = SQuence COunt COUNt_elements = not implemented yet WATEr_sort = not implemented yet
RSR_datablock = ONo RSr CONNect_file = ONo COnnect TORSion_datablock = ONo TOrs RSFIt_datablock = ONo FIt DISUlfide_ODL_file = ONo DIsulfide FIT_water_macro = ONo WAter_fit FLAG_colours = NOT SUPPORTED
STATistics = STatistics PLOT_Bs_or_Qs = BFactor PLot RADIal_B_plot = BFactor PLot RAMAchandran_plot = PRotein MC_analysis PLANar_peptides = PRotein MC_analysis BALAsubramanian_plot = NOT SUPPORTED CHI_list = PRotein SC_analysis CA_Ramachandran_plot = PRotein CA_analysis CACA_distances = PRotein CA_analysis CA_Distance_plot = DIstance PLot LIST_residue = LIst_selected GEOMetry_list = GEometry_selected SEQUence_list = LIst_selected/SQuence LIst BURIed_charges = not implemented yet DISTance_distribution = DIstance DIstribution SHORt_contacts = DIstance SHort
LIMIt_B_and_Q = BFactor/OCcupancy LImit AVERage_temp_factors = BFactor GRoup TEMP_factors_set = BFactor LImit/PRod_plus OCCUpancies_set = OCcupancy LImit/PRod_plus SMOOth_Bs = BFactor SMooth B_Q_statistics = BFactor/OCcupancy STats BONDed_Bs = BFactor BOnded NONBonded_Bs = BFactor BOnded
O2XHydrogens = ONo XPlor_hydrogens SUGGest_OT2 = CHain OT2_suggest RENUmber_atoms = NOT SUPPORTED ALTEr_residue_name = PDb NAme RESIdu_renumber = PDb NUmber ZONE_renumber = PDb NUmber CHECk_nomenclature = PRotein SC_analysis CORRect_nomenclature = not implemented yet CHAIn_name = CHain NAme_selection/REname XPLOr_ids = CHain NAme_selection/SEgid_rename FROM_chain_to_XID = CHain TO_segid XID_to_chain = CHain FRom_segid AUTO_chain_segid = CHain AUto ASK_auto_chain_segid = CHain ASk
FRACtional_to_cartesian = XYz ORthogonalise CARTesian_to_fractional = XYz FRactionalise ROTAte_molecule = XYz ROtate TRANslate_molecule = XYz TRanslate APPLy_random_rotation = XYz RAndom_rotation RANDom_shifts = XYz PErturb ORIGin_move = XYz CEntre_origin MIRRor_zone = XYz MIrror INVErt_zone = XYz INvert ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
On the whole, MOLEMAN2 provides a superset of the functionality of the old
MOLEMAN, with many additional benefits:
- removed bugs
- more use of (sensible) defaults to minimise typing (compare the new
WRite command to the one in the old MOLEMAN)
- use of atom selections to operate on only a subset of the atoms
- combined commands (e.g., the PRotein MC_analysis combines several old
MOLEMAN commands, plus new functionality)
- extended functionality (e.g., the XYz commands are much more flexible
than the combined set of old MOLEMAN commands they replace; also the
SPlit command will now auto-generate a GENERATE input file for X-PLOR
which usually requires little editing; the PDb HEtero command is new)
- the program is now easier to extend since I have actually thought a bit
about my data structures (not too much, of course, I'm still a Fortran
relic). The old MOLEMAN was initially written to do just two simple
things: add X-PLOR segment IDs and write an END card at the end of
PDB files ;-) Since then it has outgrown itself rapidly, making it
a major pain to implement or change functionality.
Not written yet.
As of version 2.5, MOLEMAN2 automatically determines the secondary structure of protein residues in its book-keeping stage (e.g., when a molecule is read in). This is done using the YASSPA algorithm and should give identical results to those you get in O (not necessarily for left-handed helices, though). There are five possible "states":
- 0 = loop or turn
- 1 = alpha helix (right-handed)
- 2 = beta strand
- 3 = left-handed alpha helix
- -1 = non-protein residues
The results can be used with the SElect commands, so you can list all left-handed helical residues, colour the helices blue in your VRML world, write out only the residues in beta strands, calculate the average temperature factor for all helical residues, etc.
If you know what you are doing, you can change the cut-off values for the algorithm using the COnstants commands (they are YALCUT, YBECUT and YLHCUT).
The default library file in Uppsala can be found in /nfs/public/lib, with name "moleman2.lib". If you set the environment variable GKLIB in your .cshrc file to /nfs/public/lib, the program will always come up with the correct default name for this name. Outside Uppsala, the library file can be found in directory pub/gerard/xutil in the compressed tar file xutil_etc.dirtar.gz
The library file must be read on start-up. The program will prompt you for the filename.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
...
Max nr of residue torsions : ( 100)
Name of library file ? (/nfs/public/lib/moleman2.lib)
Reading library ...
> ( = MOLEMAN2.LIB = VERSION 0.1 = 951106 = GJ KLEYWEGT = 118 ENTRIES =)
Lines read : ( 785)
Residue types : ( 118)
Atom types : ( 1314)
Aliases : ( 60)
First and last residue types:
Residue # 1 = GLY (PROT) = GLYCINE
Atoms | N | (T) | CA | (T) | C | (T) | O | (T)
Residue # 118 = TRS (ORGA) = TRIS TRIS(HYDROXYMETHYL)-AMINOMETHANE
Atoms | O1 | (F) | C2 | (F) | C3 | (F) | C4 | (F) | O5 | (F) | C6 | (F)
Atoms | O7 | (F) | N8 | (F)
Check integrity:
WARNING - name or alias conflict: 55 = MAL and 95 = MAL
WARNING - name or alias conflict: 60 = GLC and 61 = GLC
WARNING - name or alias conflict: 61 = GLC and 60 = GLC
WARNING - name or alias conflict: 63 = MAN and 64 = MAN
WARNING - name or alias conflict: 64 = MAN and 63 = MAN
WARNING - name or alias conflict: 95 = MAL and 55 = MAL
ERROR --- Non-unique residue names/aliases
Count types:
Nr of amino acid residue types : ( 22)
Nr of nucleic acid types : ( 4)
Nr of water types : ( 1)
Nr of metal types : ( 13)
Nr of inorganic types : ( 12)
Nr of carbohydrate types : ( 18)
Nr of organic compound types : ( 48)
Nr of other compound types : ( 0)
MOLEMAN2 commands :
...
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
As you can see, there are some duplicate names (not necessarily for identical compounds, e.g. alpha- and beta-glucose can both be called GLC). The program will use the first occurrence.
The format is as follows (in case you want to edit the file or add new residue type definitions):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- For each residue type:RES XYZ description FORMAT: (A3,1x,A3,1x,A80) - XYZ = 3-letter residue type - description = free text TYP ABCDefghijkl FORMAT: (A3,1x,A4) - ABCD = one of the defined categories, e.g. protein AKA ABC DEF GHI FORMAT: (A3,n(1x,A3)) (multiple cards allowed) - 0 or more synonyms for the residue type MCH ... FORMAT: first card (A3,1X,*) subsequent cards (4X,*) - 0 or more atom names which constitute the main chain or backbone SCH ... FORMAT: first card (A3,1X,*) subsequent cards (4X,*) - 0 or more atom names which constitute the side chain END FORMAT: (A3) - signals end of residue definition
in MCH and SCH lines, use a "-" at the end of a line to signal continuation on the next one; start the next line with 5 spaces !
any line beginning with "!" is a comment which will not be printed
any line beginning with REM is a comment which will be printed ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The pre-defined residue types are: PROTein, NUCLeic acid, WATEr, METAl ions, INORganic ions and clusters, CARBohydrates, and ORGAnic ligands, ions, substrates, co-factors etc. Anything else will be classified as HETEro.
An example:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- RES CYS cysteine TYP protein AKA CSS CSH CYH CYX MCH ' N ' ' CA ' ' C ' ' O ' SCH ' CB ' ' SG ' END ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
As of version 2.7, ring definitions can also be included (used by the ONo RIngs command).
If you want your special residue/ligand to be included in the standard distribution version of the library, or if you find any errors, E-mail me (gerard@xray.bmc.uu.se).
If you have compounds which are not in the library, it usually doesn't
matter too much, as long as you realise that:
- the compound will be assigned type HETEro; if it is in actual fact an
unusual amino acid you should add it to the library
- all atoms will be flagged as being side-chain atoms; again, if you
have unusual amino acids or nucleotides, this may not be what you want
- no check for missing/superfluous atoms can be carried out (BOok_keep
command)
Some commands produce plot files for O2D. On an SGI, you can view these plots interactively, and analyse them. On other machines, you can convert them to PostScript (or CricketGraph) files. Use the script OMAC/o2dps to do the conversion to PostScript automatically (and for lots of files at once, if you like).
Other commands directly produce PostScript files. Use your local viewer (e.g., ghostview or ghostscript) to look at these, and/or print them on a PostScript printer.
With the COnstants command a number of program parameters can be altered by the user. These include:
- BLIMLO/BLIMHI/QLIMLO/QLIMHI - used by the BFacor/OCcupancy LImit
commands
- MXCACA - maximum CA-CA distance for connected residues (used by
several commands)
- MXPP - maximum P-P distance for connected nucleic acid residues
- TORTOL - tolerance for certain impropers/dihedrals (e.g., used by
the PRotein SC_analysis and ONo TOrsion commands)
- MXBOND - maximum distance for two atoms to be considered bonded
(e.g., used by the BFactor SMooth command)
- MXNONB - maximum distance for non-bonded interactions (two atoms
are involved in a non-bonded interaction if their distance lies
in the range <MXBOND,MXNONB]); used by BFactor BOnded
- MXCYSS - maximum Cys-SG...SG-Cys distance for disulfide links
(e.g., used by the SPlit command to generate DISUlfide patches
for your X-PLOR GENERATE input file)
- ISEED - special (integer) number used to initialise the random
number generator (positive number: initialise with that number,
i.e. reproducibly; zero or negative number: initialise with the
current value of MCLOCK(), the system clock); used by the XYz
RAndom_rotation and PErturb commands
- YALCUT, YBECUT and YLHCUT - parameters for the YASSPA algorithm
that assigns the secondary structure of the protein residues
For an up-to-date list, use the COnstants LIst command. To revert to the "factory defaults", use the COnstants REset command.
Note that the values you enter are NOT checked at all. So if you want to set the maximum distance for connected CA atoms to -3.14 A, you may do so.
Syntax: ? [command]
command = name of any command which has sub-commands (e.g., XYz, ONo, etc.)
Typing a single question mark will provide you with a list of all available commands. If you supply an argument "?", you will only see the general commands. If the argument is the name of a command which has sub-commands (such as SElect, XYz, PRotein, etc.), you will only get the list of those commands.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > ? ?MOLEMAN2 commands :
? [command] (list (sub-)commands) ! (comment) QUit $ shell_command @ macro_file BOok_keeping COnstants REset COnstants SEt name value COnstants LIst STatistics GEometry_selected LIst_selected [which] MUlti_geometry which LS_plane
REad file [format] [hydro] WRite file [format] [which] APpend file [format] [hydro] SPlit file_prefix DElete_molecule
Commands with sub-commands: SElect BFactor OCcupancy CHain PDb PRotein XYz ONo DIstance SQuence AUto To see sub-commands, use for instance: ? xy ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > ? seleSElect All SElect NOne SElect HYdrogen SElect EXhydrogen SElect OR what which SElect ANd what which SElect NEgate SElect NUmeric and_or what lo hi SElect ? ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This command can be used to manipulate symbols. These are probably
only useful for advanced users who want to write fancier macros.
The command can be used in three ways:
(1) & ? -> lists currently defined symbols
(2) & symbol value -> sets "SYMBOL" to "value"
(3) & symbol -> prompts the user to supply a value for "SYMBOL"
(even if the program is executing a macro)
A few symbols are predefined:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > & ? Nr of defined symbols : ( 2) Symbol START_TIME : (Fri May 17 19:55:43 1996) Symbol USERNAME : (gerard) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The symbol mechanism is fairly simplistic and has some limitations:
- max length of a symbol name is 20 characters
- max length of a symbol value is 256 characters
- max number of symbols is 100
- symbols can not be deleted, but they can be redefined
- symbol values are accessed by supplying $SYMBOL_NAME as an
argument on the command line; the line that you type on the terminal
(or in a macro) is parsed once; if there are additional parameters
which the program prompts you for, you cannot use symbols for those
- only one substitution per argument (e.g., "$file1 $file2" will
lead to a substituion of the entire argument by the value of
symbol FILE1 only !)
- command names (first argument on any command line) cannot be
replaced by a symbol (e.g.: "$command $arg1 $arg2" is not valid)
- symbols may be equated to each other, e.g. "& file2 $file1" will
give FILE2 the same value as FILE1
- symbol substitution is not recursive (e.g., if you set the value
of FILE2 to be "$file1", any reference to $FILE2 will be replaced
by "$file1", not by the value of FILE1
- symbols on comment lines (starting with "!") are not expanded
- symbols on system command lines (starting with "$") are not expanded
Example of the use of symbols:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! Which rotation angle convention ? ! Enter CE for CCP4 Euler angles, or CP for CCP4 Polar angles: & conv ! ! Rotation angle 1 ? & alpha ! ! Rotation angle 2 ? & beta ! ! Rotation angle 3 ? & gamma ! ! Applying rotation function solution xyz rotate $conv $alpha $beta $gamma ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
If you run the program with scripts, it is sometimes useful to see input commands echoed. The parameter to the ECho command may be ON, OFf, or ? (to list the echo status).
This command calculates and prints some statistics for the currently selected set of atoms.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > st Nr of atoms : ( 2813) Nr of residues : ( 396)Nr of amino acid residues : ( 370) Nr of nucleic acids : ( 0) Nr of waters : ( 24) Nr of metals : ( 0) Nr of inorganics : ( 0) Nr of carbohydrates : ( 0) Nr of organic compounds : ( 0) Nr of other compounds : ( 2)
Nr of selected atoms : ( 2813) Ditto, hydrogen : ( 0) Ditto, ANISOU : ( 0)
Item Average St.Dev Min Max RMS Harm.ave. ---- ------- ------ --- --- --- --------- X-coord 0.000 14.956 -30.527 36.812 Y-coord 0.000 10.308 -24.280 25.566 Z-coord 0.000 8.683 -20.405 21.471 B-factor 28.669 28.761 2.000 218.470 40.610 8.843 Warning - there are B-factors > 100 A**2 ! Occpncy 1.000 0.000 1.000 1.000 1.000 1.000
The radius of gyration is 20.1 A
Range of X, Y, and Z coordinates: 67.3 A * 49.8 A * 41.9 A If you have used XYz ALign_inertia_axes, these numbers give you an indication of the dimensions of the selected molecule (or set of atoms). ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This command will re-determine where residues start and end, if there are duplicate atoms or missing atoms or extra atoms in residues that occur in the library, or if there are residues not in the library, and if all residue names are unique.
The program also checks if there are any atoms which have X ~ Y ~ Z; often, this is an indication of unset or unknown coordinates (e.g., new atoms in O will be placed at (1500,1500,1500), sometimes waters end up at (0,0,0) etc.) which may lead to all sorts of trouble later on (e.g., in map extension around the molecule or the generation of NCSRel-cards by XPAND). The tolerance used is 0.01 A.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > boTotal nr of residues : ( 239) Nr of amino acid residues : ( 137) Nr of nucleic acids : ( 0) Nr of waters : ( 101) Nr of metals : ( 0) Nr of inorganics : ( 0) Nr of carbohydrates : ( 0) Nr of organic compounds : ( 1) Nr of other compounds : ( 0)
Checking for missing/extra atoms ... ERROR --- Unknown atom in structure ATOM 1091 OXT GLU 137 26.188 -39.912 33.302 1.00 22.23 1CBS1313 ERROR --- Unknown atom in structure ATOM 1115 O HOH 300 15.524 -31.764 26.116 1.00 17.43 1CBS1337 ERROR --- Missing atom in structure RESIDUE HOH 300 1CBS Atom name : ( O1) ... ERROR --- Missing atom in structure RESIDUE HOH 399 1CBS Atom name : ( O1)
Checking uniqueness of residue names ... Non-unique residue names : # 224 = HOH 385 1CBS <-> # 230 = HOH 385 1CBS
Checking "special" positions (X~Y~Z) ... ATOM 1200 O HOH 385 0.000 0.000 0.000 1.00 32.12 1CBS1422 ATOM 1200 O HOH 385 1500.0001500.0001500.000 1.00 32.12 1CBS1422 ATOM 1210 O HOH 395 -36.656 -36.656 -36.656 1.00 35.59 1CBS1432 WARNING - Nr of atoms with X~Y~Z : ( 3) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: LIst_selected [which]
which = Residues | Atoms
You may either list all selected atoms, or the first selected atom (if any) of all residues.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > se nu and bf 50 9999 Select Numeric : ( AND B-factor 50.00000 9999.000) Selection history : (NON-HYDROGEN | AND B-factor 50.00000 9999.000 |) Nr of selected atoms : ( 8) MOLEMAN2 > li r List first selected atom of every residue ATOM 807 CE LYS 101 4.479 34.527 19.248 1.00 51.31 1CBS1029 ATOM 819 CD GLU 103 -0.383 25.503 13.395 1.00 50.23 1CBS1041 ATOM 1193 O HOH 378 9.543 16.072 11.145 1.00 50.91 1CBS1415 ATOM 1194 O HOH 379 8.174 14.289 20.240 1.00 54.21 1CBS1416 ATOM 1196 O HOH 381 5.486 15.385 24.922 1.00 50.19 1CBS1418 Nr of residues listed : ( 5) MOLEMAN2 > li a List all selected atoms ATOM 807 CE LYS 101 4.479 34.527 19.248 1.00 51.31 1CBS1029 ATOM 808 NZ LYS 101 4.917 33.952 20.559 1.00 51.14 1CBS1030 ATOM 819 CD GLU 103 -0.383 25.503 13.395 1.00 50.23 1CBS1041 ATOM 820 OE1 GLU 103 -0.130 26.346 12.499 1.00 53.12 1CBS1042 ATOM 821 OE2 GLU 103 -1.464 25.500 14.036 1.00 52.16 1CBS1043 ATOM 1193 O HOH 378 9.543 16.072 11.145 1.00 50.91 1CBS1415 ATOM 1194 O HOH 379 8.174 14.289 20.240 1.00 54.21 1CBS1416 ATOM 1196 O HOH 381 5.486 15.385 24.922 1.00 50.19 1CBS1418 Nr of atoms listed : ( 8) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This command calculates the equation of the least-squares plane
through the currently selected atoms (unit weights), and the
RMSD of the atoms to the plane.
If you want to display the plane in O, use the ONo LS_plane_odl
command instead. Also, if you want to see the distance of
the individual atoms to the plane, use the ONo LS_plane command.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > se and res rea AND atom selection With atoms for which : (RES) Equals : (REA) Selection history : (ALL | AND REsidu = REA |) Nr of selected atoms : ( 22) MOLEMAN2 > ls Nr of selected atoms : ( 22) Centre of Gravity : ( 22.065 26.283 20.209) Eigen value 1 = 515.0 Vector : 0.145303 -0.597192 0.788828 Eigen value 2 = 31.0 Vector : 0.847841 0.486099 0.211834 Eigen value 3 = 6.7 Vector : -0.509954 0.638020 0.576955 Determinant : ( 1.000) Eigenvector #3 defines the least-squares plane Equation: -0.509954 X + 0.638020 Y + 0.576955 Z = 17.176491 RMSD to plane : ( 0.552) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Note that the three eigenvalues tell you something about the shape of the selected set of atoms: in the example above (an all-trans- retinoic acid molecule), it is clearly very long, not very wide, and fairly planar (eigenvalue 1 >> 2 > 3).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ... Selection history : (ALL | AND REsidu = TRP | AND CLass = Side | AND Residue_nr 109 109 |) Nr of selected atoms : ( 10) MOLEMAN2 > ls Nr of selected atoms : ( 10) Centre of Gravity : ( 13.617 20.280 29.635) Eigen value 1 = 28.3 Vector : 0.044093 0.093234 0.994667 Eigen value 2 = 12.4 Vector : -0.373900 0.924815 -0.070112 Eigen value 3 = 0.0 Vector : 0.926420 0.368814 -0.075638 Determinant : ( -1.000) ERROR --- Negative determinant; change hand of inertia axes Eigen value 1 = 28.3 Vector : -0.044093 -0.093234 -0.994667 Eigen value 2 = 12.4 Vector : 0.373900 -0.924815 0.070112 Eigen value 3 = 0.0 Vector : -0.926420 -0.368814 0.075638 Determinant : ( 1.000) Eigenvector #3 defines the least-squares plane Equation: -0.926420 X + -0.368814 Y + 0.075638 Z = -17.853298 RMSD to plane : ( 0.029) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: RContact_order [cut_off]
cut_off = distance cut-off to decide if two residues contact each other
This option calculates the relative contact order of a protein chain as described by Plaxco et al., J Mol Biol 277, 985-994 (1998). The cut-off defaults to a value of 6.0 A (used by Plaxco et al.). Note that this calculation only makes sense for a single chain (or even domain) and that you should exclude hydrogen atoms from the contact calculations. Both conditions can be satisfied by clever use of the program's SElect commands (see the example below).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > read pdb1fss.ent [...] MOLEMAN2 > sel ex Select NON-HYDROGEN atoms Selection history : (NON-HYDROGEN |) Nr of selected atoms : ( 4742) MOLEMAN2 > sel and chain a AND atom selection With atoms for which : (CHAIN) Equals : (A) Selection history : (NON-HYDROGEN | AND CHain = A |) Nr of selected atoms : ( 4242) MOLEMAN2 > sel and type prot AND atom selection With atoms for which : (TYPE) Equals : (PROT) Selection history : (NON-HYDROGEN | AND CHain = A | AND TYpe = PROT |) Nr of selected atoms : ( 4226) MOLEMAN2 > rco Calculate relative contact order Cut-off contact distance (A) : ( 6.000) Nr of selected residues : ( 532) Nr of contacting pairs : ( 3873) Sum of separations : ( 166499) Relative contact order : ( 0.081) CPU total/user/sys : 1.7 1.7 0.0 MOLEMAN2 > MOLEMAN2 > sel ex Select NON-HYDROGEN atoms Selection history : (NON-HYDROGEN |) Nr of selected atoms : ( 4742) MOLEMAN2 > sel and chain b AND atom selection With atoms for which : (CHAIN) Equals : (B) Selection history : (NON-HYDROGEN | AND CHain = B |) Nr of selected atoms : ( 464) MOLEMAN2 > sel and typ prot AND atom selection With atoms for which : (TYP) Equals : (PROT) Selection history : (NON-HYDROGEN | AND CHain = B | AND TYpe = PROT |) Nr of selected atoms : ( 464) MOLEMAN2 > rco Calculate relative contact order Cut-off contact distance (A) : ( 6.000) Nr of selected residues : ( 61) Nr of contacting pairs : ( 344) Sum of separations : ( 4858) Relative contact order : ( 0.232) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: MUlti_geometry which
which = residue_type (must be defined in the library)
This command will list statistics (number of observations, average, standard
deviation, minimum and maximum value) for the following for all currently
selected copies of a user-specified residue type:
- bonded distances
- bond angles and 1-3 distances
- torsion angles and 1-4 distances
Note that the (torsion) angles used to be averaged in degrees, and that periodicity is not taken into account ! This means that dihedrals which are around +/-180 degrees may give seemingly large ranges !!! This has been changed in version 1.1, so that the average of -178 and +178 is now (+ or -) 180, rather than zero.
This option may be useful when creating "ideal geometry" dictionaries for a refinement program when you have several examples of the residue. In addition it can be used to look for large outliers.
The program constants LARGEB and LARGEA are used to flag bond distances and angles if they show a large range (i.e., maximum minus minimum value exceeds LARGEB for bonds or LARGEA for angles).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > mu gly Multiple copy geometry for : (GLY) Nr of atoms : ( 4) Atoms : ( N CA C O) Looking for selected residues ... RESIDUE GLY A 22 1CEL RESIDUE GLY A 23 1CEL ... RESIDUE GLY B 424 1CEL RESIDUE GLY B 427 1CEL ERROR --- Too many copies Maximum : ( 100) Nr of copies found : ( 100) Nr of bonds : ( 3) Bond distance range large if > ( 0.050) Bond angle range large if > ( 5.000)Bonded distances with cut-off : 2.000 A ========================================== N - CA # 100 Ave, Sdv, Min, Max 1.451 0.004 1.440 1.464 CA - C # 100 Ave, Sdv, Min, Max 1.517 0.006 1.501 1.529 C - O # 100 Ave, Sdv, Min, Max 1.232 0.004 1.223 1.244
Angles and 1-3 angle distances ============================== N - CA - C Angle : 100 113.89 4.23 101.49 122.24 Large range 1-3 Dist : 100 2.486 0.059 2.307 2.588 CA - C - O Angle : 100 120.44 0.96 116.96 122.29 Large range 1-3 Dist : 100 2.389 0.015 2.339 2.415
Dihedrals and 1-4 torsion distances =================================== N - CA - C - O Dihedral : 100 5.27 114.42 -178.61 179.19 1-4 Dist : 100 3.150 0.432 2.608 3.695 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > mu glc Multiple copy geometry for : (GLC) Nr of atoms : ( 12) Atoms : ( C1 C2 C3 C4 C5 C6 O1 O2 O3 O4 O5 O6) Looking for selected residues ... RESIDUE GLC 1 RESIDUE GLC 2 RESIDUE GLC 3 RESIDUE GLC 4 RESIDUE GLC 5 RESIDUE GLC 6 RESIDUE GLC 7 RESIDUE GLC 8 Nr of copies found : ( 8) Nr of bonds : ( 11) Bond distance range large if > ( 0.050) Bond angle range large if > ( 5.000)Bonded distances with cut-off : 2.000 A ========================================== C1 - C2 # 8 Ave, Sdv, Min, Max 1.533 0.013 1.513 1.548 C1 - O5 # 8 Ave, Sdv, Min, Max 1.435 0.014 1.414 1.456 C2 - C3 # 8 Ave, Sdv, Min, Max 1.519 0.013 1.503 1.543 C2 - O2 # 8 Ave, Sdv, Min, Max 1.409 0.016 1.385 1.426 C3 - C4 # 8 Ave, Sdv, Min, Max 2.528 0.413 1.497 2.875 Large range C3 - O3 # 8 Ave, Sdv, Min, Max 1.416 0.008 1.411 1.436 C4 - C5 # 8 Ave, Sdv, Min, Max 2.537 0.390 1.544 2.792 Large range C4 - O4 # 1 Ave, Sdv, Min, Max 1.413 0.000 1.413 1.413 ... C6 - O6 # 8 Ave, Sdv, Min, Max 1.410 0.016 1.374 1.426 Large range
Angles and 1-3 angle distances ============================== C2 - C1 - O5 Angle : 8 109.93 2.36 106.56 113.02 Large range 1-3 Dist : 8 2.430 0.027 2.383 2.463 C1 - C2 - C3 Angle : 8 111.72 1.48 110.48 114.24 1-3 Dist : 8 2.526 0.013 2.512 2.546 ... C1 - O5 - C5 Angle : 8 117.02 1.53 115.16 119.50 1-3 Dist : 8 2.454 0.045 2.414 2.529
Dihedrals and 1-4 torsion distances =================================== O5 - C1 - C2 - C3 Dihedral : 8 51.28 7.74 39.17 60.96 1-4 Dist : 8 2.853 0.019 2.839 2.902 O5 - C1 - C2 - O2 Dihedral : 8 37.03 167.50 -179.25 174.97 1-4 Dist : 8 3.662 0.036 3.592 3.694 ... O4 - C4 - C5 - O5 Dihedral : 1 -172.14 0.00 -172.14 -172.14 1-4 Dist : 1 3.718 0.000 3.718 3.718 ... C6 - C5 - O5 - C1 Dihedral : 8 -89.61 149.13 -176.72 168.72 1-4 Dist : 8 3.760 0.052 3.691 3.839 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This command will list the following for all currently selected atoms:
- bonded distances
- bond angles and 1-3 distances
- torsion angles and 1-4 distances
Make sure to use the SElect commands to isolate only those atoms that you are interested in ! Use the LIst_selected command before using this command to see exactly how many (and which) atoms/residues are selected.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > se an re rea AND atom selection With atoms for which : (RE) Equals : (REA) Selection history : (ALL | AND REsidu = REA |) Nr of selected atoms : ( 22) MOLEMAN2 > ge Nr of selected atoms : ( 22)Bonded distances with cut-off : 2.000 A ========================================== C1 [B 200 ] - C2 [B 200 ] = 1.546 A C1 [B 200 ] - C6 [B 200 ] = 1.564 A ... C15 [B 200 ] - O2 [B 200 ] = 1.251 A Nr of bonded distances : ( 22)
Angles and 1-3 angle distances ============================== C2 [B 200 ] - C1 [B 200 ] - C6 [B 200 ] = 109.691 deg = 2.543 A C2 [B 200 ] - C1 [B 200 ] - C16 [B 200 ] = 108.110 deg = 2.494 A ... O1 [B 200 ] - C15 [B 200 ] - O2 [B 200 ] = 121.547 deg = 2.183 A Nr of angles : ( 30)
Dihedrals and 1-4 torsion distances =================================== C6 [B 200 ] - C1 [B 200 ] - C2 [B 200 ] - C3 [B 200 ] = -42.758 deg = 2.902 A C16 [B 200 ] - C1 [B 200 ] - C2 [B 200 ] - C3 [B 200 ] = -162.723 deg = 3.847 A ... C13 [B 200 ] - C14 [B 200 ] - C15 [B 200 ] - O2 [B 200 ] = 129.005 deg = 3.505 A Nr of dihedrals : ( 32) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > se and ch m AND atom selection With atoms for which : (CH) Equals : (M) Selection history : (ALL | AND CHain = M |) Nr of selected atoms : ( 22) MOLEMAN2 > ge Nr of selected atoms : ( 22)Bonded distances with cut-off : 2.000 A ========================================== C1 [M 602 ] - O1 [M 602 ] = 1.410 A C1 [M 602 ] - C2 [M 602 ] = 1.515 A ... O5 [M 603 ] - C5 [M 603 ] - C6 [M 603 ] - O6 [M 603 ] = -51.669 deg = 2.729 A Nr of dihedrals : ( 43) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > se all ... MOLEMAN2 > se and chain a ... MOLEMAN2 > se num and res 85 87 ... MOLEMAN2 > geom Nr of selected atoms : ( 12)Bonded distances with cut-off : 2.000 A ========================================== CB [A 86 ] - CA [A 86 ] = 1.521 A C [A 86 ] - O [A 86 ] = 1.229 A ... CB [A 87 ] - CA [A 87 ] - C [A 87 ] - O [A 87 ] = 86.999 deg = 3.216 A Nr of dihedrals : ( 14) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Any command beginning with an exclamation mark will prompt the program to ignore that line. This may be useful to annotate scripts which run MOLEMAN2.
This will end you current session.
Syntax: $ shell_command
Anything following the dollar sign is passed on to the operating system shell. This can be used to list the files in a directory, or even to run another program from within MOLEMAN2.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > $ ls *.pdb 1cbs.pdb 1cel.pdb hydro.pdb q.pdb twentyz.pdb ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This resets some of the program parameters to the values that I deemed reasonable.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > co re Reset program constants to defaults ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This lists the names of those parameters than can be modified by the user.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > co li BLIMLO = B-factor default minimum : ( 2.000) BLIMHI = B-factor default maximum : ( 50.000) QLIMLO = Occupancy default minimum : ( 0.000) QLIMHI = Occupancy default maximum : ( 1.000) MXCACA = Max connected CA-CA distance : ( 4.500) TORTOL = Torsion/improper tolerance : ( 5.000) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: COnstants SEt name value
name = parameter name
value = new value for this parameter
This enables you to set the value of a program parameter. Use the COnstants LIst option to see what parameters can be set in the current version of the program
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > co set tortol 10 Set TORTOL to 10.000 MOLEMAN2 > co set junk 103 Set JUNK to 103.000 ERROR --- Name not recognised ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: REad file [format] [hydro]
file = PDB file name
format = Pdb | Alwyn
hydro = No | Yes
The Alwyn format is only required when you try to read *very* old PDB
files created with older versions of O.
By default, hydrogen atoms are *stripped* when you read a file, unless
you set the hydro parameter to y(es) !
Once the file has been read, some book-keeping is done. By default,
*all* atoms will be selected (including hydrogen atoms, if they
were read) !
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > re 1cbs.pdb Reading from file : (1cbs.pdb) in normal PDB format ignoring hydrogen atoms ==> Found file in GKPATH : (/nfs/pdb/full/1cbs.pdb) HEADER : RETINOIC-ACID TRANSPORT 28-SEP-94 1CBS 1CBS 2 AUTHOR : G.J.KLEYWEGT,T.BERGFORS,T.A.JONES 1CBS 10 REVDAT : 1 26-JAN-95 1CBS 0 1CBS 11 CRYST1 : 45.650 47.560 77.610 90.00 90.00 90.00 P 21 21 21 4 1CBS 216>>>>> END card encountered <<<<<
Nr of lines read : ( 1459) Nr of hydrogens skipped : ( 0)
Total nr of residues : ( 238) Nr of amino acid residues : ( 137) Nr of nucleic acids : ( 0) Nr of waters : ( 100) Nr of metals : ( 0) Nr of inorganics : ( 0) Nr of carbohydrates : ( 0) Nr of organic compounds : ( 1) Nr of other compounds : ( 0)
Checking for missing/extra atoms ...
Checking "special" positions (X~Y~Z), Bs and Qs ... No suspicious coordinates encountered All atoms have B <= 100 A2 All atoms have B >= 2.0 A2 All atoms have Q <= 1.0 All atoms have Q >= 0.01 No atoms with ANISOU cards
Nr of atoms now : ( 1213) Nr of residues : ( 238) Select ALL atoms Selection history : (ALL |) Nr of selected atoms : ( 1213) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: APpend file [format] [hydro]
Same parameters etc. as for the REad command. Book-keeping is done again, and *all* atoms are selected.
Syntax: WRite file [format] [which]
file = PDB file name
format = Pdb | Xplor | Ccp4
which = ALl | NO_hydro | SElected | PAla |
PGly | PSer | CAlpha
Write (a subset of) the current atoms to a PDB file. You must provide the name of the output file. If the file already exists, an error message is generated and you are asked if you want to overwrite it ("Open file as OLD (Y/N) ?"). If you don't, you can subsequently supply a different file name.
If the format is Pdb, then all records (including any REMARKS etc.) will be written, and atoms which were on HETATM cards on input will be on HETATM cards on output. Cell constants etc. are also included.
If the format is Xplor, only ATOM records will be written (even for HETATMs), and nothing else (no CRYST1, etc.).
If the format is Ccp4, the same is written as for Xplor format, but in addition the CRYST1 etc. cards will added at the top of the file.
You can specify which atoms you want to write out:
- ALl writes all atoms currently in memory
- NO_hydro writes all non-hydrogen atoms
- SElected writes only the currently selected atoms (if any)
- PGly creates a poly-Glycine file (i.e., only main-chain atoms of
protein residues and all residues will be called GLY; the program
recognizes main-chain atoms by their atom names or by the fact
that they have been labelled as such in the library file)
- PAla generates a poly-Alanine file in a similar fashion
- PSer generates a poly-Serine file (in which atoms CG, OG, SG,
OG1 and CG1 will be called OG)
- CAlpha writes only the C-alpha atoms of protein residues
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > wr q.pdb p se Output PDB file : (q.pdb) Format : (Pdb) Atoms : (SE) Number of atoms to write : ( 3220) Nr of atoms written : ( 3220) Nr of lines written : ( 3705)CPU total/user/sys : 1.0 1.0 0.0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > wr q.pdb ccp pser Output PDB file : (q.pdb) Format : (CCP) Atoms : (PSER) ERROR --- XOPXNA - error # 126 while opening NEW file : q.pdb OPEN : (UNIT= 10 STATUS=NEW CAR_CONTROL=LIST FORM=FORMATTED ACCESS=SEQUENTIAL) Error : (Connection timed out) Open file as OLD (Y/N) ? (N) y Number of atoms to write : ( 4952) Nr of atoms written : ( 4952) Nr of lines written : ( 4952)CPU total/user/sys : 1.5 1.5 0.0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: SPlit file_prefix
This option is primarily intended for X-PLOR users. As such, it removes much of the dread previously associated with the preparation of files for the GENERATE step.
You provide the prefix for the PDB file names (e.g., /Usr/Billy/Xplor/m1 or ../../xplor/m5tom6/m5 or ./m1). Upper and lower case characters in the prefix will be maintained. For each segment id found in the set of *ALL* atoms, a separate PDB file is written which contains all atoms which have that segment id (even if they are separated in the structure). The name of this file will be your prefix plus an underscore (_) plus the segment id (converted to lowercase and without any spaces) plus the extension ".pdb". For instance, if your prefix is "../Xplor/m1", then segment "PROA" will be written to a file called "../Xplor/m1_proa.pdb".
In addition to all these PDB files, an X-PLOR input file is created for the GENERATE stage. It will need some editing if your structure contains things other than protein and water (i.e.: insert topology and parameter file names; insert any patches that are necessary). The program will also look for any disulfide links and create DISU patch statements for each of these (if any). Note that in the case of for instance iron-sulfur clusters you may have to remove (some of) the DISU patch statements !
IMPORTANT: the segment id *ALONE* is used to identify different segments. In other words: the chain names are ignored (this is in agreement with the current PDB convention in which segment identifiers designate separate entities; a chain may contain multiple segments, e.g. protein + glycosylation + ligand + water).
NOTE: make sure that the segment ids make sense !! If you just read in a PDB file from O or downloaded one from Brookhaven, you probably have to use one or more of the CHain commands (e.g., CHain ASk or CHain AUto) to get correct segmentation. You have yourself to blame for any segmentation faults ;-)
Since the program writes all atoms with a certain segment id to the same file (even if they are interspersed with other segments), you can use the CHain commands to "merge" two previously distinct segments into one. For instance, if you have two-fold NCS, you may initially have refined only waters which obey the NCS and used separate segments for them (e.g., WATA and WATB). When you start to add waters which are not conserved in both molecules, you could create a third segment but this tends to get very confusing as you add and delete waters while you rebuild. Instead, you may want to merge all waters. You can do this by simply giving all of them the same segment id with the CHain commands.
NOTE: from version 0.21 onward, the program tries its best to make sure that OT1 and OT2 are named correctly. Also, if an OT2 atom is missing it will be generated on the fly and written to the PDB file (but it will not be added to your structure in memory !).
NOTE: from version 1.1.1 onward, the default is to delete hydrogen atoms and atoms with unknown coordinates.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > re test.pdb ... MOLEMAN2 > ch au ... MOLEMAN2 > split qqq Split PDB files for X-PLOR File prefix : (qqq) X-PLOR generate input file : (qqq_generate.inp)File nr 1 Segment |AAAA| File name : qqq_aaaa.pdb ATOM 1 CB SER A 4 51.238 19.799 7.294 1.00 34.72 AAAA Found & written OT1 ... Adding OT2 at : ( 39.097 17.619 13.212) Nr of lines written : ( 446) Nr of atoms written : ( 443)
File nr 2 Segment |AAAB| File name : qqq_aaab.pdb ATOM 483 N ASN B 66 26.962 19.074 20.708 1.00 2.00 AAAB Found & written OT1 Found & written OT2 Nr of lines written : ( 3747) Nr of atoms written : ( 3744)
File nr 3 Segment |AAAC| File name : qqq_aaac.pdb ATOM 4227 CB THR C 1 -3.115 5.872 13.814 1.00 77.65 AAAC Found & written OT1 ... Adding OT2 at : ( 1.912 19.586 15.804) Nr of lines written : ( 467) Nr of atoms written : ( 464)
File nr 4 Segment |AAAD| File name : qqq_aaad.pdb ATOM 4691 O1 HOH D 701 -6.674 -2.991 11.360 1.00 15.26 AAAD Nr of lines written : ( 39) Nr of atoms written : ( 36)
File nr 5 Segment |AAAE| File name : qqq_aaae.pdb ATOM 4727 ZN+2 ZNC E 901 -15.390 36.554 20.084 1.00 19.82 AAAE Nr of lines written : ( 5) Nr of atoms written : ( 2)
File nr 6 Segment |AAAF| File name : qqq_aaaf.pdb ATOM 4729 C1 NAG F 990 39.707 11.948 13.548 1.00 77.90 AAAF Nr of lines written : ( 17) Nr of atoms written : ( 14)
Nr of PDB files generated : ( 6)
Looking for disulfides ... Looking for CYS- SG atoms ... ATOM 496 SG CYS B 67 26.853 23.275 24.788 1.00 18.16 AAAB ATOM 719 SG CYS B 94 27.958 21.920 25.822 1.00 2.00 AAAB ATOM 1765 SG CYS B 231 17.706 42.764 23.358 1.00 2.00 AAAB ATOM 1944 SG CYS B 254 15.900 18.643 43.219 1.00 14.44 AAAB ATOM 2032 SG CYS B 265 17.033 17.112 43.932 1.00 13.67 AAAB ATOM 3118 SG CYS B 402 11.202 50.463 20.218 1.00 17.06 AAAB ATOM 4105 SG CYS B 521 12.171 51.649 18.881 1.00 2.00 AAAB ATOM 4247 SG CYS C 3 -0.622 9.196 15.268 1.00 34.29 AAAC ATOM 4355 SG CYS C 17 1.031 6.187 17.911 1.00 53.34 AAAC ATOM 4388 SG CYS C 22 -1.328 8.466 17.020 1.00 31.20 AAAC ATOM 4529 SG CYS C 39 2.164 5.235 19.293 1.00 20.78 AAAC ATOM 4539 SG CYS C 41 -5.604 11.002 25.701 1.00 52.29 AAAC ATOM 4620 SG CYS C 52 -4.745 12.199 24.311 1.00 29.91 AAAC ATOM 4626 SG CYS C 53 -4.229 13.247 16.868 1.00 42.61 AAAC ATOM 4669 SG CYS C 59 -4.012 11.998 15.283 1.00 12.80 AAAC Nr of CYS SG atoms : ( 15) Max SG-SG distance for link : ( 2.200) Disulfide # 1 67 AAAB <-> 94 AAAB @ 2.03 A Disulfide # 2 254 AAAB <-> 265 AAAB @ 2.03 A Disulfide # 3 402 AAAB <-> 521 AAAB @ 2.03 A Disulfide # 4 3 AAAC <-> 22 AAAC @ 2.03 A Disulfide # 5 17 AAAC <-> 39 AAAC @ 2.02 A Disulfide # 6 41 AAAC <-> 52 AAAC @ 2.03 A Disulfide # 7 53 AAAC <-> 59 AAAC @ 2.03 A Nr of disulfides : ( 7)
X-PLOR generate input file written CPU total/user/sys : 1.5 1.4 0.1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The PDB files may look as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- REMARK Created by MOLEMAN2 V. 960227/0.8 at Tue Feb 27 15:29:35 1996 for user gerard REMARK File name : m1_aaaa.pdb ATOM 1 CB ALA 86 3.109 42.928 53.312 1.00 28.54 AAAA ATOM 2 C ALA 86 4.129 45.032 52.428 1.00 27.90 AAAA ... ATOM 3319 OT1 LEU 447 38.267 47.693 63.602 1.00 18.65 AAAA ATOM 3320 OT2 LEU 447 39.049 46.653 65.371 1.00 20.12 AAAA REMARK Nr of atoms in file : 2740 END ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The GENERATE input file may look as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- remarks File m1_generate.inp - generate pdb/psf file remarks Created by MOLEMAN2 V. 960227/0.8 at Tue Feb 27 15:29:35 1996 for user gerardtopology @tophcsdx.pro @toph19.sol { add more topology files here } end
parameter @parhcsdx.pro @param19.sol { add more parameter files here }
nbonds atom cdie shift eps=8.0 e14fac=0.4 cutnb=7.5 ctonnb=6.0 ctofnb=6.5 nbxmod=5 vswitch wmin=0.5 end { dielectric constant set to 8.0 (EPS) } { close contacts printed only if dist < 0.5 A (WMIN) } end
{ protein } segment name="AAAA" chain @toph19.pep coordinates @m1_aaaa.pdb end end vector do (name="CD1") ( name CD and resname ile ) coordinates @m1_aaaa.pdb
{ CARB } segment name="BBBB" chain coordinates @m1_bbbb.pdb end end coordinates @m1_bbbb.pdb
{ HETE } segment name="CCCC" chain coordinates @m1_cccc.pdb end end coordinates @m1_cccc.pdb
{ protein } segment name="KKKK" chain @toph19.pep coordinates @m1_kkkk.pdb end end vector do (name="CD1") ( name CD and resname ile ) coordinates @m1_kkkk.pdb
{ CARB } segment name="LLLL" chain coordinates @m1_llll.pdb end end coordinates @m1_llll.pdb
{ HETE } segment name="MMMM" chain coordinates @m1_mmmm.pdb end end coordinates @m1_mmmm.pdb
{ META } segment name="XXXX" chain coordinates @m1_xxxx.pdb end end coordinates @m1_xxxx.pdb
{ WATE } segment name="WWWW" chain coordinates @m1_wwww.pdb end end coordinates @m1_wwww.pdb
{ the disulfides } patch DISU refer=1=(segid="AAAA" and resid 176) refer=2=(segid="AAAA" and resid 235) end
patch DISU refer=1=(segid="AAAA" and resid 368) refer=2=(segid="AAAA" and resid 415) end
patch DISU refer=1=(segid="KKKK" and resid 176) refer=2=(segid="KKKK" and resid 235) end
patch DISU refer=1=(segid="KKKK" and resid 368) refer=2=(segid="KKKK" and resid 415) end
flags exclude vdw elec end
hbuild selection=(hydrogen and not known) phistep=45 end
{ optimise hydrogens to get rid of clashes } constraints fix=( not hydrogen ) end flags include vdw elec end minimize powell nstep=50 end constraints fix=( not all ) end
write coordinates output=m1_gen.pdb end
write structure output=m1.psf end
stop ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This command (of which the first SIX letters should be typed - to prevent accidental deletion) removes all atoms from memory.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > dele ERROR --- Invalid command ==> (dele) MOLEMAN2 > delete ALL ATOMS AND RESIDUES DELETED !!! ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
You have the following options with this command:
- Atom_all; this will change all HETATMs to ATOMs (useful if you
want to use a model from the PDB for molecular replacement or
refinement with a program that chokes on or ignores HETATM cards);
- Deduce; the program will set all protein and nucleic acid atoms
to ATOM, and all others to HETATM (useful when you deposit your
model coordinates with the PDB).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > pd he a All atoms set to type ATOM MOLEMAN2 > pd he d Deducing ATOM/HETATM types ... Nr set to ATOM : ( 4952) Nr set to HETATM : ( 0) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
O likes to write the chemical element number of each atom/hetatm, but the PDB does not like them. Use this command to remove them.
Supply the six cell constants, the number of molecules in the unit cell (using the PDB definition), and the spacegroup symbol (using the PDB definition, i.e. with spaces). The cell constants *must* be known for CCP4-type PDB files !
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > pd cr 84 84 111.8 90 90 90 8 "P 21 21 2" Unit-cell axes (A) : ( 84.000 84.000 111.800) Unit-cell angles (deg) : ( 90.000 90.000 90.000) Unit-cell volume (A3) : ( 7.889E+05) Nr of molecules in cell : ( 8) Spacegroup symbol : (P 21 21 2) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > pdb crys 41.2 41.2 196.5 90 90 90 Nr of molecules in cell ? ( 8) Spacegroup symbol ? (P 21 21 2) P 41 21 2 Unit-cell axes (A) : ( 41.200 41.200 196.500) Unit-cell angles (deg) : ( 90.000 90.000 90.000) Unit-cell volume (A3) : ( 3.335E+05) Nr of molecules in cell : ( 8) Spacegroup symbol : (P 41 21 2) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: PDb SSbond what
what = List | Delete | Generate
Use the COnstants SEt command to change the cut-off S-S link distance if necessary.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > pdb ssb lis List SSBOND records SSBOND 1 CYS A 4 CYS A 72 1CEL 340 SSBOND 2 CYS A 19 CYS A 25 1CEL 341 SSBOND 3 CYS A 50 CYS A 71 1CEL 342 SSBOND 4 CYS A 61 CYS A 67 1CEL 343 ... SSBOND 20 CYS B 261 CYS B 331 1CEL 359 Nr of SSBOND records listed : ( 20) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > pdb ssb del Delete SSBOND records Nr of SSBOND records deleted : ( 20) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > pdb ssb gen Generate SSBOND records Looking for CYS- SG atoms ... ATOM 25 SG CYS A 4 36.618 67.989 34.228 1.00 21.90 1CEL 398 ... ATOM 5990 SG CYS B 331 -7.298 9.647 20.243 1.00 10.03 1CEL6363 ATOM 6483 SG CYS B 397 -25.330 24.877 13.503 1.00 10.62 1CEL6856 Max SG-SG distance for link : ( 2.200) SSBOND 1 CYS A 4 CYS A 72 S-S = 2.03 A SSBOND 2 CYS A 19 CYS A 25 S-S = 2.02 A ... SSBOND 19 CYS B 238 CYS B 243 S-S = 2.03 A SSBOND 20 CYS B 261 CYS B 331 S-S = 2.03 A Nr of SSBOND records generated : ( 20) MOLEMAN2 > pdb ssb l List SSBOND records SSBOND 1 CYS A 4 CYS A 72 S-S = 2.03 A SSBOND 2 CYS A 19 CYS A 25 S-S = 2.02 A SSBOND 3 CYS A 50 CYS A 71 S-S = 2.02 A ... SSBOND 19 CYS B 238 CYS B 243 S-S = 2.03 A SSBOND 20 CYS B 261 CYS B 331 S-S = 2.03 A Nr of SSBOND records listed : ( 20) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: PDb REmark text
text = text of the remark
Add information about the molecule(s) as a REMARK record (e.g., model name, current R-factor and Rfree, etc.).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
MOLEMAN2 > pdb re "Model M3 @ 960303 R=0.231 Rfree=0.273"
Add REMARK record : (Model M3 @ 960303 R=0.231 Rfree=0.273)
4: REMARK Model M3 @ 960303 R=0.231 Rfree=0.273
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: PDb LIst_remark
List the current set of REMARK records (if any).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
MOLEMAN2 > pdb li
List REMARK records
Nr of REMARK records : ( 4)
1: REMARK FILENAME="/nfs/gerard/gerard/proteins/cbh2/ibgx/xplor/m1_final_2.pdb"
2: REMARK Uses *NO* sigma or amplitude cut-offs
3: REMARK DATE:15-Jan-96 23:31:00 created by user: gerard
4: REMARK Model M3 @ 960303 R=0.231 Rfree=0.273
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: PDb DElete_remark which
which = number of the REMARK record (* means ALL)
Delete one or all REMARK records (if any).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > pdb del 3 Delete REMARK record nr: ( 3) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: PDb NAme which old new
which = Atom | Residue
old = old name to replace
new = new name
Change the atom or residue name of selected atoms. A residue is considered to be selected if at least one of its atoms is selected.
This command can be used to rename all waters (e.g., from residue HOH with atom O1 to residue WAT and atom OW). You can also write macros, for instance to convert residue and atom names for your favourite ligand or cofactor from/to X-PLOR or CCP4 or TNT or PDB or ... conventions.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > sel and type water ... MOLEMAN2 > pdb name res hoh wat Replace residue name |HOH| by |WAT| Nr of residues changed : ( 100) MOLEMAN2 > pdb name atom " o1 " " ow " Replace atom name | O1 | by | OW | Nr of atom names changed : ( 100) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The following macro would convert X-PLOR waters into PDB waters:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- select all select and type water pdb name atom " o1 " " o " ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
In the new PDB format definition, column 77-78 of each ATOM and HETATM record contains the symbol of the chemical element type of the atom and column 79-80 the charge (don't ask me why the charge has to fit inside two columns ...). This command tries to deduce this information as best as it can, using information in the atom name (4 characters) field.
Chemical element: the following four methods are tried in turn:
(1) is it one of the special hydrogen names ?
(2) are the first two characters of the atom name a valid element symbol ?
(3) is a space plus the second character a valid element symbol ?
(4) is a space plus the first character a valid element symbol ?
(5) if none of the above, generate an error message, and use "??" as
the element symbol
Charge: the following are valid charge definitions for columns 3 and 4
of the atom name, which will be recognised by the program (default
charge otherwise is " 0"):
(1) "++" or "--"
(2) "+ " or " +" or "- " or " -"
(3) "n+" or "+n" or "n-" or "-n", where n is 0,1,2,...,9
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > pdb che Deriving chemical name and charge ... Nr of atoms processed : ( 10) Unknown chemical element : ( 0) Nr of positive atoms : ( 7) Nr of negative atoms : ( 3) Nr uncharged or unknown : ( 0) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Example: the following bogus PDB file:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- HETATM 7039 CA++ CA K 440 40.443 57.977 83.935 1.00 16.86 HETATM 7039 CA2+ CA K 441 40.443 57.977 83.935 1.00 16.86 HETATM 7039 CA+2 CA K 442 40.443 57.977 83.935 1.00 16.86 HETATM 7039 S-- CA K 443 40.443 57.977 83.935 1.00 16.86 HETATM 7039 S-2 CA K 444 40.443 57.977 83.935 1.00 16.86 HETATM 7039 S2- CA K 445 40.443 57.977 83.935 1.00 16.86 HETATM 7039 AH1+ CA K 446 40.443 57.977 83.935 1.00 16.86 HETATM 7039 H+ CA K 447 40.443 57.977 83.935 1.00 16.86 HETATM 7039 'H1+ CA K 448 40.443 57.977 83.935 1.00 16.86 HETATM 7039 HX + CA K 449 40.443 57.977 83.935 1.00 16.86 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
gives the following result:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- HETATM 7039 CA++ CA A 440 40.443 57.977 83.935 1.00 16.86 AAAACA+2 HETATM 7039 CA2+ CA A 441 40.443 57.977 83.935 1.00 16.86 AAAACA+2 HETATM 7039 CA+2 CA A 442 40.443 57.977 83.935 1.00 16.86 AAAACA+2 HETATM 7039 S-- CA A 443 40.443 57.977 83.935 1.00 16.86 AAAA S-2 HETATM 7039 S-2 CA A 444 40.443 57.977 83.935 1.00 16.86 AAAA S-2 HETATM 7039 S2- CA A 445 40.443 57.977 83.935 1.00 16.86 AAAA S-2 HETATM 7039 AH1+ CA A 446 40.443 57.977 83.935 1.00 16.86 AAAA H+1 HETATM 7039 H+ CA A 447 40.443 57.977 83.935 1.00 16.86 AAAA H+1 HETATM 7039 'H1+ CA A 448 40.443 57.977 83.935 1.00 16.86 AAAA H+1 HETATM 7039 HX + CA A 449 40.443 57.977 83.935 1.00 16.86 AAAA H+1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: PDb SAnity_check
This command performs a number of sanity checks on your PDB file w.r.t. alternate locations and occupancies. Since alternate locations are often generated by manual editing of a PDB file, mistakes are easily made. This command will check for the following for each atom in your structure:
- ERROR - ALTERNATE LOCATION WITH BLANK LABEL
- ERROR - ALTERNATE LOCATIONS WITH IDENTICAL LABELS
- ERROR - ALTERNATE LOCATIONS IN IDENTICAL POSITIONS
- WARNING - OCCUPANCIES DO NOT SUM TO 1.00
- WARNING - SINGLE LOCATION WITH NON-BLANK LABEL
- WARNING - MORE THAN 3 ALTERNATE LOCATIONS
- WARNING - ALTERNATE LOCATIONS IN ALMOST IDENTICAL POSITIONS
- NOTE - LABELS NOT IN ALPHABETICAL ORDER
- NOTE - ALTERNATE LOCATIONS IN SIMILAR POSITIONS
Note: the BOok_keep command provides additional sanity-related info, and the DIstance LIst command can be used to print a list of atoms that lie too close to each other in space (e.g., DIst LIst 0 1).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > pdb sanWARNING - OCCUPANCIES DO NOT SUM TO 1.00 for the following atom, the occupancies of the 1 alternate locations add up to 0.50 instead of 1.00 (this can be okay if you are sure that the atom has partial occupancy, or if it lies in a special position, such as on a twofold axis): ATOM 845 CB GLN A 53 74.460 37.771 14.755 0.50 7.15 C [...] ERROR - ALTERNATE LOCATIONS IN IDENTICAL POSITIONS the following two atoms have alternate locations but their distance is only 0.03 A, suggesting that they are in identical positions in space and should be merged into a single location: ATOM 1245 CA ALYS A 78 73.331 23.163 -7.825 0.50 12.88 C ATOM 1246 CA BLYS A 78 73.311 23.144 -7.841 0.50 13.01 C
WARNING - ALTERNATE LOCATIONS IN ALMOST IDENTICAL POSITIONS the following two atoms have alternate locations but their distance is only 0.10 A, suggesting that they are in almost identical positions in space and could be merged into a single location: ATOM 1249 CB ALYS A 78 73.945 24.503 -7.388 0.50 12.63 C ATOM 1250 CB BLYS A 78 73.881 24.510 -7.464 0.50 12.88 C
NOTE - ALTERNATE LOCATIONS IN SIMILAR POSITIONS the following two atoms have alternate locations and their distance is 0.32 A, suggesting that they are in similar positions in space and could perhaps be merged into a single location: ATOM 1255 CG ALYS A 78 74.081 25.533 -8.510 0.50 12.41 C ATOM 1256 CG BLYS A 78 74.263 25.347 -8.691 0.50 13.05 C [...]
WARNING - OCCUPANCIES DO NOT SUM TO 1.00 for the following atom, the occupancies of the 1 alternate locations add up to 0.50 instead of 1.00 (this can be okay if you are sure that the atom has partial occupancy, or if it lies in a special position, such as on a twofold axis): ATOM 7694 O AHOH S 64 70.295 19.056 5.753 0.50 2.05 O
WARNING - SINGLE LOCATION WITH NON-BLANK LABEL the following atom has only one location, but its alternate location label is "A" instead of blank (this can be okay in some cases, e.g. for waters that only interact with one of a set of alternative conformations of an amino acid residue): ATOM 7694 O AHOH S 64 70.295 19.056 5.753 0.50 2.05 O [...] ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: PDb SEqres
This command generates a set of SEQRES records for every chain that contains amino acids or nucleic acids. Note that, by necessity, this command does NOT know if your model contains all residues of the molecule(s) that you crystallised. If this is NOT the case (e.g., if tags are missing, or loop residues, or terminal residues), then the SEQRES records do NOT contain the information they are supposed to contain and, hence, can NOT be used for deposition purposes !!!
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > read 1cbs.pdb [...] MOLEMAN2 > pdb seq Generating quick-n-dirty SEQRES records ... Add REMARK record : (Quick-n-dirty SEQRES records) 183: REMARK Quick-n-dirty SEQRES records Chain IDs found : ( )Chain ID : ( ) Nr of residues : ( 137) Nr of SEQRES records : ( 11) MOLEMAN2 > wr qq.pdb [...] MOLEMAN2 > $ grep SEQRES qq.pdb Spawn system command : ( grep SEQRES qq.pdb) REMARK Quick-n-dirty SEQRES records SEQRES 1 137 PRO ASN PHE SER GLY ASN TRP LYS ILE ILE ARG SER GLU 1CBS 202 SEQRES 2 137 ASN PHE GLU GLU LEU LEU LYS VAL LEU GLY VAL ASN VAL 1CBS 203 SEQRES 3 137 MET LEU ARG LYS ILE ALA VAL ALA ALA ALA SER LYS PRO 1CBS 204 SEQRES 4 137 ALA VAL GLU ILE LYS GLN GLU GLY ASP THR PHE TYR ILE 1CBS 205 SEQRES 5 137 LYS THR SER THR THR VAL ARG THR THR GLU ILE ASN PHE 1CBS 206 SEQRES 6 137 LYS VAL GLY GLU GLU PHE GLU GLU GLN THR VAL ASP GLY 1CBS 207 SEQRES 7 137 ARG PRO CYS LYS SER LEU VAL LYS TRP GLU SER GLU ASN 1CBS 208 SEQRES 8 137 LYS MET VAL CYS GLU GLN LYS LEU LEU LYS GLY GLU GLY 1CBS 209 SEQRES 9 137 PRO LYS THR SER TRP THR ARG GLU LEU THR ASN ASP GLY 1CBS 210 SEQRES 10 137 GLU LEU ILE LEU THR MET THR ALA ASP ASP VAL VAL CYS 1CBS 211 SEQRES 11 137 THR ARG VAL TYR VAL ARG GLU 1CBS 212 SEQRES 1 137 PRO ASN PHE SER GLY ASN TRP LYS ILE ILE ARG SER GLU SEQRES 2 137 ASN PHE GLU GLU LEU LEU LYS VAL LEU GLY VAL ASN VAL SEQRES 3 137 MET LEU ARG LYS ILE ALA VAL ALA ALA ALA SER LYS PRO SEQRES 4 137 ALA VAL GLU ILE LYS GLN GLU GLY ASP THR PHE TYR ILE SEQRES 5 137 LYS THR SER THR THR VAL ARG THR THR GLU ILE ASN PHE SEQRES 6 137 LYS VAL GLY GLU GLU PHE GLU GLU GLN THR VAL ASP GLY SEQRES 7 137 ARG PRO CYS LYS SER LEU VAL LYS TRP GLU SER GLU ASN SEQRES 8 137 LYS MET VAL CYS GLU GLN LYS LEU LEU LYS GLY GLU GLY SEQRES 9 137 PRO LYS THR SER TRP THR ARG GLU LEU THR ASN ASP GLY SEQRES 10 137 GLU LEU ILE LEU THR MET THR ALA ASP ASP VAL VAL CYS SEQRES 11 137 THR ARG VAL TYR VAL ARG GLU ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: PDb INdonesia
(Alternatively: PDb FArout)
This command uses the YASSPA-determined secondary structure assignment to generate quick'n'dirty secondary structure records (HELIX and SHEET). Save the molecule to a new PDB file to get these records. The new PDB file can then subsequently be read by Indonesia (which used to be called "FarOut" once upon a time). The records are used by Indonesia to increase the gap penalties in regions of secondary structure when you align sequences to it.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > pdb far Generating quick-n-dirty HELIX and SHEET records ... Add REMARK record : (YASSPA quick-n-dirty HELIX and SHEET records) 232: REMARK YASSPA quick-n-dirty HELIX and SHEET records Record : (SHEET 1 1 1 THR A 2 PRO A 5 0) Record : (HELIX 1 1 ILE A 7 ARG A 17 1) Record : (HELIX 2 2 ALA A 27 TYR A 29 1) Record : (SHEET 2 2 1 CYS A 32 ILE A 35 0) Record : (SHEET 3 3 1 THR A 39 PRO A 41 0) Record : (HELIX 3 3 GLY A 42 TYR A 44 1) Nr of HELIX records : ( 3) Nr of SHEET records : ( 3) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This is the old name of the PDb INdonesia command (quod vide).
Syntax: PDb NUmber first_new
Renumber the selected residues, starting from the given number.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > se and typ water AND atom selection With atoms for which : (TYP) Equals : (WATER) Selection history : (ALL | AND TYpe = WATE |) Nr of selected atoms : ( 100) MOLEMAN2 > pdb numb 501 Renumber selected residues starting at : ( 501) Nr of last changed residue : ( 600) Nr of residues changed : ( 100) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
These commands enable you to define a subset of atoms for which one or more operations have to be carried out. You can use this, for example, to get statistics about the temperature factors of all protein main-chain atoms in segment ABC3, or to set the occupancy of all calcium atoms to 0.5.
Some selection commands reset the selections (ALl, NOne, HYdrogen, and EXhydrogen). Others make it narrower (ANd), wider (OR) or invert the current selection (NEgate).
Examples:
- to select the non-hydrogen atoms of all segments except QQQQ, use:
SElect HYdrogen, SElect OR SEgid QQQQ, SElect NEgate
- to select all non-hydrogen main-chain protein atoms of chain A, use:
SElect EXhydro, SElect ANd TYpe PROT, SElect ANd CLass Main,
SElect ANd CHain A
- to select all non-hydrogen protein atoms, use: SElect EXhydro,
SElect ANd TYpe PROT
- to select all non-hydrogen protein and nucleic acid atoms, use:
SElect EXhydro, SElect ANd TYpe PROT, SElect OR TYpe NUCL
The program keeps a record of the SElection commands executed since the last time a resetting command was carried out. For instance, after selecting all non-hydrogen main-chain protein atoms, you will see:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > se ? Selection history : (NON-HYDROGEN | AND TYpe = PROT | AND CLass = MAI |) Nr of selected atoms : ( 548) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The number of selected atoms is shown with a history of the recently executed SElect commands.
This selects all atoms, including any hydrogen atoms.
This de-selects all atoms.
All atoms which had previously been selected will be de-selected, and the other way around.
No non-hydrogen atoms will be selected.
No hydrogen atoms will be selected.
If at least one atom of a residue has been selected, all atoms of the residue will be selected.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > se and res rea ... Nr of selected atoms : ( 22) MOLEMAN2 > se dist 0 3.5 ... Nr of selected atoms : ( 29) MOLEMAN2 > se by Select by residue Selection history : (ALL | AND REsidu = REA | DIstance 0.00 3.50 | BY_residue |) Nr of selected atoms : ( 55) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This can be used to select all atoms that lie in a distance shell from any given point in 3D space. In the following example, the SElect POint command is used (with others) to select the atoms of all protein residues that have at least one atom that lies within 4 Å from either the manganese or the chloride ion in PDB entry 2CHR and to write them to a small PDB file:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > read pdb2chr.ent [...] MOLEMAN2 > select all [...] MOLEMAN2 > select point and 28.850 50.835 90.295 0 4 Point (A) : ( 28.850 50.835 90.295) Minimum distance (A) : ( 0.000) Maximum distance (A) : ( 4.000) Selection history : (ALL | AND POint_distance |) Nr of selected atoms : ( 13) MOLEMAN2 > list List first selected atom of every residue ATOM 1459 CG ASP 194 29.827 52.252 93.077 1.00 18.37 2CHR1601 ATOM 1663 CG GLU 220 32.533 50.136 90.995 1.00 18.18 2CHR1805 ATOM 1859 CB ASP 245 30.976 50.114 87.466 1.00 23.09 2CHR2001 ATOM 1870 OE1 GLU 246 29.942 53.433 87.548 1.00 7.93 2CHR2012 ATOM 2789 MN MN 400 28.850 50.835 90.295 1.00 9.21 2CHR2931 ATOM 2790 CL CL 500 26.076 49.901 90.673 1.00 2.00 2CHR2932 Nr of residues listed : ( 6) MOLEMAN2 > select point or 26.076 49.901 90.673 0 4 Point (A) : ( 26.076 49.901 90.673) Minimum distance (A) : ( 0.000) Maximum distance (A) : ( 4.000) Selection history : (ALL | AND POint_distance | OR POint_distance |) Nr of selected atoms : ( 17) MOLEMAN2 > select by_residue Select by residue Selection history : (ALL | AND POint_distance | OR POint_distance | BY_residue |) Nr of selected atoms : ( 77) MOLEMAN2 > select and type protein AND atom selection With atoms for which : (TYPE) Equals : (PROTEIN) Selection history : (ALL | AND POint_distance | OR POint_distance | BY_residue | AND TYpe = PROT |) Nr of selected atoms : ( 75) MOLEMAN2 > write mncl.pdb pdb selected Output PDB file : (mncl.pdb) Format : (Pdb) Atoms : (SELECTED) Number of atoms to write : ( 75) Nr of atoms written : ( 75) Nr of lines written : ( 224) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This can be used to select, e.g. a ligand, and subsequently all atoms within 3.5 or 4 Å from this compound.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > se and res rea ... Nr of selected atoms : ( 22) MOLEMAN2 > se dist 0 3.5 ... Nr of selected atoms : ( 29) MOLEMAN2 > se by Select by residue Selection history : (ALL | AND REsidu = REA | DIstance 0.00 3.50 | BY_residue |) Nr of selected atoms : ( 55) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: SElect ANd what which
what = CHain | SEgid | TYpe | CLass |
REsidue | ATom
which = which chain, segid, etc. to use
type can prot, nucl, wate, etc.
class can be main or side chain
residue can be Ala, HOH, BGL etc.
atom can be " CA ", " O1 " etc.
This can be used to select by chain name (one character), segment name (4 characters), type (any of PROT, NUCL, WATE, META, INOR, CARB, ORGA or HETE; 4 characters), or class (main or side chain, one character). Alternatively, you can select by residue type (Ala, Asn, etc.) or by atom name (enclose in "double quotes"). Note that atom names are 4 characters (e.g., use " CA " to select C-alpha atoms).
The new selection will be those atoms that were already selected AND satisfy the new criterion. This usually reduces the selection.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > se ex Select NON-HYDROGEN atoms Selection history : (NON-HYDROGEN |) Nr of selected atoms : ( 1213) MOLEMAN2 > se an ty prot AND atom selection With atoms for which : (TY) Equals : (PROT) Selection history : (NON-HYDROGEN | AND TYpe = PROT |) Nr of selected atoms : ( 1091) MOLEMAN2 > se and cl main AND atom selection With atoms for which : (CL) Equals : (MAIN) Selection history : (NON-HYDROGEN | AND TYpe = PROT | AND CLass = MAIN |) Nr of selected atoms : ( 548) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > se ex Select NON-HYDROGEN atoms Selection history : (NON-HYDROGEN |) Nr of selected atoms : ( 5794) MOLEMAN2 > se an resi trp AND atom selection With atoms for which : (RESI) Equals : (TRP) Selection history : (NON-HYDROGEN | AND REsidu = TRP |) Nr of selected atoms : ( 280) MOLEMAN2 > se and at " CA " AND atom selection With atoms for which : (AT) Equals : ( CA) Selection history : (NON-HYDROGEN | AND REsidu = TRP | AND ATom = CA |) Nr of selected atoms : ( 20) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: SElect BUtnot what which
what = CHain | SEgid | TYpe | CLass |
REsidue | ATom
which = which chain, segid, etc. to use
type can prot, nucl, wate, etc.
class can be main or side chain
residue can be Ala, HOH, BGL etc.
atom can be " CA ", " O1 " etc.
Analogous to SElect ANd and SElect OR.
The new selection will be those atoms that were already selected AND do NOT satisfy the new criterion. This usually narrows the selection.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > sel but type prot BUtnot atom selection With atoms for which : (TYPE) Equals : (PROT) Selection history : (ALL | BUTNOT TYpe = PROT |) Nr of selected atoms : ( 906) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: SElect OR what which
what = CHain | SEgid | TYpe | CLass |
REsidue | ATom
which = which chain, segid, etc. to use
type can prot, nucl, wate, etc.
class can be main or side chain
residue can be Ala, HOH, BGL etc.
atom can be " CA ", " O1 " etc.
This can be used to select by chain name (one character), segment name (4 characters), type (any of PROT, NUCL, WATE, META, INOR, CARB, ORGA or HETE; 4 characters), or class (main or side chain, one character). Note that atom names are 4 characters (e.g., use " CA " to select C-alpha atoms).
The new selection will be those atoms that were already selected OR satisfy the new criterion. This usually increases the selection.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > se ex Select NON-HYDROGEN atoms Selection history : (NON-HYDROGEN |) Nr of selected atoms : ( 1213) MOLEMAN2 > se and type prot AND atom selection With atoms for which : (TYPE) Equals : (PROT) Selection history : (NON-HYDROGEN | AND TYpe = PROT |) Nr of selected atoms : ( 1091) MOLEMAN2 > se or type water OR atom selection With atoms for which : (TYPE) Equals : (WATER) Selection history : (NON-HYDROGEN | AND TYpe = PROT | OR TYpe = WATER |) Nr of selected atoms : ( 1191) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: SElect NUmeric and_or what lo hi
and_or = And | Or | Butnot
what = Residue_nr | B-factor | Occupancy |
X-coord | Y-coord | Z-coord |
Mass | Element | Covalent_bond_radius
lo = minimum value to select
hi = maximum value to select
Make a selection wider or narrow using numerical properties. This can be used to select a zone of residues (e.g., SEl NUm And Res 23 38), all atoms with high B-factors (SEl NUm And Bfac 50 9999), non-zero occupancy (SEl NUm And Occ 0.0 0.9999), etc.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > sel num and res 50 50 Select Numeric : ( AND Residue_nr 50 50) Selection history : (ALL | AND Residue_nr 50 50 |) Nr of selected atoms : ( 11) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > sel all Select ALL atoms Selection history : (ALL |) Nr of selected atoms : ( 7038) MOLEMAN2 > sel num and mass 40 999 Select Numeric : ( AND Mass 40.00000 999.0000) Selection history : (ALL | AND Mass 40.00000 999.0000 |) Nr of selected atoms : ( 3) MOLEMAN2 > lis List first selected atom of every residue ATOM 3244 I IBZ A 436 19.199 55.708 63.367 1.00 38.03 1CEL3617 ATOM 6763 I IBZ B 436 -19.688 12.428 7.328 1.00 32.65 1CEL7136 ATOM 7039 CA CA 440 40.443 57.977 83.935 1.00 16.86 1CEL7412 Nr of residues listed : ( 3) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > sel all ... MOLEMAN2 > se num and bfac 50 9999 Select Numeric : ( AND B-factor 50.00000 9999.000) Selection history : (ALL | AND B-factor 50.00000 9999.000 |) Nr of selected atoms : ( 8) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: BFactor STats [how]
how = Chain | Type
Lists statistics for the B-factors of all selected atoms, either split up by chain or by type. For example, to get B-factor statistics for all non-hydrogen atoms by chain, use:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
MOLEMAN2 > sel ex
Select NON-HYDROGEN atoms
Selection history : (NON-HYDROGEN |)
Nr of selected atoms : ( 7038)
MOLEMAN2 > bf st c
Chain name Atoms Bave Bsdv Bmin Bmax
A<->1CEL 3518 18.70 8.58 5.31 66.29
B<->1CEL 3518 17.23 8.68 5.91 67.75
<->1CEL 2 24.27 7.41 16.86 31.68
Nr of chains encountered : ( 3)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Ditto, but by type:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
MOLEMAN2 > bf st ty
Type Atoms Bave Bsdv Bmin Bmax
PROT 6440 17.14 8.06 5.31 67.75
WATE 529 27.65 9.99 7.05 55.30
CARB 50 20.91 5.42 12.52 34.04
HETE 19 21.67 6.61 8.66 38.03
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
To get information for only the main-chain protein atoms of chain A, use:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
MOLEMAN2 > sel ex
MOLEMAN2 > se and ty prot
MOLEMAN2 > se and ch a
MOLEMAN2 > sel an cl mai
AND atom selection
With atoms for which : (CL)
Equals : (MAI)
Selection history : (NON-HYDROGEN | AND TYpe = PROT | AND CHain = A | AND
CLass = MAI |)
Nr of selected atoms : ( 1736)
MOLEMAN2 > bf st ty
Type Atoms Bave Bsdv Bmin Bmax
PROT 1736 17.02 6.61 6.97 53.21
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Don't forget to *explicitly* exclude any hydrogen atoms you may have !
Syntax: OCcupancy STats [how]
how = Chain | Type
Lists statistics for the occupancies of all selected atoms, either split up by chain or by type. See the BFactor STats command for examples.
Don't forget to *explicitly* exclude any hydrogen atoms !
This command will remove all ANISOUs (if any are present; otherwise nothing will happen).
Syntax: BFactor LImit lo hi
Reset all B-factors less than "lo" to a value of "lo", and all those greater
than "hi" to a value of "hi". This can be used to reset very low and/or
very high B-factors, or to reset all temperature factors.
To reset very low B-factors: use a very high number for "hi" (e.g., 1000).
To reset very high B-factors: use a negative number for "lo" (e.g., -1).
To reset all B-factors, make "lo" equal to "hi".
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
MOLEMAN2 > se ex
Select NON-HYDROGEN atoms
Selection history : (NON-HYDROGEN |)
Nr of selected atoms : ( 7038)
MOLEMAN2 > bf st c
Chain name Atoms Bave Bsdv Bmin Bmax
A<->1CEL 3518 18.70 8.58 5.31 66.29
B<->1CEL 3518 17.23 8.68 5.91 67.75
<->1CEL 2 24.27 7.41 16.86 31.68
Nr of chains encountered : ( 3)
MOLEMAN2 > bf li 10 50
Reset B-factors to lie in range 10.00 to 50.00
MOLEMAN2 > bf st c
Chain name Atoms Bave Bsdv Bmin Bmax
A<->1CEL 3518 18.72 8.39 10.00 50.00
B<->1CEL 3518 17.32 8.44 10.00 50.00
<->1CEL 2 24.27 7.41 16.86 31.68
Nr of chains encountered : ( 3)
MOLEMAN2 > bf li 18 18
Reset B-factors to lie in range 18.00 to 18.00
MOLEMAN2 > bf st c
Chain name Atoms Bave Bsdv Bmin Bmax
A<->1CEL 3518 18.00 0.00 18.00 18.00
B<->1CEL 3518 18.00 0.00 18.00 18.00
<->1CEL 2 18.00 0.00 18.00 18.00
Nr of chains encountered : ( 3)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: OCcupancy LImit lo hi
Reset all occupancies less than "lo" to a value of "lo", and all those greater
than "hi" to a value of "hi". This can be used to reset very low and/or
very high occupancies, or to reset all occupancies.
See the BFactor LImit command for further discussion and examples.
Syntax: BFactor PRod_plus [prod] [plus]
prod = multiply selected Bs by this number (default 1.0)
plus = add this number to the selected Bs (default 0.0)
This can be used to change the scale of temperature factors (e.g., prior to molecular replacement with a room-temperature search model using new cryo data).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
MOLEMAN2 > stat
...
Item Average St.Dev Min Max
---- ------- ------ --- ---
...
B-factor 16.622 9.305 3.920 54.210
...
MOLEMAN2 > bf pr 0.6 2
New B = 0.6000 * Old B + 2.0000
Nr of atoms updated : ( 1213)
MOLEMAN2 > st
...
B-factor 11.973 5.583 4.352 34.526
...
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: OCcupancy PRod_plus [prod] [plus]
prod = multiply selected occupancies by this number (default 1.0)
plus = add this number to the selected occupancies (default 0.0)
This can be used to change the occupancies of the selected atoms.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > oc pr 0.5 New Q = 0.5000 * Old Q + 0.0000 Nr of atoms updated : ( 1213) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: BFactor PLot file [what]
file = O2D plot file name
what = Average | Radial
Option Average creates a plot of average B-factor per residue, using only currently selected atoms. Option Radial produces a plot of average B-factor in 2.0 A shells from the centre-of-gravity of the currently selected atoms. The plot files are for use with O2D.
For example, to plot the average B-factors for all protein residues in chain A, use: SE EX, SE ANd CHain A, SE ANd TYpe PROT (only needed if chain A contains things other than protein residues), BF PLot bave.plt a.
Example of a BFactor PLot (average).
Example of a BFactor PLot (radial).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > se ex MOLEMAN2 > se an ch a MOLEMAN2 > bf pl bave.plt a Residues with selected atoms : ( 701) MOLEMAN2 > bf pl brad.plt r Selected atoms : ( 3518) Centre-of-gravity : ( 30.052 63.904 61.356) Shell 0.0 - 2.0 A - 3 atoms; <B> = 13.80 A**2 Shell 2.0 - 4.0 A - 9 atoms; <B> = 17.73 A**2 Shell 4.0 - 6.0 A - 35 atoms; <B> = 12.22 A**2 Shell 6.0 - 8.0 A - 69 atoms; <B> = 12.69 A**2 ... Shell 32.0 - 34.0 A - 33 atoms; <B> = 25.13 A**2 Shell 34.0 - 36.0 A - 13 atoms; <B> = 35.35 A**2 Shell 36.0 - 38.0 A - 1 atoms; <B> = 43.24 A**2 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: OCcupancy PLot file [what]
file = O2D plot file name
what = Average | Radial
Option Average creates a plot of average occupancy per residue, using only currently selected atoms. Option Radial produces a plot of average occupancy in 2.0 A shells from the centre-of-gravity of the currently selected atoms. The plot files are for use with O2D.
For example, to plot the average occupancy for all protein residues in chain A, use: SE EX, SE ANd CHain A, SE ANd TYpe PROT (only needed if chain A contains things other than protein residues), OC PLot qave.plt a.
Example of a OCcupancy PLot (average).
Example of a OCcupancy PLot (radial).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > oc pl q1.plt ave Residues with selected atoms : ( 680) MOLEMAN2 > oc pl q2.plt rad Command > (oc pl q2.plt rad) Selected atoms : ( 5416) Centre-of-gravity : ( 30.728 16.687 12.025) Shell 0.0 - 2.0 A - 1 atoms; <OCC> = 1.00 Shell 2.0 - 4.0 A - 11 atoms; <OCC> = 1.00 ... Shell 52.0 - 54.0 A - 63 atoms; <OCC> = 0.89 Shell 54.0 - 56.0 A - 75 atoms; <OCC> = 0.79 Shell 56.0 - 58.0 A - 77 atoms; <OCC> = 0.88 Shell 58.0 - 60.0 A - 39 atoms; <OCC> = 0.79 Shell 60.0 - 62.0 A - 8 atoms; <OCC> = 0.62 Shell 62.0 - 64.0 A - 1 atoms; <OCC> = 1.00 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This commands calculates (for the currently selected set of atoms only) the RMS delta-B for all bonded atoms, bonded main-chain and side-chain atoms separately, and for atoms involved in non-bonded interactions (the distance cut-offs can be changed with the COnstants SEt command). Note that hydrogens are included if they are currently selected !
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
MOLEMAN2 > BF BO
Calculating RMS delta-B for (non-)bonded atoms
Max bonded distance : ( 2.000)
Max non-bonded distance : ( 3.600)
Nr of selected non-H atoms : ( 7038)
Nr of bonds (all atoms) : ( 6662)
RMS delta-B (A**2) : ( 2.099)
Nr of bonds (main chain) : ( 4278)
RMS delta-B (A**2) : ( 1.562)
Nr of bonds (side chain) : ( 3192)
RMS delta-B (A**2) : ( 2.613)
Nr of non-bonded contacts : ( 23812)
RMS delta-B (A**2) : ( 5.194)
CPU total/user/sys : 17.7 17.7 0.1
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This command will operate on all selected atoms, and replace the B-factor of each atom by the average of its own B-factor and those of all its bonded neighbours (if any). This can be useful when you make the transition from refining grouped to individual temperature factors. Use the BFactor BOnded command before and after this operation to see the effect. Note that hydrogens are included if they are currently selected !
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > BF SM Smoothing Bs for bonded atoms Max bonded distance : ( 2.000) Nr of selected non-H atoms : ( 7038) CPU total/user/sys : 34.6 34.4 0.2 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: BFactor GRoup how
how = Mc_sc | Residue | Overall
This command enables you to average B-factors for certain groups of atoms, e.g. prior to refinement of a high-resolution model against low-resolution data (e.g., a complex or mutant). Note that hydrogens are included if they are currently selected !
Grouping is carried out for all currently selected atoms in one of
three ways:
- Overall: the B-factor of each selected atom is set to the average
B-factor of all selected atoms
- Residue: the B-factors are averaged for all selected atoms for
every residue
- Mc_sc: ditto, but grouped for main-chain and side-chain atoms
separately
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > bf gr mc Group Bs for main/side chain atoms Nr of main-chain groups : ( 137) Nr of side-chain groups : ( 230) MOLEMAN2 > bf gr re Group Bs per residue Nr of residues grouped : ( 238) MOLEMAN2 > bf gr ov Group Bs for all selected atoms Nr of selected atoms : ( 1213) Average B-factor : ( 16.622) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: BFactor PSeudo how [parameters]
how = X | Y | Z | Q | A | I | R | G | D | N | C | H
With this command you can replace the B-values of a model by a range of other property values. You can use this so as to be able to colour-ramp your model by these properties, e.g. in O or Rasmol.
Note that this command only works on the B-factors of the currently selected atoms ! And before using this command you may want to "back-up" your true B-values with the BFactor SAve command (they can then be restored later with the BFactor REstore command).
The following properties have been implemented:
- X = X-coordinate
- Y = Y-coordinate
- Z = Z-coordinate
- Q = Occupancy
- A = Atom index (sequential); i.e. the first selected atom will get
a B-factor of 1.0, the second 2.0, etc.
- I = Residue index (sequential); same as A, but now the numbering
is done per residue rather than per atom
- R = Residue number (in sequence); now each atom will get a B-value
equal to the actual number of its residue (this can be used
to colour-ramp multiple protein molecules in the same way)
- G = Distance from Centre-of-Gravity (of the selected atoms); atoms
close to the centre-of-gravity will get low B-values
- D = Distance from a point; you can provide any or all of the coordinates
of a point (e.g., the coordinates of a metal ion); they will
default to zero
- N = Nr of neighbour atoms in sphere; provide the radius of a sphere
(default is 10 Å); every atom will get a B-value equal to the
number of atoms (including itself) that lie within a sphere of
the specified radius from it (related to, but different from,
the so-called Ooi number). Surface atoms will get low B-values,
and buried atoms will get high values.
- C = CX values (atomic convexity); see A Pintar et al, Bioinformatics
18, 980-984 (2002). CX is a measure for the convexity of an atom.
Note that the formula for CX can be simplified to (C/N) - 1,
where C = Vsphere / Vatom = 4 * PI * Radius**3 / (3 * Vatom).
You can supply values for Radius (default 10 Å) and Vatom (default
20 Å3).
- H = Halle B (LDM-prediction); see B Halle, PNAS 99, 1274-1279 (2002).
Halle gives a method to predict B-values from packing density
alone. His equation (7) can be used to get: B(LDM) =
4 * PI**2 * C / Nk, where Nk is the number of atoms surrounding
the atom within a sphere of radius 7.35 Å, and C is a scaling
constant that makes the observed and calculated average B-values
the same. Note that this option requires that the B-values
are the experimental ones and not some pseudo-B-values ! After
this operation, the B-values will be those computed using
Halle's method. If you plot the average of CA B-value before
and after this operation, the plots should show similar trends.
Substantial deviations may be indicative of problems in the
structure or its refined B-values.
Note that some properties can get values that are unsuitable for the B-value field in PDB files (e.g., >= 1000; some programs may also balk at non-positive B-factors). You can therefore adjust the range of values using the BF LImit, BF PRod_plus or BF SCale commands. Also, if you want to invert the colour-ramping, simply do a BF SCale with the minimum and maximum value swapped. If you want to use the properties in O, you can save the pseudo-B-values as an O datablock file with the BFactor ODb command.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > bf ps c Replace B-factors by Pseudo-B-factors ... Pseudo-B = C = CX values (atomic convexity) Radius (A) : ( 10.000) Atomic volume (A3) : ( 20.000) Nr of atoms processed : ( 1213)Minimum Pseudo-B : ( -0.089) Warning - non-positive values for Pseudo-B ! Maximum Pseudo-B : ( 5.160) Dynamic range : ( 5.249) Average Pseudo-B : ( 0.656) You may use BF LImit, BF PRod_plus and BF SCale to modify the range and values of the Pseudo-Bs MOLEMAN2 > wr cx.pdb ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Example of the use of Halle's method:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > re pdb1cbs.ent MOLEMAN2 > bf odb bexp.odb m1 MOLEMAN2 > sel and type prot MOLEMAN2 > sel and atom " CA " MOLEMAN2 > bf plot bexp.plt ave MOLEMAN2 > sel all MOLEMAN2 > sel and type prot MOLEMAN2 > bf ps halle Replace B-factors by Pseudo-B-factors ... Pseudo-B = H = Halle B (LDM-prediction) Radius (A) : ( 7.350) Nr of atoms selected : ( 1091) Average experimental B (A2) : ( 1.548E+01) Average predicted B (A2) : ( 6.474E-01) ==> Scale factor : ( 2.391E+01) Nr of atoms processed : ( 1091)Minimum Pseudo-B : ( 9.255) Maximum Pseudo-B : ( 72.619) Dynamic range : ( 63.364) Average Pseudo-B : ( 15.480) You may use BF LImit, BF PRod_plus and BF SCale to modify the range and values of the Pseudo-Bs MOLEMAN2 > bf odb bldm.odb m2 MOLEMAN2 > sel and atom " CA " MOLEMAN2 > bf pl bldm.plt ave MOLEMAN2 > wr halleb.pdb ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: BFactor SAve
Use this command prior to using the BFactor PSeudo command. Later on, you can then restire the true B-values with the BFactor REstore command. Note that the program will not allow you to use the BFactor SAvecommand when your B-values have been replaced by pseudo-B-values !
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > bf save ERROR --- Cannot save Pseudo-B-factors ! MOLEMAN2 > bf re Restored all atomic B-factors MOLEMAN2 > bf sa Saved all atomic B-factors ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: BFactor REstore
When you have backed-up your true B-values with the BFactor SAve command, you can restore them with this command (e.g., after generating pseudo-B-values).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > bf re Restored all atomic B-factors ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: BFactor SCale [min] [max]
Scale the B-values so that they lie in the range specified. This is mostly intended for manipulation of pseudo-B-values. The minimum and maximum values default to 1.0 and 100 A2, respectively.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
MOLEMAN2 > bf sc 1 100
Scale B-factors of selected atoms
Requested range (A2) : 1.000 100.000
Nr of selected atoms : ( 1213)
Current range (A2) : 3.920 54.210
B-factors scaled
MOLEMAN2 > bf st
Chain name Atoms Bave Bsdv Bmin Bmax Brms Bharm.av
<->1CBS 1213 26.00 18.32 1.00 100.00 31.81 17.01
Nr of chains encountered : ( 1)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: BFactor ODb [filename] [molname]
Save the current atomic B-values (pseudo or real) to an O-style datablock file. Such files can be read by O and ODBMAN for further use or analysis.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > bf odb b.odb cbs Save B-values in ODB file : (b.odb) Molecule name in O : (CBS) File written ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The ODB file may look as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- % 618 gerard sarek 22:09:47 gerard/junk > head b.odb ! Created by MOLEMAN2 V. 030221/3.2 at Sat Feb 22 02:38:30 2003 for gerard CBS_ATOM_B R 1213 (10F8.3) 30.050 28.820 26.590 26.840 29.240 29.290 30.710 24.040 20.790 16.750 15.230 22.810 24.290 21.870 27.940 14.690 12.620 12.430 12.120 10.740 11.850 10.900 13.260 9.120 11.760 10.300 11.240 11.300 10.390 10.240 13.530 16.760 9.870 10.860 11.210 9.910 10.410 11.060 10.330 11.280 12.950 18.080 19.520 21.230 8.660 8.740 9.630 9.450 8.000 8.010 8.290 7.600 9.200 8.730 6.990 7.670 7.580 5.920 9.390 11.560 10.560 10.140 15.200 18.520 26.260 29.220 32.480 8.210 8.080 7.860 8.380 10.700 10.950 10.700 13.230 7.080 7.450 8.490 9.490 10.280 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: NUcleic DUarte_pyle [file] [what] [chain]
file = name of output file or blank
what = Plot | ACGTU_plot | Text_file
chain = * | _ | chain_name
If you don't provide a filename, no output file is generated. If you do, the second parameter determines what type of file you will get. You can get a simple list of the ETA and THETA pseudo-torsion angles for every residue by selecting type T(ext_file). If you want a Ramachandran-like plot (PostScript format), you can select P or A. With the P option, all residues will be plotted as black plus signs. With the ACGTI command, you will get: A=black box, C=red plus, G=cyan cross, T=blue diamond, U=magenta triangle, other=green Z. Note that the plot file is already in PostScript format, so you don't have to convert it with O2D.
From version 2.9 on, there is a new (optional) parameter "chain".
This can be:
- "*" (default) : all chains will be processed in one go
- "_" : the chains will be processed one by one; in this case
"_chain_X.ps" will be appended to "file" (where "X" is
the uppercase name of each chain) to generate the name
of the PostScript file
- the (one-character) name of a specific chain
Reference: CM Duarte & AM Pyle (1998), J. Mol. Biol. 284, 1465-1478.
Example of a NUcleic DUarte_pyle plot (ACGTU).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > nu du q.ps a Command > (nu du q.ps a) => XPS_GRAF - GJK (19981216/3.1.2) Opened PostScript file : (q.ps) Date : (Fri Nov 17 20:47:20 2000) User : (gerard) Program : (MOLEMAN2) Nr of residues to check : ( 316)RESIDUE G A 103 <<<<< Start of new chain A-A 104 - 191.9 259.0 A-A 105 - 217.3 212.9 U-A 106 - 300.2 241.2 U-A 107 - 265.9 223.0 G-A 108 - 168.8 223.2 C-A 109 - 170.7 194.8 [...] U-B 259 - 166.6 209.7
RESIDUE C B 260 >>>>> End of chain
Total nr of residues checked : ( 316) Start/end residues : ( 4) Problems (missing atoms ?) : ( 0) Remaining residues in plot : ( 312) Number of A : ( 90) Number of C : ( 64) Number of G : ( 86) Number of T : ( 0) Number of U : ( 72) Others : ( 0) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: PRotein MC_analysis [file] [what] [chain]
file = name of output file or blank
what = Rama_plot | Labelled_rama | Text_file
chain = * | _ | chain_name
If you don't provide a filename, no output file is generated. If you do, the second parameter what type of file you will get. You can get a simple list of Phi, Psi, Omega and Planarity (pseudo-)torsion angles for every residue by selecting type T(ext_file). If you want a Ramachandran plot (PostScript format only; use the old MOLEMAN if you want other formats, or Balasubramanian plots, or polar Ramachandran plots), you can select R or L. With option L, the outliers will be marked with a text label in the plot; with option R they won't be. Note that the plot file is already in PostScript format, so you don't have to convert it with O2D.
From version 2.9 on, there is a new (optional) parameter "chain".
This can be:
- "*" (default) : all chains will be processed in one go
- "_" : the chains will be processed one by one; in this case
"_chain_X.ps" will be appended to "file" (where "X" is
the uppercase name of each chain) to generate the name
of the PostScript file
- the (one-character) name of a specific chain
The screen output is simply a list of "features" of your protein
main chain, including:
- start and end residues of chains (looking at CA-CA distances, *not*
chain or segment names; the maximum CA-CA distance allowed is 4.5 A);
- inability to calculate certain torsion angles (e.g., due to missing
atoms in a residue or one of its neighbours);
- type of peptide (cis, trans, or "unusual");
- planarity of the peptide bond;
- positive PHI angles (not for glycines; unusual outside the poly-Pro
area);
- outliers in the Ramachandran plot (not for glycines);
- suspected left-handed helices (check hydrogen bonding yourself to
decide if they really are helices, and, if so, if they are alpha
or 3-10 helices).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- RESIDUE HIS B 211 Warning - positive PHI = 57.1RESIDUE ALA B 212 Warning - positive PHI = 51.5
RESIDUE GLU B 214 Warning - positive PHI = 36.9 Warning - unusual PHI,PSI combination = 36.9 74.8
Left-handed helix - nr of residues : ( 6) Left-handed helix first : HIS B 211 Left-handed helix last : GLY B 216 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The Ramachandran outliers are identified using data obtained in an analysis of 403 PDB structurs (October 1995) which are mutually <= 95 % homologous (Hobohm & Sander list), and were refined at a resolution of 2.0 A or better. For the 74,893 non-Gly residues included (with temperature factors less than two standard deviations above the average for the protein), a mega-Ramachandran plot was generated using 10 degree-square bins. The set of most-populated bins containing 98% of all residues was then defined as the core of the ramachandran plot. Any residue outside this core region is called an outlier. For your average 2.0 A or better structure, one would expect ~0-5% outliers. Outliers will be shown with an asterisks (and, optionally, a text label) in the Ramachandran plot. From version 2.4.1 on, D-amino acids are treated explicitly (-phi and -psi are used to determine if they are outliers; they will be shown as red diamonds in the PostScript plot).
Reference for the most-favoured regions in the Ramachandran plot: Kleywegt, G.J. and Jones, T.A. (1996). Phi/psi-chology: Ramachandran revisited. Structure 4, 1395-1400.
Example of a PDb MC plot (labeled).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > prot mc 1cel_rama.ps lab => XPS_GRAF - GJK (2.3 @ 960209) Opened PostScript file : (1cel_rama.ps) Date : (Sun Feb 18 02:15:33 1996) User : (gerard) Program : (MOLEMAN2) Nr of residues to check : ( 868)RESIDUE PCA A 1 1CEL <<<<< Start of new chain
RESIDUE SER A 99 1CEL Warning - unusual PHI,PSI combination = -118.7 -112.1 ... RESIDUE MET A 374 1CEL Warning - positive PHI = 65.2
RESIDUE TYR A 381 1CEL Cis-peptide; omega = 0.4; next residue is PRO Warning - non-planar peptide; planarity = 5.5
RESIDUE ASN A 420 1CEL Warning - positive PHI = 47.3
RESIDUE GLY A 434 1CEL >>>>> End of chain
RESIDUE PCA B 1 1CEL <<<<< Start of new chain
RESIDUE SER B 99 1CEL Warning - unusual PHI,PSI combination = -134.0 -130.7 ... RESIDUE TYR B 381 1CEL Cis-peptide; omega = -1.1; next residue is PRO
RESIDUE ASN B 420 1CEL Warning - positive PHI = 49.6
RESIDUE GLY B 434 1CEL >>>>> End of chain
Total nr of residues checked : ( 868) Cis-peptide bonds : ( 2) Unusual OMEGA values : ( 0) Non-planar peptide bonds : ( 1) Start/end residues : ( 4) Problems (missing atoms ?) : ( 0) Glycine residues : ( 100) Remaining residues in Ramach : ( 764) In core regions : ( 759) Outliers : ( 5) Outlier percentage : ( 0.654) An average <= 2.0 A model has ~0-5% outliers ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > pr mc cbh2.list t Nr of residues to check : ( 725)RESIDUE ALA 86 AAAA <<<<< Start of new chain
RESIDUE ASN 158 AAAA Warning - unusual PHI,PSI combination = -102.6 52.9 ... RESIDUE GLN 422 KKKK Cis-peptide; omega = 0.1; next residue is PRO
RESIDUE ASN 443 KKKK Cis-peptide; omega = 1.1; next residue is PRO
RESIDUE LEU 447 KKKK >>>>> End of chain
Total nr of residues checked : ( 725) Cis-peptide bonds : ( 6) Unusual OMEGA values : ( 0) Non-planar peptide bonds : ( 0) Start/end residues : ( 4) Problems (missing atoms ?) : ( 0) Glycine residues : ( 60) Remaining residues in Ramach : ( 661) In core regions : ( 637) Outliers : ( 24) Outlier percentage : ( 3.631) An average <= 2.0 A model has ~0-5% outliers ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The text file produced in the example above may look as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Created by MOLEMAN2 V. 960217/0.4 at Sun Feb 18 02:16:43 1996 for user gerardListing of Phi, Psi, Omega and Planarity (pseudo) torsion angles for PDB file hydro.pdb
PHI = C(i-1) - N(i) - CA(i) - C(i) - usually negative PSI = N(i) - CA(i) - C(i) - N(i+1) OMEGA = CA(i) - C(i) - N(i+1) - CA (i+1) - cis=0, trans=180 PLANARITY = C(i) - CA(i) - N(i+1) - O(i) - planar < 5
An entry of "-999.9" means that the torsion angle could not be calculated (for terminal residues and residues with missing atoms).
Residue Phi Psi Omega Planarity ------- --- --- ----- ---------
ALA- 86 -AAAA -999.9 -60.2 -179.0 -0.8 THR- 87 -AAAA -73.7 142.9 -178.7 0.2 TYR- 88 -AAAA -139.9 162.0 178.3 -0.7 SER- 89 -AAAA -124.5 117.2 179.7 1.7 GLY- 90 -AAAA 86.1 -131.6 -179.6 0.4 ASN- 91 -AAAA -65.5 116.2 -179.7 -1.9 ... SER- 445 -KKKK -70.6 146.1 178.6 0.7 PHE- 446 -KKKK -98.7 -32.7 179.2 0.4 LEU- 447 -KKKK -77.7 -999.9 -999.9 -999.9 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: PRotein SC_analysis [file]
file = name of output file or blank
If you don't provide a filename, no output file is generated. If you do, you'll get a plain text file with a listing for all protein residues except Gly of the CA-chirality improper and the side chain torsion angles Chi1 to Chi5 (the latter only occurs for Arg and should be zero).
On the screen you'll get a list of "features" of your sidechains.
Things that are checked (using a tolerance of 5 degrees) include:
- CA-chirality (D/L amino acids; improper CA - N - C - CB; +34 for
L-amino acids, -34 for D-amino acids; bad if not near an ideal
value; note that the ideal value for Pro is more like 38 degrees)
- naming of equivalent sidechain 1/2 atoms (Asp, Glu, Phe, Tyr, Arg;
tested by checking if the corresponding Chi torsion i in the range
[-90,+90]; if not, a message is printed; atom names are not swapped)
- chirality of Ile CB (CB - CG1 - CG2 - CA; should be +34)
- "tetrahedral-ness" of some other carbons (Leu CG, Val CB and Thr CB)
- flatness of several atom types (not of rings; Arg CZ, Asn/Asp CG,
Gln/Glu CD, His/Phe/Tyr/Trp CG)
Example of the output:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > pr scRESIDUE ASP A 173 1CEL Warning - poor CA chirality improper = 27.3
RESIDUE PRO A 194 1CEL Warning - poor CA chirality improper = 39.1
RESIDUE PRO A 229 1CEL Warning - poor CA chirality improper = 39.8
RESIDUE TYR A 274 1CEL Warning - sidechain 1/2 atom names incorrect; Chi = 91.1
...
RESIDUE ASP B 368 1CEL Warning - poor CA chirality improper = 27.8
Nr of residues checked : ( 766) Nr of D-amino acids : ( 0) Nr with poor CA chirality : ( 9) Nr wrong 1/2 atom names : ( 3) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The output text file (optional) may look as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Created by MOLEMAN2 V. 960217/0.4 at Thu Feb 22 19:37:07 1996 for user gerardListing of Chi1-5 and Chirality (pseudo) torsion angles for PDB file 1cel.pdb
CHIRAL = CA - N - C - CB (+34=L-aa; -34=D-aa) CHI-1 = N - CA - CB - ?G(1) CHI-2 = CA - CB - ?G(1) - ?D(1) CHI-3 = CB - ?G(1) - ?D(1) - ?E(1) CHI-4 = ?G(1) - ?D(1) - ?E(1) - ?Z(1) CHI-5 = ?D(1) - ?E(1) - ?Z(1) - ?H(1)
An entry of "-999.9" means that the torsion angle could not be calculated (e.g., for residues with missing atoms).
Residue CA-chir Chi-1 Chi-2 Chi-3 Chi-4 Chi-5 ------- ------- ----- ----- ----- ----- ----- PCA-A 1 -1CEL 37.9 31.7 -30.2 -160.3 SER-A 2 -1CEL 34.3 67.1 ALA-A 3 -1CEL 35.0 CYS-A 4 -1CEL 33.1 -80.1 ... THR-B 429 -1CEL 34.5 69.0 ASN-B 431 -1CEL -1.0 -69.5 -37.0 PRO-B 432 -1CEL 36.6 -39.5 47.1 SER-B 433 -1CEL 35.4 -63.4 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: PRotein CA_analysis [file] [what] [chain]
file = name of output file or blank
what = Rama_plot | Labelled_rama | Text_file
chain = * | _ | chain_name
The meaning of the parameters is the same as for the PRotein MC_analysis command (quod vide).
The program will check:
- unusual CA-CA distances (2.9 A for cis and 3.8 for trans)
- isolated residues (a CA not connected to the previous or the next
residue in the sequence)
- unusual CA geometry (in terms of angle/torsion combinations, similar
to a Ramachandran plot)
If you select a text file for output, for each residue the following
will be listed:
- CA(i) - CA(i+1) distance
- CA(i-1) - CA(i) - CA(i+1) angle
- CA(i-1) - CA(i) - CA(i+1) - CA(i+2) pseudo-torsion angle
From version 1.0.2 onward, the program will also look for sequential stretches of residues which contain several CA-geometry outliers. Such stretches are worth closer scrutiny; sometimes they coincide with the start or end of a zone that is out-of-register with the sequence ! The program checks for zones of 8 sequential residues with at least 5 outliers, then 5 residues with at least 3 outliers and finally 3 residues with at least 2 outliers.
From version 2.9 on, there is a new (optional) parameter "chain".
This can be:
- "*" (default) : all chains will be processed in one go
- "_" : the chains will be processed one by one; in this case
"_chain_X.ps" will be appended to "file" (where "X" is
the uppercase name of each chain) to generate the name
of the PostScript file
- the (one-character) name of a specific chain
Example of a PDb CA plot (labeled).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > re /nfs/pdb/full/1chr.pdb ... MOLEMAN2 > pr ca q.ps r => XPS_GRAF - GJK (2.4 @ 960223) Opened PostScript file : (q.ps) Date : (Thu Aug 1 20:04:50 1996) User : (gerard) Program : (MOLEMAN2)RESIDUE MET A 1 1CHR <<<<< Start of new chain
RESIDUE LYS A 2 1CHR Warning - unusual CA-CA distance 3.66
...
RESIDUE SER B 370 1CHR >>>>> End of chain
Nr of residues checked : ( 743) Nr of isolated CAs : ( 0) Nr with CA-CA distance : ( 738) Nr with CA ang/torsion : ( 732) Ditto, non-Gly : ( 674)
CA-CA distances: 738 CA-CA distances Average CA-CA distance = 3.808 Sigma = 0.089 Minimum CA-CA distance = 3.482 Maxim = 4.367 Short (<= 2.8 A) CA-CA dists : 0 res = 0.00 % = 0.1 SIGMA from mean CIS (<= 3.0 A) CA-CA dists : 0 res = 0.00 % = 0.5 SIGMA from mean Poor (<= 3.7 A) CA-CA dists : 68 res = 9.21 % = 2.2 SIGMA from mean TRANS (<= 3.9 A) CA-CA dists : 579 res = 78.46 % = 2.6 SIGMA from mean Long (> 3.9 A) CA-CA dists : 91 res = 12.33 % = 2.7 SIGMA from mean
CA geometry: CORE res : 449 = 66.62 % = 0.7 SIGMA from mean Additional res : 84 = 12.46 % Generous res : 106 = 15.73 % DISALLOWED res : 35 = 5.19 % = 1.0 SIGMA from mean For <= 2.0 A structures : Core - 7.1 % area - 72.8 % (8.9) residues Additional - 5.2 % area - 12.8 % (4.0) residues Generous - 15.0 % area - 11.3 % (4.6) residues Disallowed - 72.6 % area - 3.1 % (2.2) residues
WARNING !!! At least three of five sequential residues have poor CA geometry, starting at: RESIDUE VAL A 13 1CHR
WARNING !!! At least five of eight sequential residues have poor CA geometry, starting at: RESIDUE ASP B 12 1CHR
WARNING !!! At least three of five sequential residues have poor CA geometry, starting at: RESIDUE VAL B 34 1CHR
WARNING !!! At least three of five sequential residues have poor CA geometry, starting at: RESIDUE GLY B 296 1CHR CPU total/user/sys : 1.6 1.4 0.2 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
A listing file may look as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Created by MOLEMAN2 V. 960222/0.5 at Fri Feb 23 19:24:38 1996 for user gerardListing for PDB file aspglu.pdb
CA(i) - CA(i+1) distance (2.9=cis, 3.8=trans) CA(i-1) - CA(i) - CA(i+1) angle CA(i-1) - CA(i) - CA(i+1) - CA(i+2) pseudo-torsion angle
An entry of "-999.9" means that the value could not be calculated (for near-terminal residues)
Residue Distance Angle Torsion ------- -------- ----- -------
SER- 1 - 3.7 -999.9 -999.9 THR- 2 - 3.5 75.8 58.9 ASP- 3 - 3.7 127.0 152.5 ASP- 4 - 3.8 117.4 -139.5 ALA- 5 - 3.8 106.6 75.0 SER- 6 - 3.7 123.0 -9.3 ... GLU- 327 - 3.9 129.8 -167.1 ILE- 328 - 3.9 150.3 -177.8 ASP- 329 - 3.9 -999.9 -999.9 ALA- 330 - 3.7 -999.9 -999.9 ALA- 331 - -999.9 -999.9 -999.9 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Coordinates of all selected atoms can be manipulated primarily with the XYz commands.
This command fractionalises your (selected) coordinates. This may be useful for applying fractional translations (e.g., a translation function solution), and for converting orthogonal heavy-atom coordinates (from O or RSPS, for instance) into fractional ons.
The cell constants can be entered with the PDb CRystal command if they are not present in the PDB file you have read.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > xy fr Fractionalise coordinates Cell axes : ( 45.650 47.560 77.610) Cell angles : ( 90.000 90.000 90.000) New X = 0.021906 * X + 0.000000 * Y + 0.000000 * Z New Y = 0.000000 * X + 0.021026 * Y + 0.000000 * Z New Z = 0.000000 * X + 0.000000 * Y + 0.012885 * Z ATOM 1 N PRO 1 16.979 13.301 44.555 1.00 30.05 1CBS 223 Before : ( 16.979 13.301 44.555) After : ( 0.372 0.280 0.574) Nr of transformed atoms : ( 1213) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This command orthogonalises your (selected) coordinates. This may be useful to convert refined heavy-atom coordinates (from MLPHARE, for instance) back into Cartesian ones for use with O.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > xy or Orthogonalise coordinates Cell axes : ( 45.650 47.560 77.610) Cell angles : ( 90.000 90.000 90.000) New X = 45.650002 * X + -0.000002 * Y + -0.000003 * Z New Y = 0.000000 * X + 47.560001 * Y + -0.000003 * Z New Z = 0.000000 * X + 0.000000 * Y + 77.610001 * Z ATOM 1 N PRO 1 0.372 0.280 0.574 1.00 30.05 1CBS 223 Before : ( 0.372 0.280 0.574) After : ( 16.979 13.301 44.555) Nr of transformed atoms : ( 1213) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: XYz ROtate how ang1 ang2 ang3
how = CEuler | CPolar | MEuler | MPolar | XPolar | XLattmann
(C=CCP4, M=Merlot, X=X-PLOR)
ang1-3 = the three rotation angles
Rotate the selected atoms using one of four conventions:
- CCP4 Euler angles (alpha, beta, gamma; NCODE = 1 convention !)
- CCP4 Polar angles (omega, phi, chi)
- Merlot Euler angles (alpha, beta, gamma)
- Merlot Polar angles (phi, psi, kappa)
- X-PLOR Polar angles (phi, psi, kappa)
- X-PLOR/Lattmann Euler angles (theta+, theta2, theta-)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > xy ro ce 103.4 86.2 213.4 CCP4 Euler angles : ( 103.400 86.200 213.400) New X = 0.548317 * X + 0.803665 * Y + -0.231238 * Z New Y = 0.073750 * X + 0.228964 * Y + 0.970637 * Z New Z = 0.833012 * X + -0.549271 * Y + 0.066274 * Z Crowther Alpha Beta Gamma 103.40001 86.20000 -146.60001 Spherical polars Omega Phi Chi 111.47401 -145.00000 94.48643 Direction cosines of rotation axis -0.76229 -0.53376 -0.36608 Dave Smith -86.09398 33.59056 -55.69545 ATOM 1 N PRO 1 16.979 13.301 44.555 1.00 30.05 1CBS 223 Before : ( 16.979 13.301 44.555) After : ( 9.697 47.544 9.791) Nr of transformed atoms : ( 1213) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: XYz AXis_rotate axis angle
axis = the rotation axis (X, Y or Z)
angle = the rotation angle
Rotate the selected atoms around the chosen axis by the specified angle (in degrees).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > xyz ax y 73Rotate around X, Y or Z axis Rotation axis : (Y) Angle (deg) : ( 73.000) Determinant of rotation matrix : ( 1.000E+00) New X = 0.2923718 * X + 0.0000000 * Y + -0.9563047 * Z New Y = 0.0000000 * X + 1.0000000 * Y + 0.0000000 * Z New Z = 0.9563047 * X + 0.0000000 * Y + 0.2923718 * Z Crowther Alpha Beta Gamma 180.000 73.000 180.000 Spherical polars Omega Phi Chi 90.000 -90.000 73.000 Direction cosines of rotation axis 0.000000 -1.000000 0.000000 X-PLOR polars Phi Psi Kappa *undefined* 180.000 73.000 Lattmann Theta+ Theta2 Theta- *undefined* 73.000 *undefined* ATOM 1 N SER A 1 -13.903 -4.439 3.739 1.00 34.27 1PMP 185 Before : ( -13.903 -4.439 3.739) After : ( -7.640 -4.439 -12.202) Nr of transformed atoms : ( 1039) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: XYz TRanslate tx ty tz
tx..tz = the three translation vector components
Translate the selected atoms according to the translation vector you supply.
Hint: to carry out a fractional translation, first use XYz FRact to fractionalise the coordinates, then apply the translation and then reorthogonalise with XYz ORtho (this is useful when applying translation function solutions).
Hint: to move a selected set of atoms such that their centre-of-gravity is at the origin, first use the STats command to find the coordinates of the CofG (being the average X, Y and Z coordinate), and then XYz TRanslate using a vector which is -1 times the CofG coordinates. E.g., if your CofG is at (12.4,-54.2,1.9), then use: XYz TRans -12.4 54.2 -1.9.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > xyz frac Fractionalise coordinates ... MOLEMAN2 > xy tr 0.345 0.812 0.0 Translation : ( 0.345 0.812 0.000) Length of translation vector : ( 0.882) Nr of transformed atoms : ( 1213) MOLEMAN2 > xyz ort Orthogonalise coordinates ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
MOLEMAN2 > st
Nr of atoms : ( 1213)
...
Item Average St.Dev Min Max
---- ------- ------ --- ---
X-coord 17.837 8.350 -1.464 37.101
Y-coord 20.849 6.794 2.899 34.741
Z-coord 27.423 9.907 2.776 49.501
...
MOLEMAN2 > xyz tr -17.837 -20.849 -27.423
Translation : ( -17.837 -20.849 -27.423)
Length of translation vector : ( 38.793)
Nr of transformed atoms : ( 1213)
MOLEMAN2 > st
Nr of atoms : ( 1213)
...
Item Average St.Dev Min Max
---- ------- ------ --- ---
X-coord 0.000 8.350 -19.301 19.264
Y-coord 0.000 6.794 -17.950 13.892
Z-coord 0.000 9.907 -24.647 22.078
...
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: XYz MAtrix [r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz]
new X = r11*X + r21*Y + r31*Z + tx
new Y = r12*X + r22*Y + r32*Z + ty
new Z = r13*X + r23*Y + r33*Z + tz
(defaults: 1 0 0 0 1 0 0 0 1 0 0 0)
Apply a user-defined rotation/translation operator. The determinant of the matrix must be +1 or -1 (note that -1 implies an inversion !!!).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > xyz mat 1 12 2 11 3 10 4 9 5 8 6 7Nr of NCS operators : 1
NCSOP 1 = 1.0000000 11.0000000 4.0000000 8.000 12.0000000 3.0000000 9.0000000 6.000 2.0000000 10.0000000 5.0000000 7.000 Determinant of rotation matrix -81.000000 ERROR --- Determinant differs from +-ONE by more than 0.01 ERROR --- Operation aborted ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > xyz mat -1 0 0 0 1 0 0 0 1 0 0 0Nr of NCS operators : 1
NCSOP 1 = -1.0000000 0.0000000 0.0000000 0.000 0.0000000 1.0000000 0.0000000 0.000 0.0000000 0.0000000 1.0000000 0.000 Determinant of rotation matrix -1.000000 WARNING - Determinant is -1 ! Column-vector products (12,13,23) 0.000000 0.000000 0.000000 Rotation angle 90.000000 Nr of atoms transformed : ( 1213) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > xy mat -0.9999319 0.0108257 -0.0043541 -0.0112386 -0.7931781 0.6088861 0.0031381 0.6088936 0.7932457Nr of NCS operators : 1
NCSOP 1 = -0.9999319 -0.0112386 0.0031381 0.000 0.0108257 -0.7931781 0.6088936 0.000 -0.0043541 0.6088861 0.7932457 0.000 Determinant of rotation matrix 1.000000 Column-vector products (12,13,23) 0.000000 0.000000 0.000000 Crowther Alpha Beta Gamma 89.70471 37.51013 89.59029 Spherical polars Omega Phi Chi 18.75507 -88.96022 179.33235 Direction cosines of rotation axis 0.00584 -0.32158 0.94690 Dave Smith -37.50976 90.24947 179.35606 Rotation angle 179.332367 Nr of atoms transformed : ( 1213) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: XYz DIstort [r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz]
new X = r11*X + r21*Y + r31*Z + tx
new Y = r12*X + r22*Y + r32*Z + ty
new Z = r13*X + r23*Y + r33*Z + tz
(defaults: 1 0 0 0 1 0 0 0 1 0 0 0)
Apply a user-defined operator. Note that the operator may be anything in this command, i.e., even one that inflates or deflates or otherwise psychedelically distorts your model. All at your own risk, of course !
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > xyz dis 1 0 0 0 -1 0 2 0 -1 0 0 0Nr of RT operators : 1
RT-OP 1 = 1.0000000 0.0000000 2.0000000 0.000 0.0000000 -1.0000000 0.0000000 0.000 0.0000000 0.0000000 -1.0000000 0.000 Determinant of rotation matrix 1.000000 Column-vector products (12,13,23) 0.000000 2.000000 0.000000 ERROR --- Seriously non-orthogonal column vectors Operator applied at your own risk ! Nr of atoms transformed : ( 1070) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: XYz RT file
file = LSQ operator in O format
Apply an operator in O format to the currently selected atoms. The operator may be from O (Lsq_* commands), from LSQMAN, from CELLO, from IMP, etc. Example:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
! Created by LSQMAN V. 950413/3.3 at Tue May 9 02:32:33 1995 for user gerard
.lsq_rt_m14a_to_b r 12 (3f15.7)
-0.9999319 0.0108257 -0.0043541
-0.0112386 -0.7931781 0.6088861
0.0031381 0.6088936 0.7932457
174.4427795 -1.5139760 0.7045361
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Note that, just like the XYz MAtrix command, the O file contains the operator elements in the following order: r11, r12, r13, r21, r22, r23, r31, r32, r33, tx, ty, tz and that the new coordinates are defined by the following equations:
new X = r11*X + r21*Y + r31*Z + tx
new Y = r12*X + r22*Y + r32*Z + ty
new Z = r13*X + r23*Y + r33*Z + tz
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > xyz rt rt.o==> Read NCS operator : (.LSQ_RT_M14A_TO_B)
Nr of NCS operators : 1
NCSOP 1 = -0.9999319 -0.0112386 0.0031381 174.443 0.0108257 -0.7931781 0.6088936 -1.514 -0.0043541 0.6088861 0.7932457 0.705 Determinant of rotation matrix 1.000000 Column-vector products (12,13,23) 0.000000 0.000000 0.000000 Crowther Alpha Beta Gamma 89.70471 37.51013 89.59029 Spherical polars Omega Phi Chi 18.75507 -88.96022 179.33235 Direction cosines of rotation axis 0.00584 -0.32158 0.94690 Dave Smith -37.50976 90.24947 179.35606 Rotation angle 179.332367 ERROR --- Maximum number of NCS operators read Maximum : ( 1) Nr of atoms transformed : ( 1213) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Use this command to apply a random rotation to the selected atoms.
The random-number generator seed can be set with COnstants SEt ISEED
if you want reproducile results. Note that the centre-of-gravity
is not maintained. If you do want that, use the STatistics command
to find the centre-of-gravity, then XYz TRanslate to move the
CofG to the origin (i.e., a translation of -1 * CofG vector),
then apply the random rotation, and finally XYz TRanslate back to
the original CofG.
This command can be used to generate randomly oriented molecules for
VOIDOO, for example.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > xyz rand Rotations around X,Y,Z (deg) : 109.73 242.98 38.43X Matrix : 1.0000000 0.0000000 0.0000000 0.0000000 -0.3376119 -0.9412854 0.0000000 0.9412854 -0.3376119 Determinant of X rotation matrix : ( 1.000E+00) Y Matrix : -0.4542299 0.0000000 0.8908845 0.0000000 1.0000000 0.0000000 -0.8908845 0.0000000 -0.4542299 Determinant of Y rotation matrix : ( 1.000E+00) Z Matrix : 0.7833662 0.6215605 0.0000000 -0.6215605 0.7833662 0.0000000 0.0000000 0.0000000 1.0000000 Determinant of Z rotation matrix : ( 1.000E+00) Matrix : -0.3558283 -0.2823313 0.8908845 0.8667588 0.2567523 0.4275599 -0.3494502 0.9243199 0.1533534 Determinant of random rotation matrix : ( 1.000E+00)
Random rotation matrix: New X = -0.355828 * X + -0.282331 * Y + 0.890885 * Z New Y = 0.866759 * X + 0.256752 * Y + 0.427560 * Z New Z = -0.349450 * X + 0.924320 * Y + 0.153353 * Z Crowther Alpha Beta Gamma 25.63763 81.17869 69.29031 Spherical polars Omega Phi Chi 49.30368 68.17366 118.22019 Direction cosines of rotation axis 0.28189 0.70383 0.65205 Dave Smith -70.26855 110.45370 141.56982 ATOM 1 N PRO 1 9.697 47.544 9.791 1.00 30.05 1CBS 223 Before : ( 9.697 47.544 9.791) After : ( -8.151 24.798 42.059) Nr of transformed atoms : ( 1213) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: XYz PErturb [dx] [dy] [dz] [db] [dq]
dx..dz = maximum absolute shift for the X/Y/Z coordinate (default 0 0 0)
db = maximum absolute shift for the B-factors (default 0)
dq = maximum absolute shift for the occupancies (default 0)
Applies random shift to coordinates and/or B-factors and/or occupancies. The parameters are the amplitudes of the shifts. If dx=dy=dz, then in practice the average atomic shift ~ dx. A value of zero means that no shifts will be applied (negative values will be multiplied by -1). The operation works only on the currently selected set of atoms. Note that this operation may yield unphysical values for (some) B-factors and occupancies !
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
MOLEMAN2 > xy per .1 .1 .1 10 0.02
Max allowed shifts X/Y/Z/B/Q : ( 1.000E-01 1.000E-01 1.000E-01
1.000E-01 1.000E-01)
Nr of perturbed atoms : ( 2898)
Average shifts X/Y/Z/B/Q : ( 3.618E-04 -4.027E-04 1.844E-03
4.324E-04 5.640E-04)
RMS shifts X/Y/Z/B/Q : ( 5.809E-02 5.701E-02 5.816E-02
5.701E-02 5.837E-02)
AVERAGE POSITIONAL SHIFT (A) : ( 9.588E-02)
MOLEMAN2 > stat
...
Item Average St.Dev Min Max
---- ------- ------ --- ---
...
Occpncy 1.001 0.058 0.900 1.100
Warning - there are occupancies > 1 !
...
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: XYz MIrror [xyz] [value]
xyz = type of plane to mirror in (default X)
value = "xyz" coordinate of the plane (default 0.0)
(e.g., to mirror fractionalised coordinates in the plane Z=1/2,
use: z 0.5)
Mirror the currently selected atoms in a plane. This may be useful to get a different stereo-isomer for a chiral ligand, for instance. If you mirror in the plane: X = Centre-of-Gravity(X) (or ditto for Y or Z) then the CofG will be conserved in this operation.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
MOLEMAN2 > stat
...
Item Average St.Dev Min Max
---- ------- ------ --- ---
X-coord 10.543 22.100 -33.949 54.913
...
MOLEMAN2 > xy mi x 10.543
Mirror selected atoms in plane: X = 10.543
Nr of atoms mirrored : ( 7038)
MOLEMAN2 > stat
...
Item Average St.Dev Min Max
---- ------- ------ --- ---
X-coord 10.543 22.100 -33.827 55.035
...
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: XYz INvert [icx] [icy] [icz]
icx-z = coordinates of inversion centre (default 0,0,0)
Invert the currently selected atoms. If you supply the coordinates of the centre-of-gravity as the inversion centre, the CofG will be conserved after this operation. This command may be useful to generate D-amino acids or even proteins from their all-L counterparts. However, beware that the chirality at all chiral centres will be inverted, i.e. also at Thr-CB and Ile-CB !
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
MOLEMAN2 > stat
...
Item Average St.Dev Min Max
---- ------- ------ --- ---
X-coord 17.837 8.350 -1.464 37.101
Y-coord 20.849 6.794 2.899 34.741
Z-coord 27.423 9.907 2.776 49.501
...
MOLEMAN2 > xyz inv 17.837 20.849 27.423
Invert through the point : ( 17.837 20.849 27.423)
Nr of atoms inverted : ( 1213)
MOLEMAN2 > stat
...
Item Average St.Dev Min Max
---- ------- ------ --- ---
X-coord 17.837 8.350 -1.427 37.138
Y-coord 20.849 6.794 6.957 38.799
Z-coord 27.423 9.907 5.345 52.070
...
MOLEMAN2 > pr sc
Ideal chirality improper : ( 34.000)
Ideal flatness improper : ( 0.000)
Tolerance : ( 5.000)
RESIDUE PRO 1 1CBS
Warning - D-amino acid !
RESIDUE ASN 2 1CBS
Warning - D-amino acid !
...
RESIDUE GLU 137 1CBS
Warning - D-amino acid !
Nr of residues checked : ( 129)
Nr of D-amino acids : ( 129)
Nr with poor CA chirality : ( 2)
Nr wrong 1/2 atom names : ( 0)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This will calculate the centre-of-gravity of the currently selected
atoms, and translate them by -1 times that vector, so that the
new CofG coincides with the origin at (0,0,0).
From version 1.0 onward, there is an optional "use_masses" parameter.
The default is N(o), but if you set it to Y(es), the actual masses
will be used in calculating th centre-of-gravity. Note that this
feature depends on the chemical element being recognisable for all
selected atoms (either from the atom name or the element field in
the PDB records). Also, if you don't have explicit hydrogens the
calculated CofG will be off in general.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
MOLEMAN2 > xyz cen
Moving CofG of selected atoms to (0,0,0)
Nr of selected atoms : ( 1213)
Centre-of-Gravity : ( 17.837 20.849 27.423)
CofG now at (0,0,0)
MOLEMAN2 > stats
...
Item Average St.Dev Min Max
---- ------- ------ --- ---
X-coord 0.000 8.350 -19.301 19.264
Y-coord 0.000 6.794 -17.950 13.892
Z-coord 0.000 9.907 -24.647 22.078
...
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > xy ce y Moving CofG of selected atoms to (0,0,0) Using atom masses to calculate CofG Nr of selected atoms : ( 1213) Nr of unknown elements : ( 0) Sum of masses : ( 1.632E+04) Centre-of-Mass : ( 17.831 20.824 27.406) CofG now at (0,0,0) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This will move the currently selected atoms such that their
centre-of-gravity is at the origin (0,0,0); then it will calculate
the three principal inertia axes, and align the selected atoms
such that these axes coincide with the X, Y and Z axis. This
alignment is done such that the major inertia axis coincides
with the X-axis (largest eigenvalue), and the minor inertia
axis coincides with the Z-axis (smallest eigenvalue). If the
hand of the three inertia axes is inverted (determinant = -1),
the three axes are inverted (multiplied by -1).
This is basically the same operation as the one AMORE performs
when it puts your search model inside the smallest box (TABLING
step).
As a "side-effect", the XY-plane is now the "least-squares plane"
through the selected atoms, which means that if you view your
molecule looking along the Z-axis, you get the least-cluttered
view (i.e., the least overlap between atoms).
After this operation, the "standard deviation" and range of the
X-coordinates is greater than or equal to those of the Y-coordinates,
which in turn exceed those of the Z-coordinates.
The program prints the Centre-of-Gravity vector, so if you want to
restore the old CofG, use XYz TRanslate along this vector.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ... Selection history : (ALL | AND TYpe = PROT | AND CHain = A |) Nr of selected atoms : ( 3220) MOLEMAN2 > xyz align Moving CofG of selected atoms to (0,0,0) Nr of selected atoms : ( 3220) Centre-of-Gravity : ( 30.107 63.884 61.070) CofG now at (0,0,0) Eigen value 1 = 684466.3 Vector : -0.070020 0.049714 0.996306 Eigen value 2 = 370175.8 Vector : 0.732493 0.680549 0.017521 Eigen value 3 = 298389.2 Vector : -0.677164 0.731014 -0.084067 Determinant : ( 1.000)Nr of NCS operators : 1
NCSOP 1 = -0.0700198 0.0497140 0.9963061 0.000 0.7324933 0.6805488 0.0175209 0.000 -0.6771638 0.7310143 -0.0840671 0.000 Determinant of rotation matrix 1.000000 Column-vector products (12,13,23) 0.000000 0.000000 0.000000 Crowther Alpha Beta Gamma 1.00749 94.82238 47.18999 Spherical polars Omega Phi Chi 69.42821 66.90875 103.69593 Direction cosines of rotation axis 0.36719 0.86122 0.35138 Dave Smith -168.22716 132.62241 -144.62529 Rotation angle 103.695923 MOLEMAN2 > stats ... Item Average St.Dev Min Max ---- ------- ------ --- --- X-coord 0.000 14.580 -34.834 30.615 Y-coord 0.000 10.722 -26.141 28.231 Z-coord 0.000 9.626 -22.863 23.692 ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Auto-generate chain and segment identifiers. This starts at "AAAA" for
the first residue (chain "A"), then "AAAB" (chain "B"), etc. A new
segment starts if:
- a residue is the first residue in the current structure
- a residue is not of the same type as its predecessor (e.g., from
PROTein to WATEr)
- a protein residue is too far away from its predecessor (using the
CA-CA distance to check this)
- a non-protein residue (OTHER THAN WATER) does not have a residue
number which is one higher than that of its predecessor (note that
all *consecutive* waters, irrespective of their numbering, will end
up in one segment)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > re 1cel.pdb Reading from file : (1cel.pdb) in normal PDB format ignoring hydrogen atoms ... MOLEMAN2 > ch autoRESIDUE PCA A 1 1CEL New segment : ( 1) Because : (First residue) Segment ID (4 char) : (AAAA) Chain name (1 char) : (A)
RESIDUE NAG A 435 1CEL New segment : ( 2) Because : (Different type of residue: CARB) Segment ID (4 char) : (AAAB) Chain name (1 char) : (B)
RESIDUE IBZ A 436 1CEL New segment : ( 3) Because : (Different type of residue: HETE) Segment ID (4 char) : (AAAC) Chain name (1 char) : (C)
RESIDUE GLC A 437 1CEL New segment : ( 4) Because : (Different type of residue: CARB) Segment ID (4 char) : (AAAD) Chain name (1 char) : (D)
RESIDUE HOH A 501 1CEL New segment : ( 5) Because : (Different type of residue: WATE) Segment ID (4 char) : (AAAE) Chain name (1 char) : (E)
RESIDUE PCA B 1 1CEL New segment : ( 6) Because : (Different type of residue: PROT) Segment ID (4 char) : (AAAF) Chain name (1 char) : (F) ... RESIDUE HOH 441 1CEL New segment : ( 12) Because : (Different type of residue: WATE) Segment ID (4 char) : (AAAL) Chain name (1 char) : (L)
Total number of segment/chains found : ( 12) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This command does the same as the CHain AUto command, except that you are prompted for the new segment and chain names. The program will then continue generating new segment names from the one you provided. For example, if you have three protein molecules in your file, and you call the first "PROA", the program will suggest "PROB" for the name of the second molecule, etc.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > read 1cbs.pdb Reading from file : (1cbs.pdb) in normal PDB format ignoring hydrogen atoms ... MOLEMAN2 > ch askRESIDUE PRO 1 1CBS New segment : ( 1) Because : (First residue) Segment ID (4 char) ? (AAAA) prot Chain name (1 char) ? (T) P
RESIDUE REA 200 1CBS New segment : ( 2) Because : (Different type of residue: ORGA) Segment ID (4 char) ? (PROU) RTA Chain name (1 char) ? ( ) r
RESIDUE HOH 300 1CBS New segment : ( 3) Because : (Different type of residue: WATE) Segment ID (4 char) ? (RTAB) WATR Chain name (1 char) ? (R) w
Total number of segment/chains found : ( 3) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: CHain REname old new
old = old chain name (to be replaced; * means ANY)
new = new chain name
Replaces the old by the new chain name for the selected atoms. If you type all parameters on the command line, you must enclose a space in "double quotes".
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > se all Select ALL atoms Selection history : (ALL |) Nr of selected atoms : ( 5794) MOLEMAN2 > ch ren x " " Replace chain name |X| by | | Nr of chain names replaced : ( 3) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > ch re Old chain name ? ( ) New chain name ? ( ) x Replace chain name | | by |X| Nr of chain names replaced : ( 3) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > se all ... MOLEMAN2 > se and ty prot ... MOLEMAN2 > ch re * a Replace chain name |*| by |A| Nr of chain names replaced : ( 5487) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: CHain SEgid_rename old new
old = old segment id (to be replaced; * means ANY)
new = new segment id
Replaces the old by the new segment id for the selected atoms. If you type all parameters on the command line, you must enclose segment ids with spaces in them in "double quotes".
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > ch se xxxx " a B" Replace segment id |XXXX| by | A B| Nr of segment ids replaced : ( 3) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > ch seg Old segment id ? ( ) a b New segment id ? ( ) xxxx Replace segment id | A B| by |XXXX| Nr of segment ids replaced : ( 3) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > se all ... MOLEMAN2 > se and ty prot ... MOLEMAN2 > se negate ... MOLEMAN2 > ch se * bbbb Replace segment id |* | by |BBBB| Nr of segment ids replaced : ( 307) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: CHain NAme_selection chain segid
chain = new chain name (= means no change)
segid = new segment id (= means no change)
Set the chain name and/or the segment id for all currently selected atoms. A value of "=" means that no change will take place.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > se al MOLEMAN2 > se and ty prot MOLEMAN2 > ch name = prot Give selected atoms chain name |=| and segment id |PROT| Nr of chain names replaced : ( 0) Nr of segment ids replaced : ( 5487) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: CHain FRom_segid [how]
how = AUto | ASk
Generate chain names from segment ids for all atoms. In automatic mode, the chain name will be equal to the last character of the segment id; in interactive mode, the user can set the chain name. This is useful for quickly adding chain names for O to a PDB file which comes out of X-PLOR.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > ch frRESIDUE ALA 86 AAAA New chain name : (A)
RESIDUE NAG 501 BBBB New chain name : (B)
RESIDUE I 601 CCCC New chain name : (C)
RESIDUE THR 85 KKKK New chain name : (K)
RESIDUE NAG 501 LLLL New chain name : (L)
RESIDUE I 601 MMMM New chain name : (M)
RESIDUE CD2 701 XXXX New chain name : (X)
RESIDUE HOH 801 WWWW New chain name : (W) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: CHain TO_segid [how]
how = AUto | ASk
Generate segment ids from chain names for all atoms. In automatic mode, the segment id will be equal to "four times" the chain name; in interactive mode, the user can set the chain name. This is useful for quickly adding segment ids for X-PLOR to a PDB file which comes out of O.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > ch to askRESIDUE ALA A 86 Segment id ? (AAAA) New segment id : (AAAA)
RESIDUE NAG B 501 Segment id ? (BBBB) New segment id : (BBBB) ... RESIDUE CD2 X 701 Segment id ? (XXXX) METL New segment id : (METL)
RESIDUE HOH W 801 Segment id ? (WWWW) WATR New segment id : (WATR) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This commands screens your structure to find protein chain ends and generates coordinates for the two terminal oxygens (needed for X-PLOR). The atoms are not actually added to your structure !! Protein chain ends are recognised in a way similar as that described for the CHain AUto command. For this operation to work, at least the N, CA and C atoms must be known.
NOTE: from version 0.21 onwards, the SPlit command will add an OT2 atom automagically where necessary (provided your segment IDs are correct).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > ch ot Looking for protein chain ends ...RESIDUE ILE 63 1CBS ==> OT1 NOW : 16.286 28.434 35.144 SUGGESTED : 16.306 28.432 35.120 ==> OT2 NOW : 0.000 0.000 0.000 SUGGESTED : 14.246 29.041 34.934 You must add/edit OT1/OT2 yourself !
RESIDUE LYS 98 1CBS ==> OT1 NOW : 0.000 0.000 0.000 SUGGESTED : 4.068 25.479 21.799 ==> OT2 NOW : 0.000 0.000 0.000 SUGGESTED : 4.140 26.276 23.802 You must add/edit OT1/OT2 yourself !
RESIDUE GLU 137 1CBS ==> OT1 NOW : 34.221 19.175 38.659 SUGGESTED : 34.267 19.157 38.667 ==> OT2 NOW : 0.000 0.000 0.000 SUGGESTED : 35.724 18.613 37.173 You must add/edit OT1/OT2 yourself !
Nr of chain ends found : ( 3) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: ONo RSr res_type [file] [res_nr]
res_typ = type of residue (3 characters; e.g. GLC)
file = name of output file (default: automatic)
res_nr = residue number (default: first)
Generate an O datablock for use with the RSR commands for a certain type of residue. If you don't supply a file name, a reasonable default will be generated. If you don't supply a residue number, the first residue of the specified type encountered will be used.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > ono rsr rea ONO file type : (RSR_dict) Residue type : (REA) Residue used : RESIDUE REA 200 1CBS Atoms in residue : ( 22) ATOM 1093 C1 REA 200 21.972 29.831 16.739 1.00 15.25 1CBS1315 ATOM 1094 C2 REA 200 20.921 30.524 15.841 1.00 15.61 1CBS1316 ... ATOM 1114 O2 REA 200 21.840 21.712 27.037 1.00 10.99 1CBS1336 Output file : (rea_rsr_dict.odb) Cut-off distance for bonded atoms : ( 2.000) Special torsion-angle tolerance : ( 6.000) Datablock name : (RSR_dict_REA) Datablock written ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! Created by MOLEMAN2 V. 960301/0.9 at Fri Mar 1 23:52:36 1996 for user gerard ! ! RSR datablock for REA ! RSR_dict_REA T 2 70 C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 C20 O1 O2 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: ONo FIt res_type [file] [res_nr]
res_typ = type of residue (3 characters; e.g. GLC)
file = name of output file (default: automatic)
res_nr = residue number (default: first)
Generate an O datablock for use with the RS_fit command for a certain type of residue. If you don't supply a file name, a reasonable default will be generated. If you don't supply a residue number, the first residue of the specified type encountered will be used.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > ono fit rea ONO file type : (RS_fit) Residue type : (REA) Residue used : RESIDUE REA 200 1CBS Atoms in residue : ( 22) ATOM 1093 C1 REA 200 21.972 29.831 16.739 1.00 15.25 1CBS1315 ... ATOM 1114 O2 REA 200 21.840 21.712 27.037 1.00 10.99 1CBS1336 Output file : (rea_rs_fit.odb) Cut-off distance for bonded atoms : ( 2.000) Special torsion-angle tolerance : ( 6.000) Datablock name : (rsfit_REA) Datablock written ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! Created by MOLEMAN2 V. 960301/0.9 at Fri Mar 1 23:59:24 1996 for user gerard ! ! RS-fit datablock for REA ! rsfit_REA T 2 70 C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 C20 O1 O2 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: ONo COnnect res_type [file] [res_nr]
res_typ = type of residue (3 characters; e.g. GLC)
file = name of output file (default: automatic)
res_nr = residue number (default: first)
Generate an O connectivity entry (to be included in "o.dat") for a certain type of residue. If you don't supply a file name, a reasonable default will be generated. If you don't supply a residue number, the first residue of the specified type encountered will be used. Two hydrogen atoms will not be connected. You can set the cut-off distance for bonded atoms with the COnstants SEt command (MXBOND).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > ono con rea ONO file type : (Connect) Residue type : (REA) Residue used : RESIDUE REA 200 1CBS Atoms in residue : ( 22) ATOM 1093 C1 REA 200 21.972 29.831 16.739 1.00 15.25 1CBS1315 ... ATOM 1114 O2 REA 200 21.840 21.712 27.037 1.00 10.99 1CBS1336 Output file : (rea_connect.dat) Cut-off distance for bonded atoms : ( 2.000) Special torsion-angle tolerance : ( 6.000) Nr of bonds : ( 22) Nr of ATOM records : ( 3) Nr of CONNECT ,, : ( 7) Connect file written (append to all.dat) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- REA ATOM C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 ATOM C11 C12 C13 C14 C15 C16 C17 C18 C19 C20 ATOM O1 O2 CONNECT - C1 C2 C3 C4 C5 C6 C1 C16 + CONNECT C1 C17 CONNECT C5 C18 CONNECT C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 O1 CONNECT C9 C19 CONNECT C13 C20 CONNECT C15 O2 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: ONo TOrsion res_type [file] [res_nr]
res_typ = type of residue (3 characters; e.g. GLC)
file = name of output file (default: automatic)
res_nr = residue number (default: first)
Generate an O torsion entry (include in "torsion.o") for a certain type of residue. If you don't supply a file name, a reasonable default will be generated. If you don't supply a residue number, the first residue of the specified type encountered will be used. Two hydrogen atoms will not be connected. You can set the cut-off distance for bonded atoms with the COnstants SEt command (MXBOND). The TORTOL parameter can also be set; it determines if a certain torsion is almost "special" (i.e., zero or a multiple of 180 degrees); if this is the case, the torsion is assumed to be fixed and no entry will be generated for it.
This appears to be a simple exercise, but it is not. Consider all-
trans-retinoic acid with 22 atoms and 22 bonds. This yields more than
40 dihedral angles, but only 3 torsion entries ... The trick is to
throw away every dihedral which appears to be strongly restrained,
dihedrals inside rings, etc. MOLEMAN uses the following criteria
to reduce the number of torsions:
- any dihedral which is equal to -180, 0 or +180 degrees (with a
tolerance of 5 degrees) is rejected as (probably) being strongly
restrained to its current value (e.g., in conjugated systems)
- any dihedral K->I->J->L whose rotation affects atom "K" or
"I" is rejected as (probably) being part of a ring system
- if the number of atoms affected by the torsion is >= the total
nr of atoms minus 4, the torsion is rejected. In this case,
(for example, a torsion involving a carboxylate) it makes more
sense to use the torsion defined the other way around (i.e.,
use torsion L-J-I-K which affects only 1 or 2 atoms, instead of
K-I-J-L)
- if a torsion is around the same bond as a previous torsion, and
it affects the same atoms as that previous torsion, it is rejected
as being a simple permutation. This happens, for instance, for
carboxylates and for aliphatic tails sprouting from a ring, in
which case there are two equivalent ways to define the torsion
of the tail relative to the ring)
The "surviving", freely rotatable torsion angles are written to a file. This file must be *appended* to your standard torsion file (ODAT/torsion.o, for instance), and the number of lines in the datablock must be updated accordingly.
Note that this option doesn't know anything about linkages to other residues (and therefore is less suited for use with oligomeric compounds). For instance, if you run it on a TRP residue, you'll get several unwanted torsions.
Note: at present, O can only handle a maximum of 12 torsion angles. This means you may have to remove some of them (but remember that many of them will be defined in two ways, so you can keep the one you find most useful of each such pair).
The following example shows how this works for retinoic acid (residue 200 in PDB entry 1CBS if you want to try it at home). Note that indeed only the three intuitively reasonable torsions are generated: the tail relative to the ring, the ring relative to the tail, and the carboxylate relative to the tail !
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- All-trans-retinoic is (incorrectly ;-) numbered as follows:C16 C19 C20 O21 | | | / C5 C7 C9 C11 C13 C15 /\\ / \\ / \\ / \\ / \\ / \ C4 C6 C8 C10 C12 C14 O22 | | C3 C1--C17 \ /\ C2 C18
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > ono tors rea ONO file type : (Torsion) Residue type : (REA) Residue used : RESIDUE REA 200 1CBS Atoms in residue : ( 22) ATOM 1093 C1 REA 200 21.972 29.831 16.739 1.00 15.25 1CBS1315 ... ATOM 1114 O2 REA 200 21.840 21.712 27.037 1.00 10.99 1CBS1336 Output file : (rea_torsion.dat) Cut-off distance for bonded atoms : ( 2.000) Special torsion-angle tolerance : ( 6.000) Nr of bonds : ( 22)DIHEDRAL C6 C1 C2 C3 -42.76 Skip -> ring torsion ... DIHEDRAL C1 C6 C7 C8 154.33 Affected atoms : ( C8 C9 C10 C11 C12 C13 C14 C15 C19 C20 O1 O2) OKAY ==> new torsion : (TOR1)
DIHEDRAL C5 C6 C7 C8 -32.57 Affected atoms : ( C8 C9 C10 C11 C12 C13 C14 C15 C19 C20 O1 O2) Permutation of : (TOR1) Skip -> permutation
DIHEDRAL C8 C7 C6 C1 154.33 Affected atoms : ( C1 C2 C3 C4 C5 C16 C17 C18) OKAY ==> new torsion : (TOR2)
DIHEDRAL C8 C7 C6 C5 -32.57 Affected atoms : ( C5 C1 C2 C3 C4 C16 C17 C18) Permutation of : (TOR2) Skip -> permutation
DIHEDRAL C6 C7 C8 C9 -179.29 Skip -> torsion ~ 180 ... DIHEDRAL C15 C14 C13 C20 -0.15 Skip -> torsion ~ 0
DIHEDRAL C13 C14 C15 O1 -50.98 Affected atoms : ( O1 O2) OKAY ==> new torsion : (TOR3)
DIHEDRAL C13 C14 C15 O2 129.00 Affected atoms : ( O2 O1) Permutation of : (TOR3) Skip -> permutation
DIHEDRAL O1 C15 C14 C13 -50.98 Affected atoms : ( C13 C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C16 C17 C18 C19 C20) Skip -> too many affected atoms
DIHEDRAL O2 C15 C14 C13 129.00 Affected atoms : ( C13 C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C16 C17 C18 C19 C20) Skip -> too many affected atoms
Nr of unique rotatable torsions : ( 3) Nr of lines written : ( 5) Torsion file written (append to torsion.o) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- RESIDUE REA TORSION TOR1 154. C1 C6 C7 C8 C8 C9 C10 C11 C12 C13 C14 C15 C19 C20 \ O1 O2 TORSION TOR2 154. C8 C7 C6 C1 C1 C2 C3 C4 C5 C16 C17 C18 TORSION TOR3 -51. C13 C14 C15 O1 O1 O2 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: ONo DIsulfide_odl o_mol [file] [how] [object]
o_mol = name of the molecule inside O
file = name of the ODL file (default: disulfide.odl)
how = Sticks | Lines (default: Sticks)
object = name of the ODL object in O (default: ssbond)
Generate an ODL file to draw disulfide links in O. Draw the file with the Draw command in O.
Example of the use of an ONo DIsulfide ODL file in O.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > ono dis m1 disu.odl sticks ss_st O molecule name : (M1) ODL file name : (disu.odl) Draw as Sticks ODL object name : (ss_st)Looking for disulfides ... Looking for CYS- SG atoms ... ATOM 496 SG CYS A 67 26.853 23.275 24.788 1.00 18.16 1FSS 721 ATOM 719 SG CYS A 94 27.958 21.920 25.822 1.00 2.00 1FSS 944 ATOM 1767 SG CYS A 231 17.706 42.764 23.358 1.00 2.00 1FSS1992 ATOM 1944 SG CYS A 254 15.900 18.643 43.219 1.00 14.44 1FSS2169 ATOM 2032 SG CYS A 265 17.033 17.112 43.932 1.00 13.67 1FSS2257 ATOM 3118 SG CYS A 402 11.202 50.463 20.218 1.00 17.06 1FSS3343 ATOM 4105 SG CYS A 521 12.171 51.649 18.881 1.00 2.00 1FSS4330 ATOM 4264 SG CYS B 3 -0.622 9.196 15.268 1.00 34.29 1FSS4489 ATOM 4372 SG CYS B 17 1.031 6.187 17.911 1.00 53.34 1FSS4597 ATOM 4405 SG CYS B 22 -1.328 8.466 17.020 1.00 31.20 1FSS4630 ATOM 4546 SG CYS B 39 2.164 5.235 19.293 1.00 20.78 1FSS4771 ATOM 4556 SG CYS B 41 -5.604 11.002 25.701 1.00 52.29 1FSS4781 ATOM 4637 SG CYS B 52 -4.745 12.199 24.311 1.00 29.91 1FSS4862 ATOM 4643 SG CYS B 53 -4.229 13.247 16.868 1.00 42.61 1FSS4868 ATOM 4686 SG CYS B 59 -4.012 11.998 15.283 1.00 12.80 1FSS4911 Nr of CYS SG atoms : ( 15) Max SG-SG distance for link : ( 2.200) Disulfide # 1 67 1FSS <-> 94 1FSS @ 2.03 A Disulfide # 2 254 1FSS <-> 265 1FSS @ 2.03 A Disulfide # 3 402 1FSS <-> 521 1FSS @ 2.03 A Disulfide # 4 3 1FSS <-> 22 1FSS @ 2.03 A Disulfide # 5 17 1FSS <-> 39 1FSS @ 2.02 A Disulfide # 6 41 1FSS <-> 52 1FSS @ 2.03 A Disulfide # 7 53 1FSS <-> 59 1FSS @ 2.03 A Nr of disulfides : ( 7) ODL file written ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- begin ss_st colour green stick m1 a67 sg m1 a94 sg 0.20 stick m1 a254 sg m1 a265 sg 0.20 stick m1 a402 sg m1 a521 sg 0.20 stick m1 b3 sg m1 b22 sg 0.20 stick m1 b17 sg m1 b39 sg 0.20 stick m1 b41 sg m1 b52 sg 0.20 stick m1 b53 sg m1 b59 sg 0.20 end_object ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- begin ss_li colour green move_atom m1 a67 sg line_atom m1 a94 sg move_atom m1 a254 sg line_atom m1 a265 sg move_atom m1 a402 sg line_atom m1 a521 sg move_atom m1 b3 sg line_atom m1 b22 sg move_atom m1 b17 sg line_atom m1 b39 sg move_atom m1 b41 sg line_atom m1 b52 sg move_atom m1 b53 sg line_atom m1 b59 sg end_object ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: ONo WAter_fit_macro [file]
file = name of the O macro (default: water_fit.omac)
Generate an O macro to real-space fit all waters. Execute the macro inside O with the @ command. Hint: don't use the graphics when you run the macro; this will speed up the fitting considerably !!!
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > ono water File name : (water_fit.omac) Nr of waters to be fitted : ( 50) O macro written ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
! Created by MOLEMAN2 V. 960303/0.10 at Sun Mar 3 22:11:24 1996 for user gerard
!
bell Message Set up for water fitting ...
!
symbol mymol # Molecule name ? #
mol $mymol
!
symbol mymap # Map file name ? #
map_file $mymap
rsr_map $mymap
!
rsr_setup
yes
no
conv
# RS-fit RFAC or RSCC ? #
yes
;
;
20.0
3.5
;
3
10.0
!
bell Message Fitting waters of mol $mymol in map $mymap ...
!
rs_fit J801 ;
rsr_rigid J801 ; yes
!
rs_fit J802 ;
rsr_rigid J802 ; yes
...
rs_fit J850 ;
rsr_rigid J850 ; yes
!
Message Calculating new RS-fit values
! copy_db ${mymol}//_residue_rsprefit ${mymol}//_residue_rsfit
rs_fit J801 J850
!
on_off bell Message Done
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: ONo OOps o_mol [file]
o_mol = name of the molecule inside O
file = name of the O macro file (default: pre_oops.omac)
This commands generates an O macro which, when executed, will run the standard checks and write out the necessary datablocks for use with OOPS. Your model must have been read into O before you execute this macro (with the @ command in O). It works fastest if you don't have the graphics turned on.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > ono oops m3 File name : (pre_oops.omac) O macro written ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! Created by MOLEMAN2 V. 960304/0.11 at Tue Mar 5 16:35:40 1996 for user gerard ! File: pre_oops.omac ! mol M3 yasspa M3 alpha 0.5 yasspa M3 beta 0.8 write M3_residue_name resnam.o ; write M3_residue_type restyp.o ; ! pep_flip M3 A86 W850 write M3_residue_pepflip pepflip.o ; ! rsc_fit M3 A86 W850 write M3_residue_rsc rsc.o ; ! symbol mymap # Map file name ? # map_file $mymap rsr_map $mymap ! rsr_setup yes ... 10.0 ! read odat/rsfit_all.o rs_fit M3 A86 W850 write M3_residue_rsfit rsfit_all.o ; ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: ONo XPlor_hydrogens
O mutilates HD* and HH* hydrogen atom names from X-PLOR. This command fixes them again.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > ono xpl Fixing hydrogen names for Asn and ArgRESIDUE ASN 91 ATOM 51 HD21 ASN 91 14.601 54.916 49.939 1.00 0.00 6 ATOM 52 HD22 ASN 91 15.605 53.517 50.014 1.00 0.00 6
RESIDUE ASN 101 ATOM 139 HD21 ASN 101 20.743 36.104 53.964 1.00 0.00 6 ATOM 140 HD22 ASN 101 22.169 35.310 53.410 1.00 0.00 6
RESIDUE ARG 153 ATOM 589 HH11 ARG 153 3.392 34.583 57.094 1.00 0.00 6 ATOM 590 HH12 ARG 153 2.672 33.266 56.241 1.00 0.00 6 ATOM 592 HH21 ARG 153 3.632 30.818 58.523 1.00 0.00 6 ATOM 593 HH22 ARG 153 2.799 31.153 57.036 1.00 0.00 6 ... RESIDUE ASN 443 ATOM 6855 HD21 ASN 443 51.984 102.581 98.476 1.00 0.00 6 ATOM 6856 HD22 ASN 443 51.250 104.024 99.061 1.00 0.00 6 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: ONo CEll [file] [mode] [col]
file = name of ODL file (default: cell.odl)
mode = type of graphics object in O (line or solid, default: line)
col = colour of the object (default: red)
With this command you can generate an ODL file that will draw the unit cell (as read from the CRYST1 card or entered with the PDb CRyst command) in O, either as a set of lines or a set of planes (solid mode).
Example of the use of an ONo CEll (solid) ODL file in O.
Example of the use of an ONo CEll (line) ODL file in O.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > ono cell ODL file : (cell.odl) Mode : (line) Colour : (red) Origin (fract.) : ( 0.000 0.000 0.000) Top (fract.) : ( 1.000 1.000 1.000) Origin (cart.) : ( 0.000 0.000 0.000) Top (cart.) : ( 54.124 45.617 39.426) ODL file written MOLEMAN2 > ono cell cell2.odl solid gold ODL file : (cell2.odl) Mode : (solid) Colour : (gold) Origin (fract.) : ( 0.000 0.000 0.000) Top (fract.) : ( 1.000 1.000 1.000) Origin (cart.) : ( 0.000 0.000 0.000) Top (cart.) : ( 54.124 45.617 39.426) ODL file written ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The ODL file may look as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- begin celly colour red m 0.000 0.000 0.000 l 40.430 0.000 0.000 l 47.277 39.846 0.000 l 6.847 39.846 0.000 l 0.000 0.000 0.000 m 6.847 5.771 39.426 l 47.277 5.771 39.426 l 54.124 45.617 39.426 l 13.694 45.617 39.426 l 6.847 5.771 39.426 m 0.000 0.000 0.000 l 6.847 5.771 39.426 m 40.430 0.000 0.000 l 47.277 5.771 39.426 m 47.277 39.846 0.000 l 54.124 45.617 39.426 m 6.847 39.846 0.000 l 13.694 45.617 39.426 end_object ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
And for a solid cell:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
begin celly
mode solid
colour gold
poly 4
0.000 0.000 0.000
40.430 0.000 0.000
47.277 39.846 0.000
6.847 39.846 0.000
poly 4
13.694 45.617 39.426
54.124 45.617 39.426
47.277 5.771 39.426
6.847 5.771 39.426
poly 4
0.000 0.000 0.000
40.430 0.000 0.000
47.277 5.771 39.426
6.847 5.771 39.426
poly 4
13.694 45.617 39.426
54.124 45.617 39.426
47.277 39.846 0.000
6.847 39.846 0.000
poly 4
6.847 39.846 0.000
13.694 45.617 39.426
6.847 5.771 39.426
0.000 0.000 0.000
poly 4
40.430 0.000 0.000
47.277 5.771 39.426
54.124 45.617 39.426
47.277 39.846 0.000
mode line
end_object
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: ONo RIngs [file] [obj] [col]
file = name of ODL file (default: rings.odl)
obj = name of graphics object in O (default: rings)
col = colour of the plane (default: cyan)
With this command you can generate an ODL file that will draw nice semi-transparent planes inside ring compounds (provided the atoms in the ring are defined in the "moleman2.lib" library file). All ring residues of which at least one atom is currently selected will be included.
Example of the use of an ONo RIngs ODL file (protein) in O.
Example of the use of an ONo RIngs ODL file (nucleic acid) in O.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > ono ring Command > (ono ring) Nr of rings found : ( 9) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The ODL file may look as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
! Created by MOLEMAN2 V. 000526/2.6.3 at Sat May 27 02:06:11 2000 for gerard
begin rings
mode solid
colour cyan
poly 6
17.41 17.30 15.66
16.48 18.24 15.59
15.24 17.82 15.38
15.41 16.47 15.30
16.73 16.10 15.44
17.41 17.30 15.66
poly 7
15.41 16.47 15.30
[...]
18.36 16.14 11.87
18.51 14.80 11.69
mode line
end_object
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: ONo MOlray [file] [mode] [mult] [near_far] [for_rev] [resi] [atom]
file = name of output PDB file
mode = mode selection (only mode PEPT implemented so far)
mult = multiplier (non-zero real number)
near_far = take nearest or farthest neighbours
for_rev = forward or reverse sequence order
resi = residue type to use in trace molecule (default: "HOH")
atom = residue type to use in trace molecule (default: " O ")
Generate a trace pseudo-molecule for use with MolRay (if you want to "fly" along the backbone in a movie).
In mode PEPT, points are chosen, one for every peptide plane. The normal vector to the least-squares plane of CA(i), C(i), N(i+1), CA(i+1) is calculated together with the centre-of-gravity. The trace atom is placed at the centre-of-gravity plus the (unit) normal vector multiplied by the user-defined multiplier. Note that the multiplier can be positive or negative ("above" or "below" the first peptide plane). For the second, third, etc. planes, both the positive and the negative multiplier will be used to generate two possible points. In mode "nearest", the one that is closest to the previous trace point will be accepted; in mode "farthest" the more distant one will be used instead. Just experiment with the various parameters to see what gives the best effect.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > read pdb1fss.ent [...] MOLEMAN2 > select and chain a [...] MOLEMAN2 > ono mol Trace PDB file name ? (molray_trace.pdb) 1fss_trace.pdb Mode (PEPT) ? (peptide) Multiplier ? ( 1.00) 0.5 Near or Far nbrs (NEA/FAR) ? (nearest) Forward or reverse (FOR/REV) ? (forward)Opening output file : (1fss_trace.pdb) Mode : (PEPT) Multiplier for normal vector : ( 0.500) Near/Far : (NEAR) Forward/reverse : (FORWARD) Trace residue type : (HOH) Trace atom type : ( O) Nr of residues to check : ( 532) Nr of trace atoms written : ( 531) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: ONo LS_plane_odl [file] [obj] [col] [border] [nr] [name]
file = name of ODL file (default: plane.odl)
obj = name of graphics object in O (default: _plane)
col = colour of the plane (default: cyan)
border = size of the border of the plane around the atoms (approx.)
nr = plane number (1-20) if you want to store this plane's normal vector
name = name for this plane (e.g., name of the residue)
This command does the same as the LS_plane command, plus:
- it gives a list of the distances of all atoms to the least-squares
plane
- it generates an ODL file which can be drawn in O to show the plane
- the normal vector of a plane can be stored (up to 20 planes can
be stored in total), and the angles between any of the stored
planes can subsequently be listed with the ONo ANgle_ls_planes
command
As of version 1.0.3 this command gives *much* better results (i.e., not too big planes through your selected atoms), irrespective of the orientation (before, you could get 400 A long planes if they were oriented in an unfortunate way ;-). From version 1.0.4, the size of the border around the atoms is a parameter (1 A is typically a good value, but there may be cases where you want bigger or smaller planes).
Example of the use of an ONo LS_plane ODL file in O.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > se all MOLEMAN2 > se an re rea MOLEMAN2 > ono ls rea.odl Nr of selected atoms : ( 22) Centre of Gravity : ( 22.065 26.283 20.209) Eigen value 1 = 515.0 Vector : 0.145303 -0.597192 0.788828 Eigen value 2 = 31.0 Vector : 0.847841 0.486099 0.211834 Eigen value 3 = 6.7 Vector : -0.509954 0.638020 0.576955 Determinant : ( 1.000) Eigenvector #3 defines the least-squares plane Equation: -0.509954 X + 0.638020 Y + 0.576955 Z = 17.176491ATOM 1093 C1 REA 200 Distance 0.309 ATOM 1094 C2 REA 200 Distance 0.769 ATOM 1095 C3 REA 200 Distance -0.026 ATOM 1096 C4 REA 200 Distance -0.043 ATOM 1097 C5 REA 200 Distance -0.259 ATOM 1098 C6 REA 200 Distance -0.019 ATOM 1099 C7 REA 200 Distance -0.193 ATOM 1100 C8 REA 200 Distance -0.016 ATOM 1101 C9 REA 200 Distance -0.185 ATOM 1102 C10 REA 200 Distance 0.008 ATOM 1103 C11 REA 200 Distance -0.112 ATOM 1104 C12 REA 200 Distance 0.077 ATOM 1105 C13 REA 200 Distance 0.002 ATOM 1106 C14 REA 200 Distance 0.202 ATOM 1107 C15 REA 200 Distance 0.179 ATOM 1108 C16 REA 200 Distance 1.449 ATOM 1109 C17 REA 200 Distance -0.955 ATOM 1110 C18 REA 200 Distance -0.616 ATOM 1111 C19 REA 200 Distance -0.621 ATOM 1112 C20 REA 200 Distance -0.290 ATOM 1113 O1 REA 200 Distance -0.797 ATOM 1114 O2 REA 200 Distance 1.138
RMSD to plane : ( 0.552) ODL file written ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The ODL file may look as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
! Created by MOLEMAN2 V. 960412/0.17 at Fri Apr 12 22:57:47 1996 for user gerard
begin plane
mode solid
colour cyan
poly 5
18.56 20.08 23.97
18.56 31.74 11.08
25.30 31.74 17.04
25.30 20.08 29.94
18.56 20.08 23.97
mode line
end_object
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- .. Selection history : (ALL | AND TYpe = PROT | AND CLass = Side | AND REsidu = TRP | AND Residue_nr 109 109 |) Nr of selected atoms : ( 10) MOLEMAN2 > ono ls trp109.odl Nr of selected atoms : ( 10) Centre of Gravity : ( 13.617 20.280 29.635) Eigen value 1 = 28.3 Vector : 0.044093 0.093234 0.994667 Eigen value 2 = 12.4 Vector : -0.373900 0.924815 -0.070112 Eigen value 3 = 0.0 Vector : 0.926420 0.368814 -0.075638 Determinant : ( -1.000) ERROR --- Negative determinant; change hand of inertia axes Eigen value 1 = 28.3 Vector : -0.044093 -0.093234 -0.994667 Eigen value 2 = 12.4 Vector : 0.373900 -0.924815 0.070112 Eigen value 3 = 0.0 Vector : -0.926420 -0.368814 0.075638 Determinant : ( 1.000) Eigenvector #3 defines the least-squares plane Equation: -0.926420 X + -0.368814 Y + 0.075638 Z = -17.853298ATOM 859 CB TRP 109 Distance -0.063 ATOM 860 CG TRP 109 Distance 0.034 ATOM 861 CD1 TRP 109 Distance 0.028 ATOM 862 CD2 TRP 109 Distance 0.021 ATOM 863 NE1 TRP 109 Distance -0.002 ATOM 864 CE2 TRP 109 Distance -0.009 ATOM 865 CE3 TRP 109 Distance 0.027 ATOM 866 CZ2 TRP 109 Distance -0.028 ATOM 867 CZ3 TRP 109 Distance 0.010 ATOM 868 CH2 TRP 109 Distance -0.018
RMSD to plane : ( 0.029) ODL file written ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: ONo INertia_axes_odl [file] [obj] [col] [length]
file = name of ODL file (default: inertia.odl)
obj = name of graphics object in O (default: _inert)
col = colour of the plane (default: cyan)
length = determines how long the axes will be: if length > 0,
all three axes will be given this length; if length < 0,
then the three axes will be scaled by the corresponding
eigenvalues, such that the highest eigenvalue will
have an axis of length "-length"; if length = 0, then
the three axes will be 3, 2, and 1 A in length, for
the axis with the highest, intermediate, and smallest
eigenvalue, respectively. To get the axes drawn with
lengths equal to their eigenvalues, run this command
twice, and use -1 times the largest eigenvalue as the
length the second time
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > ono in q4.odl _r321 magenta 0 Nr of selected atoms : ( 22) Centre of Gravity : ( 22.065 26.283 20.209) Eigen value 1 = 515.0 Vector : 0.145303 -0.597192 0.788828 Eigen value 2 = 31.0 Vector : 0.847841 0.486099 0.211834 Eigen value 3 = 6.7 Vector : -0.509954 0.638020 0.576955 Determinant : ( 1.000) Eigenvector #3 defines the least-squares plane Equation: -0.509954 X + 0.638020 Y + 0.576955 Z = 17.176491 Creating ODL file : (q4.odl) Object name : (_r321) Axis lengths (A) : ( 3.000 2.000 1.000) ODL file written ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The ODL file may look as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! Created by MOLEMAN2 V. 020927/3.0.5 at Fri Sep 27 23:14:42 2002 for gerard begin _r321 colour magenta m 22.07 26.28 20.21 l 22.50 24.49 22.58 m 22.07 26.28 20.21 l 23.76 27.25 20.63 m 22.07 26.28 20.21 l 21.56 26.92 20.79 end_object ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: ONo ANgle_ls_planes [nr1] [nr2]
nr1 = number of the first plane (default: all planes)
nr2 = number of the second plane (default: all planes)
Least-squares planes calculated and stored with the ONo LS_plane_odl command can be compared here. This means that the angle between pairs of planes can be calculated and listed. If you don't provide any parameters to this command, all pairs will be listed.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > ono ang 4 3 Command > (ono ang 4 3)Plane # 4 [G455 ] and plane # 3 [G454 ] COS (angle) = -0.60157 -> Angle = 126.98 = 53.02 MOLEMAN2 > ono ang 1 Command > (ono ang 1)
Plane # 1 [G452 ] and plane # 2 [G453 ] COS (angle) = 0.86964 -> Angle = 29.58 = 150.42
Plane # 1 [G452 ] and plane # 3 [G454 ] COS (angle) = -0.68560 -> Angle = 133.28 = 46.72
Plane # 1 [G452 ] and plane # 4 [G455 ] COS (angle) = 0.69565 -> Angle = 45.92 = 134.08 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: DIstance PLot file
file = name of the O2D contour plot file
This command enables you to generate a plot file for O2D to contour the distances between all currently selected atoms.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > se an ch a ... MOLEMAN2 > di pl chaina_dist.plt Distance plot file : (chaina_dist.plt) Nr of selected atoms : ( 2740) ERROR --- Too many atoms selected for 2D contour plot Maximum allowed : ( 724) MOLEMAN2 > se and atom " CA " ... MOLEMAN2 > di pl caca.plt Distance plot file : (caca.plt) Nr of selected atoms : ( 362) Nr of distances : ( 131044) Average distance : ( 25.497) St. deviation : ( 9.705) Maximum distance : ( 54.998) Plot file written CPU total/user/sys : 2.5 2.3 0.1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
REMARK Distance plot
REMARK Created by MOLEMAN2 V. 960304/0.11 at Mon Mar 4 17:12:54 1996 for user gerard
REMARK Generated from PDB file hydro.pdb
REMARK Selected atoms: NON-HYDROGEN | AND CHain = A | AND ATom = CA |
REMARK
XLABEL Selected atom
YLABEL Selected atom
NLEVEL 7
LEVELS
6 7 8 9 10 11 12
COLOUR
1 1 5 5 2 6 4
XPOINT 362
YPOINT 362
XLIMIT 1 362
YLIMIT 1 362
ZVALUE *
0.0 3.8 6.6 10.3 12.7 12.7 9.6
11.6 11.9 10.1 9.4 12.2 13.2 14.3
...
9.2 5.5 3.8 0.0
END
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: DIstance DIstribution [bin_size]
bin_size = size of distance bins (default: 2.0)
This command prints a histogram of inter-atomic distances for all selected atoms. This may be useful to find a Patterson integration radius for molecular replacement calculations.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
MOLEMAN2 > se an ch a
...
MOLEMAN2 > di di 3
Nr of selected atoms : ( 2740)
Bin size : ( 3.000)
Nr of distances : ( 3752430)
lower upper # dist # cumul % dist % cumul
0.0 3.0 8119 8119 0.216 0.216
3.0 6.0 46202 54321 1.231 1.448
6.0 9.0 103187 157508 2.750 4.197
...
54.0 57.0 704 3752393 0.019 99.999
57.0 60.0 37 3752430 0.001 100.000
CPU total/user/sys : 13.3 13.3 0.1
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: DIstance LIst [lower] [upper]
lower = min distance to list (default: 0.0)
upper = max distance to list (default: 1.0)
This will list any short distances between the currently selected atoms that lie in the selected range. This can be used to find errors in coordinate files (atoms too close to one another; use an upper cut-off of 0.8 or so if hydrogens are present).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > re pdb1bp8.ent ... MOLEMAN2 > dis lis 0 0.8 Command > (dis lis 0 0.8) Nr of selected atoms : ( 664) Lower cut-off : ( 0.000) Upper cut-off : ( 0.800)Distance: 0.78 A between: ATOM 1 O5* A A 1 -3.605 0.160 -1.035 1.00 0.00 O ATOM 2 C5* A A 1 -3.981 -0.413 -1.398 1.00 0.00 C
Distance: 0.45 A between: ATOM 928 CC7 DXB C 3 -5.454 -5.084 7.980 1.00 0.00 C ATOM 952 HM71 DXB C 3 -5.313 -4.887 7.596 1.00 0.00 H ... Distance: 0.50 A between: ATOM 1110 HM52 DXB F 3 6.115 18.492 2.924 1.00 0.00 H ATOM 1111 HM53 DXB F 3 5.873 18.325 3.326 1.00 0.00 H
Nr of distances checked : ( 220116) Nr of distances listed : ( 64) Minimum distance : ( 0.140) Maximum distance : ( 0.782) Average distance : ( 0.504) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: DIstance CHains chain1 chain2 [cut-off]
cut-off = max distance to list (default: 3.5)
This will list any contacts between the two chains provided by the user.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > read pdb1fss.ent [...] MOLEMAN2 > di ch a b 3.5 Chain 1 : (A) Chain 2 : (B) Cut-off (A) : ( 3.500) Nr of atoms in chain 1 : ( 4242) Nr of atoms in chain 2 : ( 464)Contact: 3.28 A ATOM 516 CA TYR A 70 15.296 21.623 24.210 1.00 3.71 1FSS 741 ATOM 4303 O THR B 8 13.977 18.623 24.132 1.00 2.00 1FSS4528
Contact: 3.18 A ATOM 526 OH TYR A 70 9.231 22.863 22.093 1.00 3.71 1FSS 751 ATOM 4510 O VAL B 34 7.339 20.548 23.183 1.00 7.23 1FSS4735
Contact: 2.86 A ATOM 527 N VAL A 71 14.586 20.579 22.133 1.00 24.49 1FSS 752 ATOM 4303 O THR B 8 13.977 18.623 24.132 1.00 2.00 1FSS4528 [...] Contact: 2.63 A ATOM 2593 O TYR A 334 2.776 29.911 22.350 1.00 10.53 1FSS2818 ATOM 4490 N LYS B 32 2.754 28.159 24.308 1.00 22.68 1FSS4715
Contact: 3.01 A ATOM 2647 NZ LYS A 341 4.821 24.232 8.633 1.00 19.13 1FSS2872 ATOM 4706 OH TYR B 61 4.124 21.925 10.436 1.00 25.01 1FSS4931
Nr of contacts : ( 36) CPU total/user/sys : 1.9 1.9 0.0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: DIstance SHort [cut-off]
cut-off = max distance to list (default: 2.4)
This will list any short non-bonded and non-1-3 contacts between the currently selected atoms.
NOTE!!! Any pair of atoms closer than (by default) 2.0 Å will be considered to be bonded and will therefore not be listed here (even if it is a bad contact - the program does not know any better)!!! The same applies for 1-3 contacts.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > di sh 2.6 Nr of selected atoms : ( 5794) Cut-off : ( 2.600) Ditto, bonded atoms : ( 2.000)Short contact: 2.56 A ATOM 86 O GLY 95 9.825 49.353 58.166 1.00 17.71 AAAA ATOM 662 ND2 ASN 161 9.523 47.419 59.810 1.00 26.48 AAAA
Short contact: 2.60 A ATOM 522 OE2 GLU 146 6.642 27.638 53.763 1.00 18.98 AAAA ATOM 7142 CD+2 CD2 701 5.513 25.493 52.829 1.00 19.74 XXXX ... Short contact: 2.55 A ATOM 5594 OD1 ASN 307 47.820 97.543 83.813 1.00 18.24 KKKK ATOM 7175 O1 HOH 811 49.205 95.513 83.148 1.00 15.75 WWWW
Short contact: 2.03 A ATOM 6190 SG CYS 368 51.938 82.787 85.190 1.00 10.75 KKKK ATOM 6604 SG CYS 415 52.449 81.267 83.945 1.00 13.57 KKKK
Nr of distances : ( 16782321) Nr of short contacts : ( 12) CPU total/user/sys : 11.6 11.6 0.1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: DIstance SElect [cut-off] [mode]
cut-off = max distance to list (default: 2.4)
mode = ALl = list distances to all atoms (default), or
SElected = list distances to other selected atoms, or
UNselected = list distances to unselected atoms
This will list the distances of all selected atoms to other atoms, provided they are shorter than the cut-off value provided. This can be used to quickly find the atoms that coordinate a metal, or all atoms surrounding a ligand, etc.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > read 1guh.pdb [...] MOLEMAN2 > sel num and res 209 222 [...] MOLEMAN2 > sel and type prot [...] MOLEMAN2 > sel and chain a [...] MOLEMAN2 > dist sele 3.5 unse Nr of selected atoms : ( 125) Cut-off (A) : ( 3.500) Distances to UNselected atomsDistance: 3.46 A ATOM 1672 N ASP A 209 98.442 23.509 14.741 1.00 54.82 1GUH1792 ATOM 1664 N MET A 208 96.305 21.623 12.786 1.00 41.66 1GUH1784
[...]
Distance: 3.26 A ATOM 1711 CD2 LEU A 213 94.899 24.438 20.484 1.00 36.30 1GUH1831 ATOM 880 O PRO A 110 93.705 21.664 21.714 1.00 49.62 1GUH1000
Distance: 3.17 A ATOM 1728 OE1 GLU A 215 95.617 32.077 12.568 1.00 95.20 1GUH1848 ATOM 77 CD2 PHE A 10 92.708 30.825 12.354 1.00 32.44 1GUH 197
Distance: 3.49 A ATOM 1734 CB ALA A 216 92.174 29.492 16.719 1.00 24.52 1GUH1854 ATOM 80 CZ PHE A 10 91.581 28.942 13.329 1.00 32.44 1GUH 200
Distance: 3.50 A ATOM 1761 CG2 ILE A 219 89.812 36.108 14.693 1.00 30.69 1GUH1881 ATOM 281 CG2 ILE A 35 89.641 37.143 11.354 1.00 34.96 1GUH 401
Distance: 3.47 A ATOM 1769 CD1 PHE A 220 86.603 33.420 15.496 1.00 23.64 1GUH1889 ATOM 327 CD2 LEU A 41 85.790 36.770 15.095 1.00 23.21 1GUH 447
Distance: 3.44 A ATOM 1772 CE2 PHE A 220 88.307 31.663 14.246 1.00 23.64 1GUH1892 ATOM 76 CD1 PHE A 10 90.428 30.428 11.841 1.00 32.44 1GUH 196
Distance: 3.32 A ATOM 1783 NH1 ARG A 221 86.456 39.634 18.545 1.00 86.40 1GUH1903 ATOM 335 OD2 ASP A 42 86.358 42.750 17.404 1.00 66.68 1GUH 455
Distance: 2.89 A ATOM 1784 NH2 ARG A 221 86.648 41.439 19.966 1.00 86.40 1GUH1904 ATOM 335 OD2 ASP A 42 86.358 42.750 17.404 1.00 66.68 1GUH 455
Nr of distances : ( 440125) Nr listed : ( 16) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > se an res cd2 AND atom selection With atoms for which : (RES) Equals : (CD2) Selection history : (ALL | AND REsidu = CD2 |) Nr of selected atoms : ( 3) MOLEMAN2 > di se 3.0 Nr of selected atoms : ( 3) Cut-off : ( 3.000)Distance: 2.94 A ATOM 7142 CD+2 CD2 701 5.513 25.493 52.829 1.00 19.74 XXXX ATOM 520 CD GLU 146 7.727 27.400 53.189 1.00 18.44 AAAA
Distance: 2.64 A ATOM 7142 CD+2 CD2 701 5.513 25.493 52.829 1.00 19.74 XXXX ATOM 521 OE1 GLU 146 7.842 26.597 52.237 1.00 19.27 AAAA ... Distance: 2.60 A ATOM 7144 CD+2 CD2 703 17.470 55.275 21.475 1.00 36.65 XXXX ATOM 2333 NE2 HIS 340 15.878 54.722 23.452 1.00 19.18 AAAA
Nr of distances : ( 17379) Nr listed : ( 8) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > se an re i AND atom selection With atoms for which : (RE) Equals : (I) Selection history : (ALL | AND REsidu = I |) Nr of selected atoms : ( 2) MOLEMAN2 > di se 4 Nr of selected atoms : ( 2) Cut-off : ( 4.000)Distance: 3.53 A ATOM 3531 I I C 601 30.079 30.849 34.376 1.00 23.10 CCCC ATOM 822 CB ALA A 178 30.484 31.903 31.031 1.00 21.62 AAAA
Distance: 3.21 A ATOM 3531 I I C 601 30.079 30.849 34.376 1.00 23.10 CCCC ATOM 839 O ALA A 180 30.976 27.917 33.428 1.00 24.14 AAAA ... Distance: 3.95 A ATOM 7106 I I M 601 45.445 80.203 80.802 1.00 48.25 MMMM ATOM 7241 O1 HOH W 833 42.484 77.927 82.087 1.00 11.16 WWWW
Nr of distances : ( 11586) Nr listed : ( 6) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: SQuence LIst how
how = 3-letter code | 1-letter code | Full
List the sequence (note that the one-letter codes are defined in the library file).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > sq li 1Sequence in 1-letter code: ATYCGNPFVG VTPWANAYYA CEVCCLAIPC LTGAMATAAA AVAKVPCFMW LDTLDKTPLM EQTLADIRTA NKNGGNYAGQ FVVYDLPDRD CAALACNGEY CIADGGVAKY KNYIDTIRQI ... FQAYFVQLLT NANPCFL??? ?????????? ?????????? ?????????? ?????????? ?????????? ?????????? ?? ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > sq li 3Sequence in 3-letter code: ALA THR TYR SER GLY ASN PRO PHE VAL GLY VAL THR PRO TRP ALA ASN ALA TYR TYR ALA SER GLU VAL SER SER LEU ALA ILE PRO SER ... HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH HOH ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > sq li f RESIDUE ALA 86 AAAA RESIDUE THR 87 AAAA RESIDUE TYR 88 AAAA RESIDUE SER 89 AAAA ... RESIDUE HOH 850 WWWW ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: SQuence PIr file [seq_name] [title]
file = PIR output file name
seq_nam = PIR sequence name
title = any text
Write the sequence of the currently selected residues to a PIR file. A residue is considered selected if at least one of its atoms is selected.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > re 1cel.pdb MOLEMAN2 > se and type prot MOLEMAN2 > se and chain a MOLEMAN2 > sq pir q Nr of selected residues : ( 434) Total number of residues : ( 1404) QSACTLQSET HPPLTWQKCS SGGTCTQQTG SVVIDANWRW THATNSSTNC YDGNTWSSTL CPDNETCAKN CCLDGAAYAS TYGVTTSGNS LSIGFVTQSA QKNVGARLYL MASDTTYQEF TLLGNEFSFD VDVSQLPCGL NGALYFVSMD ADGGVSKYPT NTAGAKYGTG YCDSQCPRDL KFINGQANVE GWEPSSNNAN TGIGGHGSCC SEMDIWEANS ISEALTPHPC TTVGQEICEG DGCGGTYSDN RYGGTCDPDG CDWNPYRLGN TSFYGPGSSF TLDTTKKLTV VTQFETSGAI NRYYVQNGVT FQQPNAELGS YSGNELNDDY CTAEEAEFGG SSFSDKGGLT QFKKATSGGM VLVMSLWDDY YANMLWLDST YPTNETSSTP GAVRGSCSTS SGVPAQVESQ SPNAKVTFSN IKFGPIGSTG NPSG PIR file written ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! Created by MOLEMAN2 V. 970211/1.1.3 at Tue Feb 11 17:28:33 1997 for user gerard>P1;PIRSEQ No title QSACTLQSET HPPLTWQKCS SGGTCTQQTG SVVIDANWRW THATNSSTNC YDGNTWSSTL CPDNETCAKN CCLDGAAYAS TYGVTTSGNS LSIGFVTQSA QKNVGARLYL MASDTTYQEF TLLGNEFSFD VDVSQLPCGL NGALYFVSMD ADGGVSKYPT NTAGAKYGTG YCDSQCPRDL KFINGQANVE GWEPSSNNAN TGIGGHGSCC SEMDIWEANS ISEALTPHPC TTVGQEICEG DGCGGTYSDN RYGGTCDPDG CDWNPYRLGN TSFYGPGSSF TLDTTKKLTV VTQFETSGAI NRYYVQNGVT FQQPNAELGS YSGNELNDDY CTAEEAEFGG SSFSDKGGLT QFKKATSGGM VLVMSLWDDY YANMLWLDST YPTNETSSTP GAVRGSCSTS SGVPAQVESQ SPNAKVTFSN IKFGPIGSTG NPSG * ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
List possible sites for N-glycosylation in your protein(s).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > sq gl Looking for potential N-glycosylation sites Consensus: Asn - not Pro - Ser/ThrRESIDUE ASN 289 AAAA RESIDUE ALA 290 AAAA RESIDUE SER 291 AAAA
RESIDUE ASN 310 AAAA RESIDUE ILE 311 AAAA RESIDUE THR 312 AAAA
RESIDUE ASN 289 KKKK RESIDUE ALA 290 KKKK RESIDUE SER 291 KKKK
RESIDUE ASN 310 KKKK RESIDUE ILE 311 KKKK RESIDUE THR 312 KKKK Potential sites found : ( 4) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: SQuence MOtif motif
motif = sequence motif in 1-letter code ("?" can be used as a
wild-card)
Search the sequence of your molecule(s) for a certain motif. Enter the motif in one-letter code (no spaces; question marks indicate residues which may be matched to any type).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > sq mo n?t Look for sequence motif : (N?T)RESIDUE ASN 310 AAAA RESIDUE ILE 311 AAAA RESIDUE THR 312 AAAA
RESIDUE ASN 310 KKKK RESIDUE ILE 311 KKKK RESIDUE THR 312 KKKK Nr of hits : ( 2) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > sq mo dir??nk?ggn??gq Look for sequence motif : (DIR??NK?GGN??GQ)RESIDUE ASP 151 AAAA RESIDUE ILE 152 AAAA RESIDUE ARG 153 AAAA RESIDUE THR 154 AAAA ... Nr of hits : ( 2) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This command will list the number of occurrences of each residue type defined in the library among the currently selected residues.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > se and chain a AND atom selection With atoms for which : (CHAIN) Equals : (A) Selection history : (ALL | AND CHain = A |) Nr of selected atoms : ( 3518) MOLEMAN2 > sq count Nr of selected residues : ( 701) ERROR --- Residue not in library : RESIDUE IBZ A 436 1CEL51 |G| GLY = GLYCINE 27 |A| ALA = ALANINE 46 |T| THR = THREONINE 20 |C| CYS = CYSTEINE ... 13 |K| LYS = LYSINE 1 |Q| PCA = PYROGLUTAMATE 264 |?| HOH = WATER 1 |?| NAG = N-ACETYL-GLUCOSAMINE GLCNAC 2-ACETAMIDO-2-DEOXY-D-GLUCOSE 1 |?| GLC = ALPHA-D-GLUCOSE Residues not in library : ( 1) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This command guestimates the molar extinction coefficient (using the currently selected residues; if you have non-physiological NCS or aggregation make sure to select only the physiological entities).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > se and chain a ... MOLEMAN2 > sq ext Reference: Gill & Von Hippel, Anal. Biochem. 182: 319-326 (1989). e280 = (1280*TYR + 5690*TRP + 120*CYS) accuracy roughly 5%; units M-1 cm-1 Nr of selected residues : ( 701) Nr of TYR : ( 20) Nr of TRP : ( 9) Nr of CYS : ( 20) e280 (M-1 cm-1) ~ ( 7.921E+04) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
These commands can be used to generate bits of poly-Ala helix and
strand out of the blue (a.k.a., "to spink" atoms).
All new atoms will be added to any atoms you already have in memory,
so you may want to use the DELETE command prior to issuing an
AUto command.
Automatically generated strands tend to give poor planarity
messages in the PRotein MC command, even though omega is ~180
degrees. Some minor idealisation should fix that.
Since in the AUto BOnes and AUto SSe commands only two points are
used per helix or strand, the rotation aroudn its axis is
undefined. Therefore, inside O, you probably have to use
Move_zone (or RSR_rigid) in order to fit the density.
NOTE: the algorithm is much better than that used in the old MOLEMAN (the latter sometimes gave rubbish for small bits of structure !!!). Also, it no longer uses the random-number generator ;-)
Syntax: AUto SPink type nr_res
type = Alpha | Beta
nr_res = number of residues to generate
This command has been named in memory of Neil Spink who first suggested a new O command to "spink" atoms out of the blue (FEBS course in Aarhus, 1992).
A helix or strand of the requested number of residues will be generated. The first CA will be at (0,0,0). The N-th CA will be roughly at X=1.41*N for a helix, or at X=3.30*N for a strand with zero Y and Z coordinates (these formulae are only used if N > 10; if 1 < N < 11, the actual numbers are different; the program keeps them in two small tables so it can "predict" appropriate start and end coordinates).
Other atom and residue attributes are set as follows (most can be
modified afterwards, if you want):
- atom numbering will be continuous
- residue numbering: starts at 1, if there are no atoms in memory,
or at I+2, where I is the residue number of the last atom
currently in memory
- chain name will be 'Z' if there aren't any atoms, or one higher
in the alphabet than that of the last atom in memory (but never
"exceeding" 'Z' of course)
- residue type will be ALA; atom names as usual for alanines
- insert character is blank
- all Bs are set to 20.0 A2; all occupancies to 1.0
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > auto spink beta 3 Length (A) : ( 6.610) Start CA coordinates : ( 0.000 0.000 0.000) End CA coordinates : ( 6.610 0.000 0.000) Nr of residues : ( 3) Nr of new atoms : ( 15) Actual distance terminal CAs (A) : ( 6.610) Actual N-term CA : ( 0.000 0.000 0.000) Actual C-term CA : ( 6.610 0.000 0.000) RMSD (A) : ( 0.000)Total nr of residues : ( 3) Nr of amino acid residues : ( 3) Nr of nucleic acids : ( 0) Nr of waters : ( 0) Nr of metals : ( 0) Nr of inorganics : ( 0) Nr of carbohydrates : ( 0) Nr of organic compounds : ( 0) Nr of other compounds : ( 0)
Checking for missing/extra atoms ... MOLEMAN2 > au sp alpha 3 Length (A) : ( 5.540) Start CA coordinates : ( 0.000 0.000 0.000) End CA coordinates : ( 5.540 0.000 0.000) Nr of residues : ( 3) Nr of new atoms : ( 15) Actual distance terminal CAs (A) : ( 5.537) Actual N-term CA : ( 0.000 0.000 0.000) Actual C-term CA : ( 5.537 0.000 0.000) RMSD (A) : ( 0.002)
Total nr of residues : ( 6) Nr of amino acid residues : ( 6) Nr of nucleic acids : ( 0) Nr of waters : ( 0) Nr of metals : ( 0) Nr of inorganics : ( 0) Nr of carbohydrates : ( 0) Nr of organic compounds : ( 0) Nr of other compounds : ( 0)
Checking for missing/extra atoms ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
When saved, the PDB file may look as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- REMARKCreated by MOLEMAN2 V. 960414/0.18 at Mon Apr 15 01:06:26 1996 for user gerard CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 ATOM 1 N ALA Z 1 -1.214 0.817 0.081 1.00 20.00 ATOM 2 CA ALA Z 1 0.000 0.000 0.000 1.00 20.00 ATOM 3 C ALA Z 1 1.211 0.932 -0.081 1.00 20.00 ATOM 4 O ALA Z 1 1.155 1.974 -0.777 1.00 20.00 ATOM 5 CB ALA Z 1 -0.004 -0.896 -1.251 1.00 20.00 ATOM 6 N ALA Z 2 2.094 0.809 0.892 1.00 20.00 ... ATOM 15 CB ALA Z 3 6.525 -1.059 -1.126 1.00 20.00 ATOM 16 N ALA Z 5 0.389 1.419 -0.158 1.00 20.00 ... ATOM 27 CA ALA Z 7 5.537 0.000 0.000 1.00 20.00 ATOM 28 C ALA Z 7 5.285 -0.699 1.326 1.00 20.00 ATOM 29 O ALA Z 7 6.166 -1.424 1.825 1.00 20.00 ATOM 30 CB ALA Z 7 5.785 1.503 0.276 1.00 20.00 END ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: AUto BOnes type x1 y1 z1 x2 y2 z2
type = Alpha | Beta
x1..z2 = coordinates of first and last CA atom
This command can be used if you want to generate a helix or strand
between two particular points in space. Usually, these will
be coordinates read from a skeleton (bones) in O. Note the
directionality: (x1,y1,z1) specifies the N-terminus.
If you want to generate more than one helix or strand, use the
AUto SSe command instead.
Atom and residue attributes are set in the same fashion as with
the AUto Spink command (quod vide).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > aut bones alpha 46 9 112 43 13 110 Length (A) : ( 5.385) Start CA coordinates : ( 46.000 9.000 112.000) End CA coordinates : ( 43.000 13.000 110.000) Nr of residues : ( 3) Nr of new atoms : ( 15) Actual distance terminal CAs (A) : ( 5.537) Actual N-term CA : ( 46.000 9.000 112.000) Actual C-term CA : ( 42.915 13.113 109.944) RMSD (A) : ( 0.107)Total nr of residues : ( 3) Nr of amino acid residues : ( 3) Nr of nucleic acids : ( 0) Nr of waters : ( 0) Nr of metals : ( 0) Nr of inorganics : ( 0) Nr of carbohydrates : ( 0) Nr of organic compounds : ( 0) Nr of other compounds : ( 0)
Checking for missing/extra atoms ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Syntax: AUto SSe filename
filename = name of a DEJAVU SSE file
If you have delineated secondary structure elements (SSEs) in your skeleton (bones) already, for instance to search the fold database with DEJAVU, you can easily generate poly-Ala fragments corresponding to the SSEs you found. Such an SSE file (see the DEJAVU manual) looks as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! === test ! MOL test NOTE sse test file moleman2 PDB ./m1a.pdb ! ALPHA 'A1' 'A82' 'A87' 6 43.023 3.630 102.404 51.740 7.245 100.634 ALPHA 'A2' 'A89' 'A91' 3 49.811 10.893 104.060 54.432 12.827 103.655 BETA 'B1' 'A99' 'A101' 3 52.141 14.649 111.454 51.195 21.767 112.558 ALPHA 'A3' 'A103' 'A110' 8 56.050 25.675 109.872 52.074 27.789 101.676 ALPHA 'A4' 'A118' 'A127' 10 49.546 30.795 110.663 39.466 20.855 114.772 BETA 'B2' 'A135' 'A137' 3 50.470 15.703 117.437 47.613 11.238 114.386 ALPHA 'A5' 'A138' 'A141' 4 46.482 8.779 111.744 43.362 12.567 109.661 ENDMOL ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
All lines except those beginning with 'ALPHA' or 'BETA' are ignored.
Each SSE is defined by one ALPHA or BETA line. The other items on
such a line are:
- 'A1' = name of the SSE (ignored)
- 'A82' 'A87' - name of first and last residue; these are used to
derive the chain and insert name (in this case, 'A' and blank,
respectively); also, if the second residue number is *LOWER*
than the first, the program will swap the start and end coordinates
- 6 - the number of residues; if positive, this will be the actual
number of residues generated; if zero or negative, the program will
figure out the number of residues from the distance between the
start and end points itself
- 43.023 3.630 102.404 = approximate coordinates of first CA atom
- 51.740 7.245 100.634 = approximate coordinates of last CA atom
In other words: the first and last residue name define the directionality and the names of the new residues; if you don't know exactly how many residues there are, use zero or a negative number for the number of residues. Other atom and residue parameters are set in the same fashion as with the AUto SPink command (quod vide).
Executing this command with the SSE file shown above yields:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > au sse trca.sse MOLEMAN2 > au sse trca.sse > (MOL trca) > (NOTE calmodulin m1a) > (PDB ./m1a.pdb)> (ALPHA 'A1' 'A82' 'A87' 6 43.023 3.630 102.404 51.740 7.245 100.634) Length (A) : ( 9.601) Start CA coordinates : ( 43.023 3.630 102.404) End CA coordinates : ( 51.740 7.245 100.634) Nr of residues : ( 6) Nr of new atoms : ( 30) Actual distance terminal CAs (A) : ( 8.201) Actual N-term CA : ( 43.023 3.630 102.404) Actual C-term CA : ( 50.469 6.718 100.892) RMSD (A) : ( 0.990)
...
> (BETA 'B1' 'A99' 'A101' 3 52.141 14.649 111.454 51.195 21.767 112.558) Length (A) : ( 7.265) Start CA coordinates : ( 52.141 14.649 111.454) End CA coordinates : ( 51.195 21.767 112.558) Nr of residues : ( 3) Nr of new atoms : ( 15) Actual distance terminal CAs (A) : ( 6.610) Actual N-term CA : ( 52.141 14.649 111.454) Actual C-term CA : ( 51.280 21.125 112.458) RMSD (A) : ( 0.463)
...
> (ALPHA 'A5' 'A138' 'A141' 4 46.482 8.779 111.744 43.362 12.567 109.661) Length (A) : ( 5.331) Start CA coordinates : ( 46.482 8.779 111.744) End CA coordinates : ( 43.362 12.567 109.661) Nr of residues : ( 4) Nr of new atoms : ( 20) Actual distance terminal CAs (A) : ( 5.086) Actual N-term CA : ( 46.482 8.779 111.744) Actual C-term CA : ( 43.505 12.393 109.757) RMSD (A) : ( 0.173) > (ENDMOL) New atoms : ( 186)
Total nr of residues : ( 37) Nr of amino acid residues : ( 37) Nr of nucleic acids : ( 0) Nr of waters : ( 0) Nr of metals : ( 0) Nr of inorganics : ( 0) Nr of carbohydrates : ( 0) Nr of organic compounds : ( 0) Nr of other compounds : ( 0)
Checking for missing/extra atoms ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
From version 2.0 on, MOLEMAN2 can produce VRML files of your molecule (VRML = Virtual Reality Modelling Language). Rather than writing a dedicated set of routines to display molecules, use of of VRML is trivial for the programmer, and easy for the user.
Some things you may need to know:
- VRML files have the extension ".wrl"
- use your favourite browser with VRML viewer plug-in to inspect
the displays (you can launch it from inside MOLEMAN2, e.g.:
"$ netscape test.wrl &")
- colours can be defined by name or by RGB values (red-green-blue,
three numbers in the range 0-1). The VRml LIst_colours command
will list all (> 400) predefined colour names and their RGB
values
The following set of commands would produce a pretty picture of cellobiohydrolase I (PDB ID 1CEL; try it yourself !):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! read PDB file re /nfs/pdb/full/1cel.pdb ! ! reset VRML parameters vr in vr reset ! ! draw yellow CA trace for chain A sel all sel and chain a vr tr yellow ! ! draw green CA trace for chain B sel all se an cha b vr tr green ! ! draw CPK models for inhibitor, NAG, Calcium sel all vr rad 1.5 0.0 sel and res glc sel or res ibz sel or res nag sel or res " ca" vr cp ! ! all-atom stick model for the tryptophans sel all sel and res trp vr stick ! ! magenta ball-and-stick for the active site residues vr reset sel all vr rad 0.0 0.3 sel num and res 212 212 sel num or res 214 214 sel num or res 217 217 vr ball 0.2 magenta ! ! draw the unit cell vr cell purple ! ! close the file vr close ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The VRML interface was written for two purposes:
- quick inspection of a structure without the need to fire up a
separate graphics program
- creating VRML files which you can include in your web pages (in
this case, don't forget to compress the files with the "gzip"
command to reduce their size !)
You will want to use the SElect commands to tailor your VRML files (see the example above). Experiment !
Example of a VRML display (of 1PMP) generated with MOLEMAN2.
With this command you can define the following parameters:
- the central atom type for the VRml TRace option (" CA " for proteins)
- the maximum allowed distance between two subsequent central
atoms for them to be connected on the display (4.5 Å is a
reasonable cut-off for CA-CA distances in proteins)
- the background colour (default is black)
- the default colour for molecules (default is yellow)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > vr set Central atom type ? ( CA) Central atom type : ( CA) Max central atom distance ? ( 4.50) Max central atom distance : ( 4.500) Background colour ? (0.000 0.000 0.000) black Background colour : (0.000 0.000 0.000) Default colour ? (1.000 1.000 0.000) white Default colour : (1.000 1.000 1.000) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The current VRML file is not closed until you open a new VRML file, or use this command. It may be necessary to close the file so that the output buffer is flushed properly and your VRML browser can read the file.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > vr close Command > (vr close) Closed VRML file ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This command opens a new VRML file (default: same file name as before if the file name is not provided). To actually write molecules to it, use the VRml TRace etc. commands
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > vr in Open VRML file : (moleman2.wrl) Opened VRML file ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
To help you find colours, more than 400 colour names have been predefined. This command will list their names and their RGB values.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- LSQMAN > vr li Nr of colours : ( 411) # 1 (black ) = 12595212 RGB 0.000 0.000 0.000 # 2 (red ) = 12596212 RGB 1.000 0.000 0.000 # 3 (green ) = 13619212 RGB 0.000 1.000 0.000 # 4 (blue ) = 1061171212 RGB 0.000 0.000 1.000 # 5 (yellow ) = 13620212 RGB 1.000 1.000 0.000 # 6 (magenta ) = 1061172212 RGB 1.000 0.000 1.000 # 7 (cyan ) = 1062195212 RGB 0.000 1.000 1.000 # 8 (light_grey ) = 852276012 RGB 0.800 0.800 0.800 # 9 (grey ) = 537395712 RGB 0.500 0.500 0.500 # 10 (dark_grey ) = 222515412 RGB 0.200 0.200 0.200 # 11 (white ) = 1062196212 RGB 1.000 1.000 1.000 # 12 (gainsboro ) = 917351274 RGB 0.862 0.862 0.862 # 13 (honeydew ) = 1000330169 RGB 0.941 1.000 0.941 # 14 (mistyrose ) = 938355700 RGB 1.000 0.894 0.882 ... # 407 (dodgerblue2 ) = 991454330 RGB 0.110 0.525 0.933 # 408 (lightsteelblue3 ) = 855328391 RGB 0.635 0.709 0.803 # 409 (green3 ) = 13417484 RGB 0.000 0.803 0.000 # 410 (orangered4 ) = 12745261 RGB 0.545 0.146 0.000 # 411 (mediumorchid1 ) = 1061582714 RGB 0.878 0.401 1.000 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > vr re Resetting atom colours and radii ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Prior to generating a CPK model you will want to increase the standard (covalent bond) radii, e.g. by a factor of 2. Prior to generating a ball-and-stick model you will want to set them to e.g. 0.5 times their normal value, or set all radii e.g. to 0.3 Å.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > vr rad Multiply radii by ? (1.0) 0 Increase radii by ? (0.0) 0.4 Nr of radii changed : ( 7038) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Use this, e.g. to colour a whole chain green before using the VRml TRace command.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
how = REsi_nr | BFactor | OCcupancy | MAss | ELement | RAdius | ATom_nr | X | Y | Z
With this command you can colour-ramp the currently selected atoms by various atomic properties. (Note: ATom_nr is the number of each atom in the PDB file, ELement is the number of the chemical.) Hint: if an external program can put other numbers in the B-factor field of your PDB file (e.g., charge, distance from a certain point, or whatever), you can then ramp on that property by selecting BFactors here.
At present, ramping goes from blue for low values, to red for high values. Note that the ramping is carried out for all selected atoms, so if you want a colour-ramped CA trace from blue to red, you will have to deselect all your hetero-compounds, waters, etc., and then ramp on residue number.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > vr cr bfact Colour-ramping by B-factor ... Nr of atoms selected : ( 2553) Lowest value found : ( 3.430E+00) Highest value found : ( 6.726E+01) Ramping done ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Generate a trace, e.g. of the CA atoms. This is always monochrome !
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > vr tr purple VRML Trace ... Nr of central atoms written : ( 434) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Generate a fat (turd-like) trace, e.g. of the CA or P atoms. You must supply the fatness (e.g., 0.3-1.0 Å), and may specify the colour. If you don't specify a colour, the atoms will be drawn in their current individual colours.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > vr fa 0.5 purple VRML Fat trace ... Nr of central atoms written : ( 434) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
If you don't specify the colour, the current colour of each atom will be used. You have to supply the radius for all atoms.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > vr cpk 1.2 VRML CPK ... Nr of atoms written : ( 2553) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
If you don't specify the colour, the current colour of each atom will be used. The current individual atomic radii will be used.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > vr sphe VRML Sphere ... Atoms without bonds : ( 252) Terminal atoms : ( 709) Nr of atoms : ( 2553) Nr of bonds : ( 2381) CPU total/user/sys : 1.9 1.9 0.0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
If you don't specify a colour, the atoms will be drawn in their current individual colours. The current individual atomic radii will be used.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > vr ball Stick radius (A) ? (0.2) VRML Ball-and-stick ... Nr of atoms written : ( 252) Nr of bonds written : ( 270) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Supply the radius that will be used for both the spheres and the cylinders to give that yummy liquorice look. If you don't specify a colour, the atoms will be drawn in their current individual colours.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > vr ball Stick radius (A) ? (0.2) VRML Ball-and-stick ... Nr of atoms written : ( 252) Nr of bonds written : ( 270) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
A stick model consists of lines rather than cylinders, which makes for fast manipulation in your VRML browser. If you don't specify a colour, the atoms will be drawn in their current individual colours.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > vr st VRML Stick ... Nr of atoms written : ( 252) Nr of bonds written : ( 270) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
If you don't specify a colour, the atoms will be drawn in their current individual colours.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > vr st VRML Stick ... Nr of atoms written : ( 252) Nr of bonds written : ( 270) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MOLEMAN2 > vr cel purple VRML Cell : ( 84.000 86.200 111.800 90.000 90.000 90.000) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
None, at present ("peppar, peppar").
Created at Tue Aug 26 16:53:04 2008
by MAN2HTML version 070111/2.0.8 . This manual
describes MOLEMAN2, a program of the Uppsala
Software Factory (USF), written and maintained by Gerard Kleywegt. © 1992-2007.
