Program : MAPMAN
Version : 080625
Author : Gerard J. Kleywegt & T. Alwyn Jones,
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 electron-density maps
Package : RAVE
Reference(s) for this program:
* 1 * T.A. Jones & S. Thirup (1986). Using known substructures in protein model building and crystallography. EMBO J 5, 819-822. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=3709525&dopt=Citation]
* 2 * T.A. Jones (1992). A, yaap, asap, @#*? A set of averaging programs. In "Molecular Replacement", edited by E.J. Dodson, S. Gover and W. Wolf. SERC Daresbury Laboratory, Warrington, pp. 91-105.
* 3 * G.J. Kleywegt & T.A. Jones (1994). Halloween ... Masks and Bones. In "From First Map to Final Model", edited by S. Bailey, R. Hubbard and D. Waller. SERC Daresbury Laboratory, Warrington, pp. 59-66. [http://xray.bmc.uu.se/gerard/papers/halloween.html]
* 4 * G.J. Kleywegt & T.A. Jones (1996). xdlMAPMAN and xdlDATAMAN - programs for reformatting, analysis and manipulation of biomacromolecular electron-density maps and reflection data sets. Acta Cryst D52, 826-828. [http://scripts.iucr.org/cgi-bin/paper?gr0468]
* 5 * 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]
* 6 * G.J. Kleywegt & R.J. Read (1997). Not your average density. Structure 5, 1557-1569. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=9438862&dopt=Citation]
* 7 * G.J. Kleywegt & T.A. Jones (1999). Software for handling macromolecular envelopes. Acta Cryst D55, 941-944. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=10089342&dopt=Citation] [http://scripts.iucr.org/cgi-bin/paper?se0256]
* 8 * 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]
* 9 * R.J. Read & G.J. Kleywegt (2001). Density modification: theory and practice. In: "Methods in Macromolecular Crystallography" (D Turk & L Johnson, Eds.), IOS Press, Amsterdam, pp. 123-135.
* 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 * 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.
930409 - 0.5 - first production version; first manual
930410 - 0.6 - implemented HISTO, SCALE, ZERO
930413 - 0.7 - implemented UVW, SPACEGROUP
930416 - 0.8 - bug fix (reading XPLOR maps)
930420 - 0.9 - more formats supported
930510 - 1.0 - implemented EXTRACT
930513 - 1.1 - removed bugs in (NEW)EZD scale calculation
930602 - 1.3 - made smaller ESV version (only 3 maps of
approximately 3 MW each); print program
dimensioning with "?" option
930608 - 1.4 - implemented MOMENTS, $ and NORMALISE options
930615 - 2.0 - new production version; implemented ADD
930705 - 2.1 - new options MIN_MAX and CORRELATE
930803 - 2.2 - implemented PICK commands
930805 - 2.3 - implemented new READ format DSN6/BRICK,
so that you may RECONSTRUCT OLD BRICK files !
930806 - 2.4 - implemented CELL option to change cell
constants of a map (sometimes needed when
reconstructing an old BRICK file)
930825 - 2.5 - made NEW-EZD format compatible with O 5.9.1
930901 -2.5.1- removed bug from reading NEW-EZD files
930928 - 3.0 - implemented BONES and SWAPBYTES options
931001 - 3.1 - implemented BONES PRUNE (for iterative
skeletonisation)
931004 -3.1.1- sped up BONES PRUNE by a factor of ~200
931109 - 3.2 - implemented 3DMATRIX (from XPLOR) input
format to enable display of rotation and
translation functions with O and O2D
931117 - 3.3 - extended ODl command
931124 - - made paper manual; drastically shortened this one
940303 - - store spare bones randomly throughout skeleton
940323 - 3.4 - Steve Muchmore (Purdue) implemented TNT input format
940415 - 3.5 - improved O2D plot files
940525 - 3.6 - option DH produces Density Histogram
940806 - 3.7 - new output format ENVELOPE (for CCP4 masks)
950118 - 3.8 - sensitive to environment variable CCP4_OPEN
950207 -3.8.1- removed minor bug in LIst command
950216 -3.8.2- removed sign-reversal bug from NOrmalise command
(it used to *add* rather than subtract the average)
950512 - 3.9 - implemented BRix command; added PHASES and FSMASK
input formats for PHASES maps and masks, respectively
(both are *UN*tested !)
950630 -3.9.1- minor bug fixes; added 1D_projection and 2D_projection
950717 - 4.0 - implemented loads of "filters"
950719 -4.0.1- fixed bug in reading DSN6 files (should now work properly
on all machine types, little- and big-endian)
951020 - 4.1 - new command ERase, INtegrate, PAste and FRame
951102 - 4.2 - new PIck INtegrate command; fixed bug which made that
peak interpolation only worked the first time PI PE/IN
was used, but not thereafter
951113 - 4.3 - added WRite format X-PLOR (ASCII only); changed X-PLOR
reading routine to utilise X-PLOR version 4 addition of
average and sigma at end of map file
960124 -4.3.1- minor bug fix; print prod/plus and dynamic range
whenever any of them changes
960125 -4.3.2- new VAlue_at command to list density value at a certain
grid point (plus those of its neighbours)
960215 - 4.4 - try to restore lost changes (yet another disk crash ...);
recalculate & display Prod & Plus whenever the dynamic
range of the map changes; improve error message when
Prod out of bounds; new VAlue_at command (different
from the version before the disk crash); new CHange_value
command to set all map values within a certain range
to another value
960409 - 4.5 - macro mechanism (@ filename)
960411 -4.5.1- picked peaks can now be written as an AMORE rotation
function solution file
960415 -4.5.2- minor bug fixes
960517 - 4.6 - implemented simple symbol mechanism
960629 -4.6.1- changed mask output format to OMASK
960827 -4.6.2- map statistics now do get updated for the MI, CO and AD
commands
961121 - 4.7 - implemented PIck HIgh option (e.g., to pick high values
in a rotation function map, rather than just the peaks)
961125 - 5.0 - implemented dynamic memory allocation
970501 -5.0.1- MStats command to get statistics about map points
inside/outside a mask
970626 - 5.1 - support initialisation macro (setenv GKMAPMAN macrofile)
970628 - 5.2 - several minor changes; new PEek commands
970630 - 5.3 - removed "MAXREC=" from OPEN statements for DSN6 files
(this stemmed from the PDP11 days !); implemented
reading of BRIX maps; added map type "XPLOR" (easier
to type than "X-PLOR" ;-)
971120 -5.3.1- NEWEZD files shouldn't contain null characters any
longer (I hope; only happened on SGIs); the EZD format
has been renamed to OLDEZD. From now on, "the EZD" format
by default refers to the (NEW)EZD format. (NEW)EZD files
can be contoured directly in O using the fm_* commands
980113 - 5.4 - added new map output format "AMORE" which will write
*binary* maps for use with Jorge Navaza's version of
AMORE (*not* the CCP4 version as far as I know !). They
cannot be read back into MAPMAN at present, but if anyone
needs that, let me know.
980428 -5.4.1- fixed bug which caused a crash if all points in a
map have the same value
980715 -5.4.2- added option Mean to the "mode" parameter of the PEek
CUbe and PEek SPhere commands
980922 -5.4.3- removed bug so that BRIX files are now read correctly
on little-endian machines (DEC ALPHA) as well
980929 - 5.5 - new ZP_restart command to re-start the program with
different memory allocation
981008 -5.5.1- new QInvert command to do quick-and-dirty inversion of
a map (i.e., swap rho(1,1,1) and rho(NX,NY,NZ) etc.)
981021 -5.5.2- new ECho command to echo command-line input (useful
in scripts)
981022 - 5.6 - implemented command history (# command)
990129 -5.6.1- BOnes commands will print more information when allocated
storage space is exceeded
990319 -5.6.2- changed maximum number of maps allowed to 100
990503 - 5.7 - implemented the NEw commands to generate empty maps
990505 -5.7.1- new input format EM08 (KI-Stockholm-style EM maps), but
it doesn't work yet :-)
990506 -5.7.2- added OMAP as input and output format (same as DSN6);
writing a map with output format DSN6 or OMAP will now
actually do the mappage step for you, and writing a
map with output format BRIX will do just that (i.e.,
no need to use the separate MAppage and BRix commands
any longer)
990823 - 5.8 - new ROughness command to calculate the local RMS
density and assess map interpretability a la
Terwilliger and Berendzen (Acta Cryst D55, 501-505, 1999)
991203 -5.8.1- minor bug fix
000307 - 5.9 - new OPerate command to combine two maps
001107 -5.9.1- increased dimensioning of arrays used in skeletonisation
001129 -5.9.2- WHere_value command to locate specific density
values (with a certain tolerance) in your map
001130 - 6.0 - VRml commands implemented
010122 - 7.0 - use C routines to do dynamic memory allocation
and port to Linux
010227 -7.0.1- fixed mini-bug in peak picking (crashed on Alpha
and Linux; didn't do any harm on SGI)
010301 -7.0.2- minor changes to dimensioning
010403 - 7.1 - implemented input format MPI (for MPI-style EM maps)
010409 -7.1.1- minor changes
010424 -7.1.2- enable separate X/Y/Z pixel sizes with MPI format
010502 - 7.2 - SEt_value command; implemented output format TURBO
(DSN6 maps for Turbo-Frodo)
010514 -7.2.1- implemented input format AMBER (for AMBER-style
X-PLOR maps, but written by AMBER in a wrong format)
010806 - X - added some example figures to demonstrate some of
the options that produce plots
011010 -7.2.2- changed default atom name for picked peaks to " O "
(instead of " O1 "; note that the defaults can be
changed with the PIck PDb command)
011023 -7.2.3- minor changes
011025 -7.2.4- minor changes
011127 - 7.3 - implemented RS_fit command *** TO BE DOCUMENTED ***
011128 -7.3.1- continued with RS_fit command
011130 -7.3.2- implemented MF_map command *** TO BE DOCUMENTED ***;
WRite for mask now has an extra parameter, namely the
comparator (<, LT, >, GT, <=, LE, >=, or GE; default >)
to define which points should be set when writing a map
as a mask file; continued with RS_fit command
011204 -7.3.3- continued with RS_fit command
011205 -7.3.4- minor changes
011220 -7.3.5- minor changes
011221 - 7.4 - sped up RS_fit command by a factor of 5-10; documented
RS_fit command; implemented Sphere option for MF_map
command (now the default although it is a factor two
slower)
020306 -7.4.1- minor changes (renamed MF to LC command for "local
correlation maps")
020702 -7.4.2- minor changes
020715 -7.4.3- RS_fit command more robust against and informative
about errors
020730 -7.4.4- minor changes
020827 -7.4.5- RS_fit command now tries to figure out for each residue
whether it is an Amino acid, Nucleic acid, Water, or
Hetero-entity and prints this in the list file
020905 -7.4.6- minor changes
020912 -7.4.7- RS_fit command prints more statistics
020913 -7.4.8- RS_fit command prints more statistics
020913 -7.4.9- RS_fit command prints more statistics; also now handles
SCALE1/2/3 cards and if the fractionalisation matrix
calculated from the cell constants (read from the
CRYST1 card) differ from that provided on the SCALEn
cards, then all coordinates will be fractionalised
(using SCALEn) and then re-orthogonalised (using
the CRYST1 cell)
020925 - 7.5 - RS_fit command: if a negative radius is supplied, it is
assumed to be the resolution (*-1) and the radius is
calculated according to: (1) if resolution < 0.6 A then
radius = 0.7 A; (2) if resolution > 3.0 A then radius =
resolution/2 A; (3) else radius = 0.7 + (resolution-0.6)/3 A;
new parameter to determine how obs_map and cal_map are to
be scaled: Q = Quick-n-dirty (ratio of sums of absolute
densities, summed over all grid points in the maps), or
M = Masked (only sum over grid points within the envelope
of the total set of atoms; this is slower but better)
020926 -7.5.1- minor bug fix
020927 -7.5.2- minor changes
020930 -7.5.3- minor changes
021122 -7.5.4- new output format MPI (for MPI-style EM maps)
030227 - X - added information about the various formats
030328 - 7.6 - new option DRange
030704 - X - added information about the meaning of grid, origin and extent
030915 - 7.7 - new options TRanslate and GTranslate
040224 -7.7.1- minor bug fix (for Linux only)
040602 -7.7.2- minor bug fix (now several options involving two maps,
such as ADd, will also work with 2D maps)
040701 -7.7.3- changed checks of dynamic memory allocation to allow
for pointers with negative values as returned by
some recent Linux versions
040916 -7.7.4- the PEek commmand now also lists the results to the
screen (stdout) and warns when atoms lie outside the
limits of the map
041015 - 7.8 - fixed several horrible bugs in the PAste command (thanks to
Jeff Bolin; I hope he was the first ever to use this
command ...);
these bugs also brought to light errors in the subroutine
calls used by the VAlues and the INtegrate command, both
of which were fixed
050302 -7.8.1- minute change
061124 -7.8.2- fixed bug in writing ASCII CNS maps (last line should
contain 0 and 1 instead of the actual average and
st. dev. of the density, since the maps are not scaled)
070913 -7.8.3- adjusted for PDB changes in nucleotide nomenclature
071204 -7.8.4- RS_fit stats file now also includes occupancy-weighted
centre-of-gravity coordinates for every residue/entity
080625 -7.8.5- suppress error messages if more than 10 of them
From version 5.1 on, MAPMAN 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 GKMAPMAN to point to a MAPMAN macro file, e.g.:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- setenv GKMAPMAN /home/gerard/mapman.init ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
From version 5.0 onward, MAPMAN allocates memory for maps dynamically. This means that you can increase the size and number of maps that the program can handle on the fly:
1 - through the environment variables MAPSIZE and NUMMAPS (must be in capital letters !), for example put the following in your .cshrc file:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- setenv MAPSIZE 8000000 setenv NUMMAPS 3 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
2 - by using command-line arguments MAPSIZE and NUMMAPS (need not be in capitals), for example:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- run mapman mapsize 20000000 nummaps 1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Note that command-line arguments take precedence over environment variables. So you can set the environment variables in your .cshrc file to "typical" values, and if you have to deal with a map which is bigger than that, you can use the command-line argument(s).
From version 5.5 on, you can also use ZP_restart from within the program itself to increase memory allocation. WARNING : all memory is reset, so any unsaved data will be lost !!!
If sufficient memory cannot be allocated, the program will print a message and quit. In that case, increase the amount of virtual memory (this will not help, of course, if you try to allocate more memory than can be addressed by your machine (for 32-bit machines, something 2**32-1 bytes, I think), or reduce the size requirements.
MAPMAN needs space for NUMMAPS + 1 maps.
MAPMAN is a program for manipulation of electron-density files. Its applications comprise:
1 - map exchange among different machines through intermediate
EZD files
2 - conversion of maps produced by different programs
3 - producing DSN6-files for "O"/FRODO (a la MAPPAGE or BRIX)
4 - simple mathematics on maps
5 - combination of different maps
6 - peak picking
7 - creating BONES skeletons
8 - swap bytes on VAX maps
MAPMAN allows you to work with several maps simultaneously ! The wild-card character "*" can be used for most single-map options if you want to carry out an operation for all maps in memory.
When you read a map, you give it a name by which you can refer to it later. All names are converted to uppercase, so "m1" and "M1" are the same maps ! MAPMAN checks that you don't use duplicate map names.
MAPMAN is command-driven; the first TWO letters of each command are unique (so you don't have to type the rest); the commands are automatically converted to uppercase, so no worries there either.
Parameters to commands may be supplied on the same line as the command itself. MAPMAN will prompt you for the values of any parameters that were not supplied in this way.
MAPMAN runs in interactive mode by default. This means that if
(a) a file can not be opened, MAPMAN will ask you what to do
(b) if you delete a map which has unsaved changes, MAPMAN will
ask you if you're absolutely sure
(c) if you quit and there are maps with unsaved changes, MAPMAN
will ask you if you really want to quit
You may run MAPMAN in batch mode by supplying the command line option -b (or -batch). In that case, MAPMAN will crash if she can't open a file and any unsaved changes (with QUIT or DELETE) are lost forever. You may want to use this mode if you run MAPMAN in batch (using an input script).
NOTE: all output files are opened as "UNKNOWN", which means that any existing files will be overwritten !
Grid, origin, extent - what do all these numbers mean ? A brief explanation:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Fm> Grid ................. 224 104 120 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
A map is simply a three-dimensional array. Grid is the number of divisions along the axes of one entire unit cell. So, in this case, the a ("x") direction has 224 divisions (from 0 to 223), b ("y") has 104, and c ("z") has 120. These divisions are typically chosen automatically by the program that calculates the map, and usually such as to get a grid spacing equal to a fraction f times the resolution (f is usually 1/4 or 1/3). The grid spacing you can calculate by dividing a cell axis length by its grid size. E.g., for the a axis, it would be 40.81 A (see below) / 224 which is ~0.18 A. Since the resolution is 0.54 A it means that the grid spacing is ~1/3 of the resolution.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Fm> Origin ............... -30 -13 -50 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This is the point in space where the map begins, i.e. the smallest a, b and c values. If your map would have contained a complete unit cell, these three numbers would all have been zero. In this case they aren't because the map has been carved out such that it covers the molecule.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Fm> Extent ............... 175 142 165 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The extent is the number of grid points that the map contains in all three directions. You can calculate how many points are in the map by multiplying these three numbers. Note that the end point of the map is equal to (extent + origin - 1) for all directions. For instance, the end point in the c direction here is: 165 + (-50) - 1 = 114.
You can now calculate the fractional coordinates of any point in the map as follows: fract = (point + origin - 1) / grid. For instance, grid point number 66 along b would be: 66 + -13 - 1 / 104 = 0.500.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Fm> Fast, medium, slow.... X Y Z ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This is a technical detail - don't worry about it.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Fm> Cell axes ............ 40.81 18.50 22.36 Fm> Cell angles .......... 90.00 90.46 90.00 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The cell constants (needed to convert fractional to cartesian and vice versa).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Fm> Prod ................. 48.46 Fm> Plus ................. 70 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Technical details (see elsewhere in the MAPMAN manual if you really want to know more).
At present, the following map formats are supported:
Input formats : ( PROTEIN FFT-Y TENEYCK2 CCP4 X-PLOR OLDEZD MASK NEWEZD BINXPLOR BRICK DSN6 3DMATRIX TNT PHASES FSMASK BRIX XPLOR CNS EZD EM08 OMAP MPI AMBER)
Output formats : ( CCP4 OLDEZD MASK NEWEZD ENVELOPE X-PLOR DSN6 BRIX XPLOR CNS EZD AMORE OMAP TURBO MPI)
Some more information about these formats (note that several are "legacy formats" and quite a few are untested):
- 3DMATRIX (ASCII; input only) - this is a file that contains a 3D matrix of numbers and is produced by X-PLOR. It is typically used to store the results of rotation and translation functions. As a user, you need to supply the extent of the grid (the number of points along the three axes) since this cannot be deduced from the file contents. Similarly, you have to provide (real or dummy) cell constants.
- AMBER (ASCII; input only) - AMBER's interpretation of the ASCII X-PLOR format (almost, but not quite, the same). Untested.
- AMORE (BINARY; output only) - AMORE-style binary map. Untested.
- BINXPLOR (BINARY; input only) - binary X-PLOR format (not recommended)
- BRICK (BINARY; input only) - treated as DSN6
- BRIX (BINARY; input and output) - similar to DSN6, but has a human-readable first record that contains the cell constants etc.
- CCP4 (ASCII or BINARY; input and output) - the CCP4 format. Input maps may be ASCCI, but output maps are always BINARY.
- CNS (ASCII; input and output) - CNS (and X-PLOR) maps (the difference being that CNS maps contain an extra line at the bottom with the average and standard deviation of the electron density values in the map)
- DSN6 (BINARY; input and output) - the famous O format (and previously Frodo) as produced by MAPMAN and loads of old MAPPAGE and BRICK-ing programs
- EM08 (BINARY; input only) - for electron microscopy maps ("KI Stockholm" format). The user needs to provide the number of points along the three axes and the pixel size. Not sure if this actually works.
- ENVELOPE (BINARY; output only) - CCP4 masks. DOES NOT WORK PROPERLY !
- EZD (ASCII; input and output) - treated as NEWEZD
- FFT-Y (BINARY; input only) - annotated in the code as "Ten Eyck style maps". The user needs to supply cell constants, grid size, etc. Not sure if this works and , if so, with what programs.
- FSMASK (BINARY; input only) - PHASES mask format. Untested.
- MASK (ASCII; input and output) - MAMA/O style mask (envelope) format (see the MAMA manual). On output, masks are written in compressed O format. On input, all varieties are handled automatically (NEW, OMASK, OEXPLICIT, COMPRESSED, and Alwyn's old format).
- MPI (BINARY; output only) - for electron microscopy maps ("MPI" format). The user needs to supply the pixel sizes in all three directions. Only the 4 byte per pixel variant is supported. Not sure if this actually works.
- NEWEZD (ASCII; input and output) - the New E-Z Density format (read by O and sometimes produced by VOIDOO, CNS, and SOLVE)
- OLDEZD (ASCII; input and output) - an older version of the E-Z Density format
- OMAP (input and output) - treated as DSN6
- PHASES (BINARY; input only) - PHASES map format. Untested.
- PROTEIN (BINARY; input only) - Steigemann's PROTEIN map format. Untested.
- TENEYCK2 (BINARY; input only) - see FFT-Y (small difference in the file header)
- TNT (BINARY; input only) - TNT map format. The user needs to supply cell constants etc. Untested.
- TURBO (BINARY; output only) - Turbo-Frodo variant of the DSN6 format.
- XPLOR (ASCII; input and output) - treated as CNS
- X-PLOR (ASCII; input and output) - treated as CNS
NOTE: only binary XPLOR files produced by 32-bit versions of the program can be read !
NOTE: if you write a map as a mask file (format MASK or ENVELOPE) you must provide a cut-off to decide between solvent and protein density; the output file will contain zeros and ones.
NOTE: this program is sensitive to the environment variable CCP4_OPEN. If this variable has *not* been set, you will not be able to create any CCP4 maps. If this happens, the program will print a warning message. To fix this, put the following line in your .login or .cshrc file: setenv CCP4_OPEN UNKNOWN
NOTE: FORTRAN code for writing MASK and EZD files is available from the O ftp-server (directory pub/gerard/extras/fortran).
Some examples that may help you recognise ASCII map formats:
OLDEZD:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
0 0 0
72 72 72
72 72 432
74.373 74.373 432.373 90.000 90.000 120.000
MAP (13f6.1) 2.188054E+02
-495.4 -89.3 138.1 0.0-251.8-349.2-300.5-316.8-373.6-227.4 81.2 219.3 97.5
32.5 186.8 292.4 194.9 8.1 -89.3 -8.1 219.3 357.4 219.3 -16.2 -56.9 24.4
16.2 -48.7 -89.3-186.8-308.6-259.9 -32.5 138.1 138.1 48.7-105.6-219.3 -56.9
[...]
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
NEWEZD and EZD:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EZD_MAP ! Created by MAPMAN V. 021122/7.5.4 at Thu Feb 27 18:08:44 2003 for gerard CELL 74.373 74.373 432.373 90.000 90.000 120.000 ORIGIN 0 0 0 EXTENT 72 72 72 GRID 72 72 432 SCALE 2.18805374E+02 MAP -495.4 -89.3 138.1 0.0 -251.8 -349.2 -300.5 -316.8 -373.6 -227.4 81.2 219.3 97.5 32.5 186.8 292.4 194.9 8.1 -89.3 -8.1 219.3 [...] ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
MASK (the OMASK variety):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- .MASK_INPUT ! Created by MAPMAN V. 021122/7.5.4 at Thu Feb 27 18:09:41 2003 for gerard ORIGIN 0 0 0 EXTENT 72 72 72 GRID 72 72 432 CELL 74.3733 74.3733 432.3733 90.0000 90.0000 120.0000 COMPRESSED 3 3 11 18 21 23 26 27 [...] ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
CNS, X-PLOR and XPLOR:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----2 REMARKS FILENAME="q.q" REMARKS Created by MAPMAN V. 021122/7.5.4 at Thu Feb 27 18:10:56 2003 for gerard 72 0 71 72 0 71 432 0 71 7.43733E+01 7.43733E+01 4.32373E+02 9.00000E+01 9.00000E+01 1.20000E+02 ZYX 0 -2.26429E+00-4.08315E-01 6.31032E-01 0.00000E+00-1.15071E+00-1.59614E+00 -1.37342E+00-1.44766E+00-1.70750E+00-1.03935E+00 3.71195E-01 1.00223E+00 4.45434E-01 1.48478E-01 8.53749E-01 1.33630E+00 8.90869E-01 3.71195E-02 [...] ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
BINARY map files are usually more difficult to recognise, but sometimes the following Unix command may provide a clue: od -c yourmapfilename | more The command's output for a BRIX file will always start with a line that looks like this (note the string ":-) Origin") :
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- 0000000 : - ) O r i g i n 0 [...] ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
A CCP4 map may contain a line like this (note the string "MAP "):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- [...] 0000320 M A P 021 021 \0 \0 = ] G 217 \0 \0 \0 001 [...] ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
If nothing works, just try reading the map into MAPMAN with different formats until one of them (if any) gives reasonable results.
MAPMAN welcomes you with the current array dimensions and a list of supported formats for input and output files. It then gives you a list of all available commands:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- *** MAPMAN *** MAPMAN *** MAPMAN *** MAPMAN *** MAPMAN *** MAPMAN ***Version - 001130/6.0 (C) 1992-2000 Gerard J. Kleywegt & T. Alwyn Jones, BMC, Uppsala (S) User I/O - routines courtesy of Rolf Boelens, Univ. of Utrecht (NL) Others - T.A. Jones, G. Bricogne, Rams, W.A. Hendrickson Others - W. Kabsch, CCP4, PROTEIN, E. Dodson, etc. etc.
Started - Thu Nov 30 21:53:38 2000 User - gerard Mode - interactive Host - sarek ProcID - 16172 Tty - /dev/ttyq13
*** MAPMAN *** MAPMAN *** MAPMAN *** MAPMAN *** MAPMAN *** MAPMAN ***
Reference(s) for this program:
* 1 * T.A. Jones & S. Thirup (1986). Using known substructures in protein model building and crystallography. EMBO J 5, 819-822. [http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=3709525&form=6&db=m&Dopt=r]
* 2 * T.A. Jones (1992). A, yaap, asap, @#*? A set of averaging programs. In "Molecular Replacement", edited by E.J. Dodson, S. Gover and W. Wolf. SERC Daresbury Laboratory, Warrington, pp. 91-105.
* 3 * G.J. Kleywegt & T.A. Jones (1994). Halloween ... Masks and Bones. In "From First Map to Final Model", edited by S. Bailey, R. Hubbard and D. Waller. SERC Daresbury Laboratory, Warrington, pp. 59-66. [http://xray.bmc.uu.se/gerard/papers/halloween.html]
* 4 * G.J. Kleywegt & T.A. Jones (1996). xdlMAPMAN and xdlDATAMAN - programs for reformatting, analysis and manipulation of biomacromolecular electron-density maps and reflection data sets. Acta Cryst D52, 826-828. [http://www.iucr.ac.uk/journals/acta/tocs/actad/1996/actad5204.html]
* 5 * 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]
* 6 * G.J. Kleywegt & R.J. Read (1997). Not your average density. Structure 5, 1557-1569. [http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=9438862&form=6&db=m&Dopt=r]
* 7 * G.J. Kleywegt & T.A. Jones (1999). Software for handling macromolecular envelopes. Acta Cryst D55, 941-944. [http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=10089342&form=6&db=m&Dopt=b] [http://journals.iucr.org/d/issues/1999/04/00/se0256]
* 8 * G.J. Kleywegt (1999). Experimental assessment of differences between related protein crystal structures. Acta Cryst. D55, 1878-1857. [http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=10531486&form=6&db=m&Dopt=b] [http://journals.iucr.org/d/issues/1999/11/00/se0283]
* 9 * G.J. Kleywegt & T.A. Jones (2027 ?). Convenient single and multiple crystal real-space averaging. To be published ???
* 10 * G.J. Kleywegt, J.Y. Zou, M. Kjeldgaard & T.A. Jones (2000). Chapter 17.1. Around O. Int. Tables for Crystallography, Vol. F. (In press.)
==> For manuals and up-to-date references, visit: ==> http://xray.bmc.uu.se/usf ==> For downloading up-to-date versions, visit: ==> ftp://xray.bmc.uu.se/pub/gerard
*** MAPMAN *** MAPMAN *** MAPMAN *** MAPMAN *** MAPMAN *** MAPMAN ***
Allocate maps of size : ( 5000000) Max number of maps : ( 3)
Max nr of maps in memory : 3 Max nr of points in map : 5000000 Max nr of picked peaks : 65536 Max size of density buffer : 1048576 Max nr of BONES points : 500000 Max nr of BONES branches : 500000 Max nr of BONES connections : 1000000 Record length for DSN6/BRIX : 128
Input formats : ( PROTEIN FFT-Y TENEYCK2 CCP4 X-PLOR OLDEZD MASK NEWEZD BINXPLOR BRICK DSN6 3DMATRIX TNT PHASES FSMASK BRIX XPLOR CNS EZD EM08 OMAP)
Output formats : ( CCP4 OLDEZD MASK NEWEZD ENVELOPE X-PLOR DSN6 BRIX XPLOR CNS EZD AMORE OMAP)
Initialising : (XVRML - 990924/0.7) Nr of predefined colours : ( 411)
Symbol START_TIME : (Thu Nov 30 21:53:39 2000) Symbol USERNAME : (gerard)
MAPMAN's options :
? (list options) ! (comment) QUit $ shell_command & symbol value & ? (list symbols) @ macro_file ZP_restart mapsize nummaps ECho on_off # parameter(s) (command history)
REad map file fmt WRite map file fmt [cutoff] DElete map LIst [map] HIsto map x1 x2 x3 [...] EXtract map file type plane MOments map DH map plot_file nr_bins 1D_proj map file type 2D_proj map file type first last
MAppage map file BRix map file SWapbytes brick_file
NEw ? (list defaults) NEw ORigin o1 o2 o3 NEw CEll a b c al be ga NEw EXtent e1 e2 e3 NEw GRid g1 g2 g3 NEw SAme oldmap NEw ENcompass oldmap NEw MAke mapname
UVw map u v w SPacegroup map ispcgr LAbel map text CEll map a b c al be ga PRod_plus map prod plus RAnge map low high MUltiply map factor DIvide map factor PLus map value ODl map odl_file type mode SCale map low high ZEro map low high NOrmalise map ERase map e1 .. e6 INtegrate map e1 .. e6 FRame map type e1 e2 e3 VAlue_at map e1 .. e6 CHange_value map lo hi new WHere_value map value toler
SImilarity map1 map2 DUplicate map oldmap ADd map map_to_add MIn_max map1 map2 OPerate map oper map2 COrrelate map1 map2 MStats map mask_map cutoff QInvert map oldmap PAste map1 e1 .. e6 map2 e1 e2 e3 ROughness map oldmap npos nneg box plot_file nr_bins
BOnes SKel map base step nr_spares BOnes COnnect file id mc BOnes ? BOnes PRune file mc bfac
PIck PDb res atom first PIck LImits e1 .. e6 PIck LEvel threshold PIck ? PIck PEaks map file format PIck INtegrate map file format PIck HIgh map file format
PEek VAlue map pdb_in pdb_out mode PEek CUbe map pdb_in pdb_out mode nr_points PEek SPhere map pdb_in pdb_out mode radius
FIlter ? FIlter EDge map a b FIlter MEdian map size FIlter AVerage map size FIlter MInimum map size FIlter MAximum map size FIlter SMooth map FIlter SIgnal/noise map size FIlter GRadient map FIlter LAplace map FIlter KHighest map size k FIlter KLowest map size k FIlter VAr_thr map size a b FIlter STat_diff map size a b c
VRml SEtup central_atom max_dist backgr_col default_col VRml INit [filename] VRml COlour_list VRml TRace pdb_file [colour] VRml BOx map [colour] [line_solid] VRml CEll map [colour] [line_solid] [x_offset] [y_offset] [z_offset] VRml DOts map low high [colour] VRml DRaw map level [colour] VRml CLose_file
Max nr of maps in memory : 3 Max nr of points in map : 5000000 Max nr of picked peaks : 65536 Max size of density buffer : 1048576 Max nr of BONES points : 500000 Max nr of BONES branches : 500000 Max nr of BONES connections : 1000000 Record length for DSN6/BRIX : 128
Execute initialisation macro : (/home/gerard/mapman.init) ... Opened macro file : (/home/gerard/mapman.init) ... On unit : ( 61) Command > (! MAPMAN initialisation macro) Command > (echo on) 1 @ /home/gerard/mapman.init 2 ! MAPMAN initialisation macro 3 echo on ... End of macro file ... Control returned to terminal MAPMAN > ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
A very frequently-asked question is the following:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- I'm getting this error with MAPMAN converting XPLOR maps to O for the first time:ERROR --- PROD > 327.66; reset prod/plus yourself ! Or multiply your map with 10 or 100 or ... This error ONLY affects the MAppage command, not the BRix command ! ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The value of PROD and PLUS are used to scale the density values to integer values between 0 and 255 (which are subsequently stored in the DSN6 file): PROD = 255.0 / dynamic_range_of_map .
In the DSN6 format, there are only two bytes available to store the value of 100*PROD, so PROD can only lie between -327 and +327 (roughly).
If your map has a very small dynamic range, the required value of PROD may well be bigger than this, but that means it cannot be stored.
Easiest fix: use the NOrmalise command in MAPMAN; this will give your map an average of 0 and a sigma of 1; then MUltiply the map by 10 (which gives you a sigma of 10); then MAppage your map (and remember to contour at a level of 10).
How does using the PROD/PLUS command help in fixing this problem ? It doesn't ! E.g., forcing PROD to be 327 applies a "ceiling" function to your density !!!
NOTE: BRIX files do not suffer from this problem; only "DSN6" (old-fashioned "mappage") files.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > $ xterm & MAPMAN > $ ls -FartCos m1*E 3435 -r--r--r-- 1 gerard 1758288 Jun 2 23:54 m1_start.E 1634 -rw-r--r-- 1 gerard 836224 Jun 8 13:46 m1_startx.E ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Example of a MAPMAN macro:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! mappage10.mapmac ! ! read a map, set sigma level to 10.0, mappage for O ! ! enter map file name, then map type read m1 ! ! normalise map to get sigma level at 1.0 norm m1 ! ! multiply by 10 to get sigma level at 10.0 multiply m1 10 ! ! enter O map file name mappage m1 ! ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
When executed, this gives:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > @mappage10.mapmac ... Opened macro file : (mappage10.mapmac) ... On unit : ( 61) > (!) > (! enter map file name, then type) > (read m1) File name ? (not_defined) /nfs/scr_uu1/gerard/scratch/all4_amore.map Format ? (CCP4) Read header ... CPU total/user/sys : 3.3 1.9 1.4 > (!) > (! normalise map) > (norm m1) Normalise : (M1) Subtract average : ( 2.566E-07) Divide by sigma : ( 1.407E+00) ... CPU total/user/sys : 3.9 3.9 0.0 > (!) > (! multiply by 10 to get sigma level at 10.0) > (multiply m1 10) Multiply : (M1) ... CPU total/user/sys : 1.9 1.9 0.0 > (!) > (! enter O map file name) > (mappage m1) Brick file ? (10) /nfs/scr_uu1/gerard/scratch/q.E Opening DSN6 file : (/nfs/scr_uu1/gerard/scratch/q.E) Little-endian machine; will swap bytes Scale constant for cell : ( 80) Pages along X, Y and Z : ( 21 21 38) Nr of records written : ( 16759) CPU total/user/sys : 8.0 6.3 1.7 > (!) ... End of macro file ... Control returned to terminal ----- 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 ----- MAPMAN > & ? Nr of defined symbols : ( 4) Symbol PROGRAM : (MAPMAN) Symbol VERSION : (960517/4.6) Symbol START_TIME : (Fri May 17 20:26:49 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
NOTE: binary XPLOR maps can only be read if they were created by an XPLOR version which uses 32 bits for reals and integers !!!
NOTE: you may also read old mappaged files (BRICK or
DSN6 files) ! This enables you to convert ancient
VAX PROTEIN maps into UNIX CCP4 format:
- create or read from tape your old PROTEIN map
- run AMAPPAGE on your VAX
- FTP (binary) the DSN6 file to your UNIX box
- run MAPMAN and do: SWapbytes old.map
- REad M1 old.map dsn6
- WRite M1 new.E ccp4
NOTE: from version 5.3, BRIX maps can also be read back into MAPMAN
If you have saved the full range of electron density
values when you mappaged the file, you should be able
to get correlation coefficients of ~0.998 between the
original map and the new CCP4 map !
Note that the spacegroup is set to P1 by default.
Note that the program knows if it should do a swap-bytes
on the header record of the brick file, so you can read
BRICK files made on any type of machine into MAPMAN
running on any type of machine.
Sometimes the cell constants are slightly altered when
moving from VAX to UNIX (round-off error plus intermediate
conversion to integers); in such cases, use the CELL
command to get them right again.
From version 4.3 onwards, X-PLOR version 4 maps are recognised by the fact that they have the original average and sigma density stored at the end of the map. If these values are found, the map will be changed such that the original density values are restored (in e-/A3).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
MAPMAN > re m1 x ?
Supported formats : ( PROTEIN FFT-Y TENEYCK2 CCP4 X-PLOR EZD MASK NEWEZD
BINXPLOR BRICK DSN6 3DMATRIX TNT)
MAPMAN > re m1 p21_start.E ccp4
Read header
Filename : (p21_start.E)
...
Fourier parameters as read from the data-set
Origin ................................ 0 0 0
Extent ................................ 70 48 88
Grid .................................. 70 48 88
uvw (fast, medium, slow) .............. Z X Y
Header done
Map read into memory
CPU total/user/sys : 2.2 1.6 0.5
MAPMAN > re m2 map.tnt tnt
Read header
Input map : (map.tnt)
Title : (*Density map produced by RFACTOR)
Title : (*Density map calculated by inverting coefficients.)
Title : (*Coefficients were of type 2FO-FC)
Title : ( Map file PUNCHed on 11-Mar-94 11:54:15.)
Fast, medium, slow axes ? ( 1 2 3)
Number of sections ? ( 10) 170
Unit cell constants ? ( 100.000 100.000 100.000 90.000 90.000
90.000) 109.900 138.800 79.900 90.000 116.500 90.000
Parameters as read from the map file
Origin ...................... -39 0 -62
Extent ...................... 232 167 170
Grid ........................ 160 200 120
Cell axes ................... 109.90 138.80 79.90
Cell angles ................. 90.00 116.50 90.00
UVW (fast, medium, slow) .... X Y Z
Header done
Not in core
Reading levels ...
Level number : ( 10)
Level number : ( 20)
...
Level number : ( 160)
Level number : ( 170)
Sum of density in map : ( 9.406E+05)
Map read into memory
Closing TNT map on unit : ( 1)
CPU total/user/sys : 32.0 29.4 2.6
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > re m4 q.xplor x-plor Read header Input map : (q.xplor) Title : (REMARKS FILENAME="q.xplor") Title : (REMARKS Created by MAPMAN V. 951113/4.3 at Mon Nov 13 19:50:32 1995 for user ger) ... Header done Not in core Reading levels ... Level number : ( 10) Level number : ( 20) Level number : ( 30) Level number : ( 40) Level number : ( 50) Level number : ( 60) This is an X-PLOR version 4 map ! Average density : ( 1.411E-04) Sigma level : ( 6.193E+00) Restoring original density values (e-/A3) Sum of density in map : ( 1.689E+02) Map read into memory Closing XPLOR map on unit : ( 1) CPU total/user/sys : 2.3 2.2 0.1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > re m1 ../test/trimer1.em ? Supported formats : ( PROTEIN FFT-Y TENEYCK2 CCP4 X-PLOR OLDEZD MASK NEWEZD BINXPLOR BRICK DSN6 3DMATRIX TNT PHASES FSMASK BRIX XPLOR CNS EZD EM08 OMAP MPI) MAPMAN > re m1 ../test/trimer1.em mpi Opening MPI map : (../test/trimer1.em) Reading header ... # X/Y/Z : ( 32 32 61) Comment : ($) EM data : ( 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00) Bytes per pixel : ( 4) Pixel size (A) ? ( 7.580) Cell axes (A) : ( 758.000 758.000 758.000) Cell angles (d) : ( 90.000 90.000 90.000) Grid axes (pts) : ( 100 100 100) Origin (pts) : ( 0 0 0) Extent (pts) : ( 32 32 61) Points in map : ( 62464) Reading data ... File read OK Spacegroup set to P1 Map read into memory - calculating statistics Sum of density in map : ( 4.206E+01) Requested dynamic range : -1.1687E+00 1.4186E+00 Value of Prod and Plus : 9.8558E+01 115 Actual dynamic range : -1.1668E+00 1.4205E+00 MAPMAN > li m1 Nr of maps in memory : ( 1)Map 1 = M1 File = ../test/trimer1.em Grid = 100 100 100 Origin = 0 0 0 Extent = 32 32 61 Cell = 758.000 758.000 758.000 90.000 90.000 90.000 UVW = 2 1 3 Spcgrp = 1 Nr of points = 62464 Density min = -1.169E+00 Max = 1.419E+00 Average = 6.733E-04 Sigma = 2.376E-01 Variance = 5.644E-02 Mappage Prod= 9.856E+01 Plus = 115 Dyn. range = -1.167E+00 To = 1.420E+00 Cell vol. = 4.355E+08 Voxel vol. = 4.355E+02 Grid vol. = 2.720E+07 %Cell vol. = 6.25 Origin frac = 0.00000 0.00000 0.00000 Origin Cart = 0.000 0.000 0.000 Top frac = 0.31000 0.31000 0.60000 Top Cart = 234.980 234.980 454.800 Spacing = 7.580 7.580 7.580 Top = 31 31 60 Changes = F Label = Read from ../test/trimer1.em ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
From version 4.3 onwards, ASCII X-PLOR maps can also be written (in the format of X-PLOR version 4).
From version 7.3.2 - when writing a map as a mask there is a new comparator parameter (<, LT, >, GT, <=, LE, >=, or GE; default >) to determine which points should be set
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > wr m3 x ? Supported formats : ( CCP4 OLDEZD MASK NEWEZD ENVELOPE X-PLOR DSN6 BRIX XPLOR CNS EZD AMORE OMAP TURBO) MAPMAN > wr m3 rscc8.mask mask 0.8 <= Writing MASK ... Set mask points if map value <= 8.0000E-01 Nr of mask points set : ( 725474) Writing mask (compressed O format) Grid points : ( 1191330) Stretches : ( 33993) Mask points : ( 725474) Mask write OK CPU total/user/sys : 1.7 1.7 0.0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > map m1 p21_start.map Opening DSN6 file : (p21_start.map) Big-endian machine; will NOT swap bytes Pages along X, Y and Z : ( 9 6 11) Nr of records written : ( 649) CPU total/user/sys : 3.8 3.3 0.4 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > br m1 m1_1.brix Opening DSN6 file : (m1_1.brix) Little-endian machine; will swap bytes Pages along X, Y and Z : ( 11 11 10) Nr of records written : ( 1211) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > range m1 -50 100 Range : (M1) Requested dynamic range : -5.0000E+01 1.0000E+02 Value of Prod and Plus : 1.7000E+00 85 Actual dynamic range : -5.0000E+01 1.0000E+02 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > drange m1 -50 100 Cap dynamic range for map : (M1) ... Lower before : ( -6.323E+01) ... Upper before : ( 8.682E+01) Requested dynamic range : -5.0000E+01 8.6821E+01 Value of Prod and Plus : 1.8637E+00 93 Actual dynamic range : -4.9899E+01 8.6922E+01 ... Lower after : ( -4.990E+01) ... Upper after : ( 8.692E+01) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Note that indices are assumed to start at zero (i.e., index value of zero corresponds to a value of zero for the fractional coordinate).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > fr Which map ? (M1) Input Indices/Fractional/Cartesian (I/F/C) ? (I) Value for X ? (0.0000000E+00) 20 Value for Y ? (0.0000000E+00) 40 Value for Z ? (0.0000000E+00) 77 Indices : ( 20 40 77) Fractional : ( 0.333 0.417 0.642) Cartesian : ( 3.017 31.292 57.333) Point lies inside the map ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > fr m1 fr 0.333 0.417 0.642 Fractional : ( 0.333 0.417 0.642) Indices : ( 20 40 77) Cartesian : ( 2.994 31.317 57.363) Point lies inside the map ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > fr m1 cart 3.017 31.292 57.333 Cartesian : ( 3.017 31.292 57.333) Fractional : ( 0.333 0.417 0.642) Indices : ( 20 40 77) Point lies inside the map ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > in m1 10 50 20 60 30 70 Limits : ( 10 50 20 60 30 70) Integrate : (M1) Nr of points summed : ( 68921) Sum of density : ( 1.105E+02) Sum of | density | : ( 5.356E+04) Average zeroed density : ( 1.603E-03) Average | zeroed dens | : ( 7.771E-01) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > er m1 10 50 20 60 30 70 Limits : ( 10 50 20 60 30 70) Erase : (M1) Nr of points set to zero : ( 68921) Sum of zeroed density : ( 1.105E+02) Sum of | zeroed dens | : ( 5.356E+04) Average zeroed density : ( 1.603E-03) Average | zeroed dens | : ( 7.771E-01) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > where m1 -66 0.3 Command > (where m1 -66 0.3) Density value : ( -6.600E+01) Tolerance : ( 3.000E-01) Checking map : (M1) Value @ X, Y, Z 16 44 33 = -6.6265E+01 Value @ X, Y, Z 34 66 1 = -6.6265E+01 Value @ X, Y, Z 66 11 31 = -6.6265E+01 Value @ X, Y, Z 84 99 63 = -6.6265E+01 Nr of points listed : ( 4) Nr of points in map : ( 704000) Percentage listed : ( 0.001) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > va m1 -20 -20 -20 -20 -20 -20 Limits : ( 8 8 20 20 -15 -15) List values : (M1) Nr of map points to list : ( 1)X Y Z Density 8 20 -15 0.0000E+00
Nr of points listed : ( 1) Sum of density : ( 0.000E+00) Sum of | density | : ( 0.000E+00) Average density : ( 0.000E+00) Average | dens | : ( 0.000E+00) MAPMAN > va m1 40 42 70 72 40 42 Limits : ( 40 42 70 72 40 42) List values : (M1) Nr of map points to list : ( 27)
X Y Z Density 40 70 40 8.1301E+00 40 70 41 9.2141E+00 40 70 42 1.0705E+01 40 71 40 8.1301E+00 40 71 41 9.6206E+00 40 71 42 1.1789E+01 40 72 40 5.2846E+00 40 72 41 7.8591E+00 40 72 42 1.1111E+01
X Y Z Density 41 70 40 1.3008E+01 41 70 41 1.3008E+01 41 70 42 1.3686E+01 41 71 40 1.3008E+01 41 71 41 1.3008E+01 41 71 42 1.4092E+01 41 72 40 1.0705E+01 41 72 41 1.2195E+01 41 72 42 1.4092E+01
X Y Z Density 42 70 40 1.5176E+01 42 70 41 1.5447E+01 42 70 42 1.5176E+01 42 71 40 1.5176E+01 42 71 41 1.5447E+01 42 71 42 1.5176E+01 42 72 40 1.4905E+01 42 72 41 1.5447E+01 42 72 42 1.5176E+01
Nr of points listed : ( 27) Sum of density : ( 3.358E+02) Sum of | density | : ( 3.358E+02) Average density : ( 1.244E+01) Average | dens | : ( 1.244E+01) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
With the PEek VAlue command, the density at the atomic centre will be
extracted; the "mode" parameter may be:
* N = Nearest - this will extract the value at the nearest grid point
* I = Interpolate - this will do linear interpolation of the 8 grid points
surrounding each atom
* S = Spline - this will do spline interpolation using a 4 * 4 * 4 cube
surrounding each atom
With the PEek CUbe command, density in the neighbourhood of atomic
positions will be extracted; the "mode" parameter may be:
* I = Integrate - simply add up the density values inside the cube
* M = Mean - calculate the average of the density values inside the cube
* A = Absolute integral - add up the absolute density values
* R = Rms - calculate the root-mean-square density
You need to supply the number of grid points around each atom that
will be included in the calculations (e.g., 1 or 2). Using a
margin of 1 grid point means that 27 grid points will be considered
(in general: (1+2*N)**3, where N is the number you supply).
Note that the affected bit of the map is cubic only for cubic cells;
in general it will be a parallellopiped.
The PEek SPhere command is very similar to the PEek CUbe command, except that a sphere of points around each atom is used. You must supply the mode (same options as for PEek CUbe), and the radius around each atom.
In the following example, we use a 1.5 A anomalous difference map to locate iodide ions that were part of the crystallisation soup and to get a rough estimate of their occupancies. First read the map and multiply it by -1 to get positive rather than negative peaks:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > read m1 fourier_ano.map cns Read header Input map : (fourier_ano.map) Title : ( REMARKS FILENAME="fourier_ano.map") Title : ( REMARKS resolution: 500. - 1.5) Title : ( REMARKS sg= P2(1)2(1)2) Title : ( REMARKS a= 164.577 b= 110.98 c= 56.295 alpha= 90 beta= 90 gamma= 90) Title : ( REMARKS map is scaled to sigma units : true) Title : ( REMARKS map 1 : anomalous difference map:) Title : ( REMARKS fom * [ FOBS+ - FOBS- ] * exp(i [ phase -90 ] )) [...] Level number : ( 120) Closing XPLOR map on unit : ( 1) Map read into memory - calculating statistics Sum of density in map : ( 1.669E+00) Requested dynamic range : -1.8609E+01 5.0324E+00 Value of Prod and Plus : 1.0786E+01 201 Actual dynamic range : -1.8635E+01 5.0064E+00 CPU total/user/sys : 25.9 25.2 0.7 MAPMAN > mu m1 -1 Multiply : (M1) Requested dynamic range : -5.0324E+00 1.8609E+01 Value of Prod and Plus : 1.0786E+01 54 Actual dynamic range : -5.0064E+00 1.8635E+01 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Next, pick peaks at a level of 4 sigma:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > pick level 4 MAPMAN > pick peaks m1 peaks.pdb pdb Pick level : ( 4.000E+00) Pick limits : ( 1 179) Pick limits : ( 1 119) Pick limits : ( 1 119) Nr of points in pick volume : ( 2534819) Nr of points >= pick level : ( 542) Picking ... Interpolate intensity Nr of peaks found : ( 64) CPU total/user/sys : 4.7 4.4 0.2 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Now integrate the peaks (sphere of radius 3 A - since the anomalous map is rather sparsely populated with signal and since iodides are pretty big, we need to and can use a fairly large radius):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > peek sphere m1 peaks.pdb peaksint.pdb int 3.0 Grid spacing (A) : ( 0.457 0.462 0.469) Peeking ... ATOM 1 O HOH 1001 --> PEEK-A-BOO --> 1.3495E+02 ATOM 2 O HOH 1002 --> PEEK-A-BOO --> 1.1562E+02 ATOM 3 O HOH 1003 --> PEEK-A-BOO --> 1.8002E+02 ATOM 4 O HOH 1004 --> PEEK-A-BOO --> 2.1915E+02 ATOM 5 O HOH 1005 --> PEEK-A-BOO --> -4.3614E+01 ATOM 6 O HOH 1006 --> PEEK-A-BOO --> 7.7073E+01 [...] ATOM 63 O HOH 1063 --> PEEK-A-BOO --> 1.5240E+02 ATOM 64 O HOH 1064 --> PEEK-A-BOO --> -1.4394E+02 New PDB file created Nr of atoms read and processed : ( 64) Nr outside the limits of the map : ( 0) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Finally, remove negative peaks and sort by the value of the integral (which now resides in the B-factor column - these provide an estimate of the relative occupancies, e.g. 1.0, 0.75, 0.5):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > $ grep '^ATOM' peaksint.pdb | grep -v '1.00-' | sort +9 -nbr > sortedpeaks.pdb Spawn system command : ( grep '^ATOM' peaksint.pdb | grep -v '1.00-' | sort +9 -nbr > sortedpeaks.pdb) MAPMAN > $ head -10 sortedpeaks.pdb Spawn system command : ( head -10 sortedpeaks.pdb) ATOM 28 O HOH 1028 33.523 20.307 17.481 1.00 661.6 ATOM 54 O HOH 1054 72.750 38.427 50.551 1.00 613.9 ATOM 46 O HOH 1046 63.181 6.273 18.911 1.00 488.3 ATOM 11 O HOH 1011 16.672 49.706 41.221 1.00 444.5 ATOM 8 O HOH 1008 7.219 30.900 10.554 1.00 391.7 ATOM 51 O HOH 1051 68.944 44.094 20.249 1.00 390.7 ATOM 58 O HOH 1058 75.050 46.867 11.731 1.00 376.3 ATOM 26 O HOH 1026 29.320 20.591 12.238 1.00 337.7 ATOM 33 O HOH 1033 53.067 44.703 25.872 1.00 336.6 ATOM 12 O HOH 1012 18.022 6.181 45.398 1.00 334.7 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Edward Berry explains the similarity index much clearer than I:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- If you take each map and string out the 3-dimensional array of pixel values into one dimension (in any order, but the same order), and consider these N=nx*ny*nz values as the elements of an ordered N-tuple or vector in N-dimensional space, then the similarity index between two maps is the scalar (inner) product of the two normalized vectors, i.e.SI = <A/sqr<A.A> . B/sqr<B.B>> = <A.B>/sqr(<A.A><B.B>)
This is the value of the cosine between the two vectors, or if both maps have mean zero (or equal?) it is the same as the correlation coefficient. Unlike the correlation coefficient, the S.I. will be sensitive to a constant offset of one map relative to the other. ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > si m1 m2 Similarity Map : (M1) Similarity Map : (M2) ... Nr of points in common grid : ( 295680) Correlation coefficient : ( 1.000) R-factor w.r.t. map 1 : ( 35.424) R-factor w.r.t. map 2 : ( 0.973) RMS difference : ( 1.961E+02) Shape similariy index : ( 0.239) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The map and the "mask map" must have the same grid and cell.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
MAPMAN > re m1 m11_2fofc.map dsn6
...
MAPMAN > re m2 m1.mask mask
...
MAPMAN > mstats m1 m2 0.5
Masked stats Map : (M1)
Mask : (M2)
Lower limits common volume : ( -56 -51 -46)
Upper limits common volume : ( 71 63 69)
Limits first map : ( 1 128 1 115 1
116)
Limits second map : ( 11 138 14 128 17
132)
Number of common map points : ( 1707520)
Density inside the mask :
Nr of points : ( 280522)
Average density : ( 2.528E-02)
St. deviation : ( 1.803E+01)
Minimum value : ( -5.488E+01)
Maximum value : ( 1.000E+02)
Sum of values : ( 7.091E+03)
Density outside the mask :
Nr of points : ( 2910308)
Average density : ( -3.621E-01)
St. deviation : ( 1.432E+01)
Minimum value : ( -5.488E+01)
Maximum value : ( 9.756E+01)
Sum of values : ( -1.054E+06)
CPU total/user/sys : 10.0 9.7 0.3
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > oper m1 * m2 Command > (oper m1 * m2) Store Map : (M1) Other Map : (M2) Operator : (*) Lower limits common volume : ( 0 0 0) Upper limits common volume : ( 99 109 63) Limits first map : ( 1 100 1 110 1 64) Limits second map : ( 1 100 1 110 1 64) Number of common map points : ( 704000) Requested dynamic range : -4.5609E+02 5.1340E+03 Value of Prod and Plus : 4.5617E-02 21 Actual dynamic range : -4.6036E+02 5.1297E+03 CPU total/user/sys : 1.9 1.9 0.0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > pa m1 10 50 20 60 30 70 m3 10 20 30 Limits : ( 10 50 20 60 30 70) Nr of points copied : ( 68921) Sum of OLD density : ( 1.879E+02) Sum of NEW density : ( 1.105E+02) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This will calculate a new map that contains the local RMS density
divided by the RMS ( RMS local density ). This can help in
deciding whether you have an interpretable map or not. Parameters
are:
- name of new map (will be created)
- name of existing map (for which you want to do this calculation)
- npos, nneg = number of positive and negative peaks that will be
masked out in the calculation (to get rid of heavy-atom artefacts);
the suggested value for both is two times the number of heavy-atom
sites (in the entire input map !)
- box = half the size of the box; a value of 1 yields 3*3*3 cubes,
a value of 2 gives 5*5*5 cubes (recommended), etc.
- plot_file = O2D histogram plot file with a histogram of the RMS
local density (see Figure 2 in Terwilliger & Berendzen)
- nr_bins = number of bins to use in the histogram
Example of a ROughness density histogram plot.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > rough m2 m1 8 8 2 Command > (rough m2 m1 8 8 2) O2D plot file ? (dens_hist.plt) Number of bins ? (100) Initialising map and mask ... Removing highest peaks ... Peak value : ( 1.000E+02) [...] Peak value : ( 9.791E+01) Removing lowest peaks ... Peak value : ( -3.351E+01) [...] Peak value : ( -3.351E+01) Calculating local RMS density ... Box size : ( 125) Finishing touch ... Nr of masked points : ( 690140) RMS (local RMS dens) : ( 1.135E+01) Minimum : ( 1.276E-01) Maximum : ( 3.172E+00) Average : ( 8.501E-01) St.dev. : ( 5.267E-01) Calculating histogram ... O2D file written CPU total/user/sys : 50.8 50.5 0.3 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Note: for these calculations to be interpretable, it is important that your map covers an integral number of asymmetric units (e.g., one asymmetric unit, or one unit cell) !
The standard deviation listed above (5.267E-01) is of interest: if it is small (say, 0.2 or lower for 5*5*5 cubes; see Figure 3 in Terwilliger & Berendzen), the map is probably very poor. If it is high (say, 0.3 or above), it looks more hopeful.
Also have a look at the histogram produced by the program (compare to Figure 2 in Terwilliger & Berendzen). If the histogram is unimodal (one peak centered near 1.0), the map is poor. If the map contains traces of protein, you should get a bimodal distribution, with one sharp solvent distribution peaking near 0.3 or so, and a broader protein distribution peaking near 1.2 or so. To see the histogram, convert the plot file to PostScript with the program O2D. (Note: the large peak at 0.0 in the histogram is due to the points in the map for which the RMS density was not calculated.)
With this command you can calculate RS-fit values (both correlation coefficients, RSCC, and R-values, RSR) on a per-residue basis for a model, given its "observed" and "calculated" maps. Normally, the "observed" map would be (2mFo-DFc, PHIc) and the "calculated" map would be (Fc, PHIc). If you use CNS ("model_map.inp", for instance), use:
- u=2; v=1; map_type="sigmaa"; for the observed map
- u=0; v=-1; map_type="unweighted"; for the calculated map
If you NOrmalise both maps before using the RS_fit command, you will get the lowest RSR values (the RSCC values are not affected).
Note that this implementation differs from both O and CNS. It uses all atoms in each residue (incl. partial occupancies) to define a mask, with a radius of 1.5 Å around these atoms. O uses a more complicated masking algorithm and also uses a "faked" calculated map (a sum of Gaussians with all atoms given a B of 20 Å2) - both were born of necessity since O doesn't deal with reflection data. The CNS implementation is even stranger: the RSCC is estimated as an average point-by-point map correlation and the RSR is simply nonsense (calculated as "RSR" = 1.0 - RSCC).
A summary of the results for each residue is listed on the screen, and more extensive output is written to a list file. The list file can also be used by OOPS2 ! Note that the average B-value <B> is occupancy-weighted: <B> = (SUM B*Q)/(SUM Q) .
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > read m1 1f83_2mfodfc.xE ccp4 [...] MAPMAN > read m2 1f83_fc.xE ccp4 [...] MAPMAN > rsfit m1 m2 /db/pub/pdb/data/structures/all/pdb/pdb1f83.ent 1f83_stat.lis 1.5 Real-space fit calculation: Obs_map (e.g., 2mFo-DFc,PHIc) : M1 Calc_map (Fc,PHIc) : M2 Model PDB file : /db/pub/pdb/data/structures/all/pdb/pdb1f83.ent Result list output file : 1f83_stat.lis Masking radius around atoms (A) : 1.500 Initialising ... Grid spacing (A) : ( 0.666 0.651 0.675) Max size of mini-maps : ( 1398101) Sum |obs_map| : ( 2.275E+05) Sum |cal_map| : ( 2.414E+05) Scale factor for cal_map : ( 9.422E-01) Processing ... # 1 [PRO A 1 ] Nat 7 RSCC 0.807 RSR 0.547 <B> 50.59 # 2 [VAL A 2 ] Nat 7 RSCC 0.937 RSR 0.172 <B> 33.13 # 3 [THR A 3 ] Nat 7 RSCC 0.962 RSR 0.132 <B> 27.92 # 4 [ILE A 4 ] Nat 8 RSCC 0.909 RSR 0.216 <B> 24.00 # 5 [ASN A 5 ] Nat 8 RSCC 0.906 RSR 0.177 <B> 25.10 [...] # 424 [SER A 424 ] Nat 6 RSCC 0.579 RSR 0.320 <B> 94.51 # 425 [LYS A 425 ] Nat 6 RSCC 0.451 RSR 0.632 <B> 110.06 # 426 [VAL B 53 ] Nat 7 RSCC 0.380 RSR 0.685 <B> 126.19 # 427 [LEU B 54 ] Nat 8 RSCC 0.537 RSR 0.489 <B> 132.46 # 428 [GLU B 55 ] Nat 9 RSCC 0.600 RSR 0.584 <B> 132.87 # 429 [ARG B 56 ] Nat 11 RSCC 0.474 RSR 0.696 <B> 138.74 [...] # 457 [LEU C 84 ] Nat 8 RSCC 0.219 RSR 0.936 <B> 140.63 # 458 [LYS C 85 ] Nat 9 RSCC 0.530 RSR 0.615 <B> 135.86 # 459 [ARG C 86 ] Nat 11 RSCC 0.510 RSR 0.561 <B> 130.91 # 460 [LYS C 87 ] Nat 9 RSCC 0.504 RSR 0.476 <B> 106.16 # 461 [TYR C 88 ] Nat 13 RSCC 0.653 RSR 0.570 <B> 117.07 # 462 [ ZN A 500 ] Nat 1 RSCC 0.609 RSR 0.279 <B> 34.94 # 463 [HOH 601 ] Nat 1 RSCC 0.974 RSR 0.141 <B> 11.46 # 464 [HOH 602 ] Nat 1 RSCC 0.978 RSR 0.120 <B> 15.75 [...] # 742 [HOH 926 ] Nat 1 RSCC 0.589 RSR 0.512 <B> 59.71 # 743 [HOH 927 ] Nat 1 RSCC 0.786 RSR 0.408 <B> 85.91Nr of lines read from file : ( 4463) Nr of hydrogen atoms skipped : ( 0) Nr of zero-occ atoms : ( 0) Nr of non-H atoms read : ( 4028) Nr of residues encountered : ( 743) ... of which amino acids : ( 461) ... of which nucleic acids : ( 0) ... of which waters : ( 281) ... of which heteros : ( 1) Nr with alt. conf. : ( 0) Nr with HETERO atoms : ( 282) Nr with zero summed occup. : ( 0) Nr with odd summed occup. : ( 0) Nr not calculated at all : ( 0) Nr with computation errors : ( 0) Total nr with errors : ( 0) CPU total/user/sys : 1.6 1.6 0.0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The list file contains the following information:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
!
! Created by MAPMAN V. 020827/7.4.5 at Tue Aug 27 20:52:14 2002 for eds
!
! RS-fit list file 1f83_stat.lis
!
! Obs_map M1 = 1f83_2mfodfc.xE
! Calc_map M2 = 1f83_fc.xE
! Model = /db/pub/pdb/data/structures/all/pdb/pdb1f83.ent
! Masking radius around atoms = 1.500 A
!
! Sum |obs_map| = 2.275E+05
! Sum |cal_map| = 2.414E+05
! Scale factor for cal_map = 9.422E-01
!
! # = sequential residue index
! residue_id = columns 18:27 of the ATOM/HETATM card
! RSCC = residue-based real-space correlation coefficient
! RSR = residue-based real-space R-value
! wgtBave = occupancy-weighted average B = (SUM B*Q)/(SUM Q)
! Natom = nr of atoms encountered in residues
! S occ = sum of their occupancies (normally same as Natom)
! Nhet = number of HETATM cards encountered in residue
! AC = alternative conformation flag (T or F)
! Scale RHOc = residue-based density scale (not used)
! Ngridpts = nr of grid points summed for RSCC and RSR
! R? = Error? = computation-error flag (T or F)
! K = Kind = kind of residue (Amino, Nucleic, Water, Hetero)
!
! 1 2 3 4 5 6 7 8 9 10
!23456789+123456789+123456789+123456789+123456789+123456789+123456789+123456789+123456789+123456789+
! # [residue_id] RSCC RSR wgtBave Natom S occ Nhet AC Scale RHOc Ngridpts R? K
1 [PRO A 1 ] 0.807 0.547 50.59 7 7.00 0 F 4.6114E-01 254 F A
2 [VAL A 2 ] 0.937 0.172 33.13 7 7.00 0 F 8.8460E-01 272 F A
3 [THR A 3 ] 0.962 0.132 27.92 7 7.00 0 F 8.4815E-01 258 F A
4 [ILE A 4 ] 0.909 0.216 24.00 8 8.00 0 F 8.2670E-01 298 F A
5 [ASN A 5 ] 0.906 0.177 25.10 8 8.00 0 F 8.6668E-01 295 F A
[...]
425 [LYS A 425 ] 0.451 0.632 110.06 6 6.00 0 F 3.6789E-01 203 F A
426 [VAL B 53 ] 0.380 0.685 126.19 7 7.00 0 F 1.0287E+00 271 F A
427 [LEU B 54 ] 0.537 0.489 132.46 8 8.00 0 F 6.7260E-01 294 F A
428 [GLU B 55 ] 0.600 0.584 132.87 9 9.00 0 F 5.7221E-01 333 F A
429 [ARG B 56 ] 0.474 0.696 138.74 11 11.00 0 F 9.9605E-01 411 F A
430 [ASP B 57 ] 0.475 0.453 98.11 8 8.00 0 F 6.6769E-01 289 F A
[...]
457 [LEU C 84 ] 0.219 0.936 140.63 8 8.00 0 F 9.7687E-01 313 F A
458 [LYS C 85 ] 0.530 0.615 135.86 9 9.00 0 F 1.6995E+00 346 F A
459 [ARG C 86 ] 0.510 0.561 130.91 11 11.00 0 F 1.1015E+00 425 F A
460 [LYS C 87 ] 0.504 0.476 106.16 9 9.00 0 F 9.4747E-01 324 F A
461 [TYR C 88 ] 0.653 0.570 117.07 13 13.00 0 F 1.9071E+00 420 F A
462 [ ZN A 500 ] 0.609 0.279 34.94 1 1.00 1 F 1.0757E+00 53 F H
463 [HOH 601 ] 0.974 0.141 11.46 1 1.00 1 F 8.9061E-01 53 F W
[...]
743 [HOH 927 ] 0.786 0.408 85.91 1 1.00 1 F 1.2506E+00 53 F W
!
! Nr of lines read from file : 4463
! Nr of hydrogen atoms skipped : 0
! Nr of zero-occ atoms : 0
! Nr of non-H atoms read : 4028
! Nr of residues encountered : 743
! ... of which amino acids : 461
! ... of which nucleic acids : 0
! ... of which waters : 281
! ... of which heteros : 1
! Nr with alt. conf. : 0
! Nr with HETERO atoms : 282
! Nr with zero summed occup. : 0
! Nr with odd summed occup. : 0
! Nr not calculated at all : 0
! Nr with computation errors : 0
! Total nr with errors : 0
!
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > hi m1 -100 -50 -30 -20 -10 0 10 20 30 40 50 100 Histrogram limits : ( -1.000E+02 -5.000E+01 -3.000E+01 -2.000E+01 -1.000E+01 0.000E+00 1.000E+01 2.000E+01 3.000E+01 4.000E+01 5.000E+01 1.000E+02) Histogram : (M1)Nr of values < -100.00 : 0 ( 0.000 %) Nr of values >= -100.00 and < -50.00 : 780 ( 0.264 %) Nr of values >= -50.00 and < -30.00 : 15222 ( 5.148 %) Nr of values >= -30.00 and < -20.00 : 23328 ( 7.890 %) Nr of values >= -20.00 and < -10.00 : 42825 ( 14.484 %) Nr of values >= -10.00 and < 0.00 : 77377 ( 26.169 %) Nr of values >= 0.00 and < 10.00 : 66974 ( 22.651 %) Nr of values >= 10.00 and < 20.00 : 28849 ( 9.757 %) Nr of values >= 20.00 and < 30.00 : 16553 ( 5.598 %) Nr of values >= 30.00 and < 40.00 : 11028 ( 3.730 %) Nr of values >= 40.00 and < 50.00 : 6946 ( 2.349 %) Nr of values >= 50.00 and < 100.00 : 5797 ( 1.961 %) Nr of values >= 100.00 : 1 ( 0.000 %) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Example of an EXtracted map plot.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > li m1 ... File = crabp.difpat Grid = 40 40 200 Origin = 0 0 0 Extent = 40 21 200 Cell = 41.500 41.500 203.500 90.000 90.000 90.000 ... MAPMAN > ex m1 z25.o2d z 50 O2D file written MAPMAN > ex m1 z50.o2d z 100 O2D file written ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Example of an 1D_projection plot.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > 1d Which map ? (m1) O2D plot file ? ( ) c.plt ONTO which axis (X/Y/Z) ? (Z) Nr of points in projection : 301 Average density : 3.9404E+01 Standard deviation : 2.3940E+03 Minimum density : -4.5252E+03 Maximum density : 4.9876E+03 O2D file written ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Example of a 2D_projection plot.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > 2d Which map ? (M1) O2D plot file ? ( ) ab.plt ALONG which axis (X/Y/Z) ? (Z) Start plane ? (0) End plane ? (300) Nr of points in projection : 16641 Average density : 7.1369E-01 Standard deviation : 2.8884E+02 Minimum density : -8.0051E+02 Maximum density : 1.2097E+03 O2D file written CPU total/user/sys : 3.6 3.4 0.2 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ... Density min,max,ave = -7.2651E+01 1.0000E+02 1.5338E-08 Sigma, variance = 1.9707E+01 3.8836E+02 Mappage prod/plus = 1.4770E+00 107 Mappage dyn. range = -7.2446E+01 1.0021E+02 ... MAPMAN > sc m1 -1 1 Scale : (M1) MAPMAN > li Nr of maps in memory : ( 1)Map 1 = M1 ... Density min,max,ave = -1.0000E+00 1.0000E+00 -1.5841E-01 Sigma, variance = 2.2829E-01 5.2117E-02 Mappage prod/plus = 1.2750E+02 127 Mappage dyn. range = -9.9608E-01 1.0039E+00 ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ... Density min,max,ave = -7.2651E+01 1.0000E+02 1.5338E-08 Sigma, variance = 1.9707E+01 3.8836E+02 Mappage prod/plus = 1.4770E+00 107 Mappage dyn. range = -7.2446E+01 1.0021E+02 ... MAPMAN > zero m1 0 40 Zero : (M1) Less than lower bound : ( 159532) Greater than upper bound : ( 12744) MAPMAN > li m1 Nr of maps in memory : ( 1)Map 1 = M1 ... Density min,max,ave = 0.0000E+00 3.9999E+01 5.0790E+00 Sigma, variance = 8.9967E+00 8.0940E+01 Mappage prod/plus = 6.3751E+00 0 Mappage dyn. range = 0.0000E+00 3.9999E+01 ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > ch Which map ? (m1) Lower bound ? ( -1.0000E+04) -0.001 Upper bound ? ( 9.9900E-01) 0.001 New value ? ( 0.0) -100 Change : (M1) Nr of points changed : ( 61484) Requested dynamic range : -1.0000E+02 1.6125E+01 Value of Prod and Plus : 2.1959E+00 220 Actual dynamic range : -1.0019E+02 1.5939E+01 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
map (i,j,k) = start + (i-1)*dx + (j-1)*dy + (k-1)*dz
(start, dx, dy and dz are arguments to this command; the
latter three are optional and default to zero).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > set m1 0 0 0 1 Command > (set m1 0 0 0 1) Set values : (M1) Start value : ( 0.000E+00) DX increment : ( 0.000E+00) DY increment : ( 0.000E+00) DZ increment : ( 1.000E+00) Requested dynamic range : 0.0000E+00 1.5000E+01 Value of Prod and Plus : 1.7000E+01 0 Actual dynamic range : 0.0000E+00 1.5000E+01 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
NOTE: NOT TESTED
NOTE: DOES NOT CHANGE THE SYMMETRY OPERATORS IN CCP4 MAPS !!! USE MAPFIX TO DO THIS.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > tr m1 Old origin : ( 0 0 0) Grid : ( 100 100 100) Nr of UNIT CELLs translation in X ? (0) 1 Nr of UNIT CELLs translation in Y ? (0) 2 Nr of UNIT CELLs translation in Z ? (0) 3 New origin : ( 100 200 300) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > gt m1WARNING !!! This option will change the origin of your map by any number of grid points that you specify. This is bound to upset the compatibility between this map and your model/data. Only use this option if you understand this and know what you are doing ...
Old origin : ( 100 200 300) Grid : ( 100 100 100) Nr of GRID POINTs translation in X ? (0) 11 Nr of GRID POINTs translation in Y ? (0) -22 Nr of GRID POINTs translation in Z ? (0) 33 New origin : ( 111 178 333) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > mom m1 Moments : (M1)Extensive map statistics Number of data points ................... 439296 Average electron density ................ -1.18879E-07 RMS density ("sigma") ................... 1.24695E+01 Mean Absolute Deviation from the mean ... 8.93063E+00 Variance ................................ 1.55488E+02 Standard deviation ...................... 1.24695E+01 Skewness (third moment) ................. 7.29890E-01 Sigma(skewness) estimate ................ 3.69570E-03 Skewness / Sigma(skewness) .............. 1.97497E+02 Asymmetric tail extending towards positive density Kurtosis (fourth moment) ................ 2.47488E+00 Sigma(kurtosis) estimate ................ 7.39140E-03 Kurtosis / Sigma(kurtosis) .............. 3.34832E+02 Leptokurtic (sharp) distribution ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > list m1 ... Nr of points = 208800 Density min,max,ave = -4.5111E+01 1.0000E+02 -5.0106E-03 Sigma, variance = 4.3394E+00 1.8831E+01 Mappage prod/plus = 1.7573E+00 79 Mappage dyn. range = -4.4956E+01 1.0016E+02 ... MAPMAN > no m1 Normalise : (M1) Subtract average : ( -5.011E-03) Divide by sigma : ( 4.339E+00) CPU total/user/sys : 1.5 1.4 0.0 MAPMAN > li m1 ... Nr of points = 208800 Density min,max,ave = -1.0397E+01 2.3043E+01 -2.3120E-03 Sigma, variance = 1.0000E+00 1.0000E+00 Mappage prod/plus = 7.6256E+00 79 Mappage dyn. range = -1.0360E+01 2.3080E+01 ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > sw q2.map Origin 0 0 0 Extent 85 66 157 Grid 84 128 156 Cell 49.10 75.80 92.90 89.99 103.20 89.99 Prod/Plus 1.00 0 Scale1/2 100 100 Bricks in x,y,z 11 9 20 Nr of records 1981 Total number of records written = 1981 CPU total/user/sys : 7.0 1.7 5.3 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Example of a DH density histogram plot.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > dh m1 m1bins.plt 500 Calculating histogram ... O2D file written CPU total/user/sys : 2.7 2.5 0.1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- % 420 gerard rigel 00:51:31 dirs/p2 > o2dps m1bins.plt hi... o2dps ... convert O2D plot files to PostScript ...
Will convert m1bins.plt to m1bins.ps with option hi ...
Running O2D ...
Lowest X-value : ( -6.610E+01) Highest X-value : ( 8.682E+01) Lowest Y-value : ( 0.000E+00) Highest Y-value : ( 3.158E+05) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
With the NEw commands, you can create empty maps which you can subsequently 'fill' by combining them with one or more existing maps, e.g. using the ADd or PAste commands. [These commands are very similar to the corresponding commands in the mask manipulation program MAMA.]
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > new ? Command > (new ?)Current defaults for the next NEW map: Grid = 100 100 100 Origin = 0 0 0 Extent = 100 100 100 Cell = 100.000 100.000 100.000 90.000 90.000 90.000 Nr of points = 1000000 Max = 5000000 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > new sam m1 Command > (new sam m1) MAPMAN > new ? Command > (new ?)Current defaults for the next NEW map: Grid = 45 80 90 Origin = -50 -55 -43 Extent = 109 110 124 Cell = 23.900 45.300 46.900 90.000 90.000 90.000 Nr of points = 1486760 Max = 5000000 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > new enc m1 Command > (new enc m1) Current NEw ORigin : ( -55 -60 -48) Current NEw EXtent : ( 100 100 100) Current map origin : ( -50 -55 -43) Current map extent : ( 109 110 124) New origin : ( -55 -60 -48) New extent : ( 114 115 129) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > new make m2 Command > (new make m2) WARNING --- All map points have identical values ! Requested dynamic range : 0.0000E+00 0.0000E+00 Value of Prod and Plus : 1.0000E+00 0 Actual dynamic range : 0.0000E+00 2.5500E+02 New (empty) map created (P1) ! MAPMAN > li m2 Command > (li m2) Nr of maps in memory : ( 2)Map 2 = M2 File = not_defined Grid = 45 80 90 Origin = -55 -60 -48 Extent = 119 120 134 Cell = 23.900 45.300 46.900 90.000 90.000 90.000 UVW = 1 2 3 Spcgrp = 1 Nr of points = 1913520 Density min = 0.000E+00 Max = 0.000E+00 Average = 0.000E+00 Sigma = 0.000E+00 Variance = 0.000E+00 Mappage Prod= 1.000E+00 Plus = 0 Dyn. range = 0.000E+00 To = 2.550E+02 Cell vol. = 5.078E+04 Voxel vol. = 1.567E-01 Grid vol. = 2.999E+05 %Cell vol. = 590.59 Origin frac = -1.22222 -0.75000 -0.53333 Origin Cart = -29.211 -33.975 -25.013 Top frac = 1.40000 0.73750 0.94444 Top Cart = 33.460 33.409 44.294 Spacing = 0.531 0.566 0.521 Top = 63 59 85 Changes = T Label = Created from scratch with NEw MAke ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > pi ?Peak residue & atom names : |HOH| O1 | First peak residue number : 1001 Peak threshold level : 6.0000E+00 Pick limits : 0 0 0 0 0 0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > pick pdb H2O " O " 501 MAPMAN > pi ?Peak residue & atom names : |H2O| O | First peak residue number : 501 Peak threshold level : 6.0000E+00 Pick limits : 0 0 0 0 0 0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > pi lim 0 0 10 -10 5 Upper bound for Z ? (0) 95 MAPMAN > pi ?Peak residue & atom names : |H2O| O | First peak residue number : 501 Peak threshold level : 6.0000E+00 Pick limits : 0 0 10 -10 5 95 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > pi lev 5.5 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > pi pea m1 peaks.pdb pdb Pick level : ( 5.500E+00) Pick limits : ( 1 64) Pick limits : ( 1 87) Pick limits : ( 5 64) Nr of points in pick volume : ( 334080) Nr of points >= pick level : ( 820) ... Nr of peaks found : ( 52) MAPMAN > $ cat peaks.pdb REMARK Created by MAPMAN V. 930803/2.2 at Tue Aug 3 17:14:32 1993 for user gerard REMARK 52 peaks picked above level 5.500000 REMARK Map file ../../scratch/am/crabp21.difpat REMARK Map name M1 REMARK Map text Read from ../../scratch/am/crabp21.difpat REMARK CRYST1 37.127 106.501 40.495 90.00 110.05 90.00 REMARK Peak # 1 @ 3.220 16.397 46.593 $ 5.985534E+00 ATOM 1 O H2O 501 -7.990 9.922 26.855 1.00 20.00 ... REMARK Peak # 52 @ 65.191 73.900 33.332 $ 5.892479E+00 ATOM 52 O H2O 552 29.660 44.718 19.212 1.00 20.00 END ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > pi pea m1 multi_roting.log amore Pick level : ( 1.000E+00) Pick limits : ( 1 46) Pick limits : ( 1 71) Pick limits : ( 1 142) Nr of points in pick volume : ( 463772) Nr of points >= pick level : ( 174271) Picking ... Interpolate intensity Nr of peaks found : ( 340) CPU total/user/sys : 1.0 1.0 0.1 MAPMAN > $ cat multi_roting.log REMARK Created by MAPMAN V. 960411/4.5.1 at Thu Apr 11 20:49:51 1996 for user gerard REMARK 340 peaks picked above level 1.000000 REMARK Map file multi_rot.map REMARK Map name M1 REMARK Map text Read from multi_rot.map SOLUTIONRC 1 2.19 40.87 190.94 0.00000 0.00000 0.00000 3.0 0.0 SOLUTIONRC 1 1.43 56.65 354.18 0.00000 0.00000 0.00000 2.9 0.0 SOLUTIONRC 1 2.78 71.59 156.24 0.00000 0.00000 0.00000 3.7 0.0 SOLUTIONRC 1 1.25 85.11 105.13 0.00000 0.00000 0.00000 3.3 0.0 ... SOLUTIONRC 1 113.66 140.50 322.90 0.00000 0.00000 0.00000 3.7 0.0 SOLUTIONRC 1 114.53 156.38 25.65 0.00000 0.00000 0.00000 4.0 0.0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > pick int m1 integrate.pdb pdb Pick level : ( 4.850E+01) Pick limits : ( 9 176) Pick limits : ( 27 233) Pick limits : ( 26 257) Nr of points in pick volume : ( 8068032) Nr of points >= pick level : ( 3903) Picking ... Integrate intensity Nr of peaks found : ( 436) CPU total/user/sys : 17.7 17.6 0.1 MAPMAN > $ head -10 integrate.pdb REMARK Created by MAPMAN V. 951102/4.2 at Thu Nov 2 21:55:50 1995 for user gerard REMARK 436 peaks picked above level 48.50000 REMARK Map file /nfs/scr_uu1/gerard/scratch/m2_fofc.xE REMARK Map name M1 REMARK Map text Read from /nfs/scr_uu1/gerard/scratch/m2_fofc.xE REMARK CRYST1 49.100 75.800 92.900 90.00 103.20 90.00 REMARK Peak # 1 @ 9.346 134.124 169.783 $ 9.681636E+02 ATOM 1 O1 HOH 1001 -14.274 66.886 80.822 1.00 20.00 REMARK Peak # 2 @ 11.919 161.172 115.088 $ 1.303484E+03 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > re m1 all1_amore.map ccp4 MAPMAN > his m1 30 32 34 36 38 39 40 MAPMAN > pick lev 39 MAPMAN > pick high m1 Output file ? (peaks.pdb) Format (Pdb|Amore) ? (PDB) amo Pick level : ( 3.900E+01) Pick limits : ( 1 82) Pick limits : ( 1 119) Pick limits : ( 1 250) Nr of points in pick volume : ( 2439500) Nr of points >= pick level : ( 156) Picking ... High-density values Nr of peaks found : ( 156) CPU total/user/sys : 8.7 8.5 0.2 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > bo ?Current BONES parameters and defaults : Current BONES map : M1 From file : test.E Skeletonised with base level 5.000 and step 2.000 And including 100 spare points Yielding 2373 points and 2555 connections BONES file : sgi.bones BONES ID for O : SKL Minimum length for main-chain fragments = 4 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > bo sk m1 5 2 100 Constructing envelope with base level 5.000 Level increment ..................... 2.000 Number of levels (max. 10) .......... 10 Nr of points (level > 0) in input map 12802 Ditto, in skeletonised map .......... 2273Nr of points in the bones : 2373 (includes spare points !) Nr of spare points : 100 Nr of connections : 2555 Nr of branch-points : 741
Nr of fragments Size less than or equal to 1 = 18 Size less than or equal to 2 = 30 Size less than or equal to 3 = 9 ... Size less than or equal to 100 = 0 Size greater than 100 = 1 Maximum fragment size = 919
CPU total/user/sys : 80.2 78.8 1.4 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > bo co sgi.bones skl Min length main-chain fragments ? ( 5) 4 Min length for main-chain fragments : 4 Nr of main-chain connections : 1879 Nr of side-chain connections : 675 eq 1 1 2273 Histogram of bones types 1,2,3.... Bone type : 1 481 1791 100 0 0 0 0 0 0 Type 2 = side-chain; 3 = main-chain Type 1 = left-overs; 4 = spare parts ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > bo pr bones.pdb 6 5.0 Min length for main-chain fragments : 6 Nr of main-chain connections : 5074 Nr of side-chain connections : 5912 Nr of BONES with 0 neighbours = 372 Nr of BONES with 1 neighbours = 3713 Nr of BONES with 2 neighbours = 5396 Nr of BONES with 3 neighbours = 715 Nr of BONES with 4 neighbours = 22 Nr of BONES with 5 neighbours = 0 Nr of BONES with 6 neighbours = 0 Pruning BONES ... Nr of BONES written to PDB file : ( 6424) Nr of BONES with code 1,2,... written: Nr : (0 1479 4945 0 0 0 0 0 0 0) Nr of BONES with code 1,2,... NOT written: Nr : (1 3793 0 0 0 0 0 0 0 0) CPU total/user/sys : 5.3 5.0 0.3 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
From version 6.0 on, MAPMAN can produce VRML files of masks and molecules (VRML = Virtual Reality Modelling Language). Rather than writing a dedicated set of routines to display these, 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 MAPMAN, 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 COlour_list command
will list all (> 400) predefined colour names and their RGB
values
A typical series of commands would be:
- (generate or read mask)
- VRml SEtup (if necessary)
- VRml INit filename
- VRml DRaw map level
(or: VRml DOts map low_level high_level)
- VRml TRace pdbfile
- VRml CEll mask
- VRml BOx mask
- VRml CLose_file
The VRML interface was written for two purposes:
- quick inspection of maps
- creating files with maps and models 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 !)
Example of a VRML display generated with MAPMAN.
With this command you can define the following parameters:
- the central atom type (" 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 white)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > vr set " CA " 4.5 black white Central atom type : ( CA) Max central atom distance : ( 4.500) Background colour : (0.0000000E+00 0.0000000E+00 0.0000000E+00) Default colour : (1.000000 1.000000 1.000000) ----- 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 masks and molecules to it, use the VRml DRaw/DOts/TRace etc. commands
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > vr in mapman.wrl Open VRML file : (mapman.wrl) Opened VRML file ----- 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 ----- MAPMAN > vr close Closed 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 ----- MAPMAN > vr col 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 -----
Adds the central-atom trace of the molecule in the PDB file you supply, in the colour you specify (if any), to the current VRML file. Use the VRml SEtup command to define the central atom type and the maximum distance between sequential central atoms for them to be connected.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > vr trace 1pmp.pdb yellow VRML - Trace of CA atoms for PDB file 1pmp.pdb Nr of atoms written : ( 393) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Adds a unit cell. You must supply the map name. Optionally, you can specify the drawing colour, whether the cell should be drawn as lines or as a solid body, and you can supply offsets (integeral numbers of unit cells) so you can show other unit cells than the one with x,y,z = 0->1.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > vr cell m1 blue VRML - Cell for map M1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Adds the box of a selected map.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > vr box m1 green VRML - Box for map M1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
You supply the name of the map, a lower and an upper level and (optionally) a colour. All map points whose density falls in the selected range will be drawn as dots.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > vr dots m1 60 100 red Nr of points written : ( 219) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
You supply the name of the map, the contour level and (optionally) a colour. Instructions to draw a chicken wire representation of the entire map will be added to the VRML file.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > vr draw m1 12 cyan Contour planes perpendicular to : (X) Number of planes : ( 57) Nr of contours drawn : ( 598) Nr of points included : ( 10736) Contour planes perpendicular to : (Y) Number of planes : ( 62) Nr of contours drawn : ( 584) Nr of points included : ( 10820) Contour planes perpendicular to : (Z) Number of planes : ( 67) Nr of contours drawn : ( 586) Nr of points included : ( 10760) Contours written CPU total/user/sys : 5.7 5.7 0.0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Some (early) observations:
- MEdian, AVerage, SMooth and VAr_thr reduce noise somewhat
- MAximum and KHighest smear out the density
- SIgnal/noise may bring out density for surface side chains
- LAplace shows the edges of the molecule (sometimes)
- EDge and STat_diff are rather neutral operations
- KLowest, GRadient and MInimum are rather useless
These filters are intended to clean up your density a bit, or to
enhance real features.
An as yet unexplored application lies in the use of these techniques
in density modification.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAPMAN > filter ?Filter options: --------------- MEdian - replace point by median value in local cube MInimum - replace point by minimum value in local cube MAximum - replace point by maximum value in local cube AVerage - replace point by average value in local cube i.e., convolution with 1 1 1 1 1 1 1 1 1 (1/27) * 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 SMooth - convolution with 1 2 1 2 3 2 1 2 1 (1/55) * 2 3 2 3 5 3 2 3 2 1 2 1 2 3 2 1 2 1 EDge - convolution with A A A A A A A A A (1/B) * A A A A B-26A A A A A (A<0, B>0) A A A A A A A A A SIgnal/noise - replace point by average/sigma in local cube GRadient - convolution with (-1 0 +1) in 3 directions LAplace - convolution with (-1 2 -1) in 3 directions KLowest - replace point by average of K lowest nbrs KHighest - replace point by average of K highest nbrs VAr_thr - variable threshold (A, B in <0,1]): NEW = old - (A*sigma + B*ave) STat_diff - statistical differencing (A, B, C in <0,1]): NEW = (1-A)*old + (old-ave)*B*C/(C+B*sigma)
Parameters: Size = one-sided size of small, local cube (usually, 1) A,B,C = parameters that determine the convolution matrix (the program suggests sensible defaults) K = number of neigbours to use in averaging
Further reading : Wayne Niblack, "An Introduction to Digital Image Processing", Prentice-Hall International, London, 1986. ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
MAPMAN > fil smo m1
SMooth - working ...
Filter : ( 1.000 2.000 1.000 2.000 3.000 2.000 1.000
2.000 1.000 2.000 3.000 2.000 3.000 5.000 3.000
2.000 3.000 2.000 1.000 2.000 1.000 2.000 3.000
2.000 1.000 2.000 1.000)
Sum : ( 55.000)
CPU total/user/sys : 3.9 3.9 0.0
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Some of the input and output formats don't work properly (yet).
Created at Thu Jun 26 11:57:39 2008
by MAN2HTML version 070111/2.0.8 . This manual
describes MAPMAN, a program of the Uppsala
Software Factory (USF), written and maintained by Gerard Kleywegt. © 1992-2007.