Program : MAMA
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 improvement of O/RAVE-style masks
(molecular envelopes)
Package : RAVE
Reference(s) for this program:
* 1 * 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.
* 2 * G.J. Kleywegt & T.A. Jones (1993). Masks Made Easy. CCP4/ESF-EACBM Newsletter on Protein Crystallography 28, May 1993, pp. 56-59. [http://xray.bmc.uu.se/usf/factory_1.html]
* 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 & 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]
* 5 * 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]
* 6 * G.J. Kleywegt (1999). Experimental assessment of differences between related protein crystal structures. Acta Cryst. D55, 1878-1857. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=10531486&dopt=Citation] [http://scripts.iucr.org/cgi-bin/paper?se0283]
* 7 * 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.
* 8 * 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.
930224 - 0.1 - initial version; max 8 masks of 1 MegaWord each;
reasonably well debugged, but no visual tests
done yet !!!
930226 - 0.2 - doubled max size of masks to 2 MegaWord;
implemented CPU-timing;
new options DUPLICATE, NOT, NBR_COUNT, UNITE,
NEW ?, NEW ORIGIN, NEW EXTENT, NEW GRID,
NEW CELL, NEW MAKE, NEW RT_OPERATOR, NEW RADIUS,
NEW PDB, NEW BONES (not tested), NEW COPY,
NEW SAME, NEW FACTOR;
did visual checks (looks good, especially when
using semi-transparent surfaces in "O" !!!)
930301 - 0.3 - added option NEW PAD; print delta-CPU-time only
if it exceeds 1.0 seconds; calculate smoothness
in NBR_COUNT; give more info in LIST; NEW_MASK
format; error traps in mask i/o routines;
COMPRESSED_MASK format; use argument for LIST
930302 - 1.0 - first production version; manual up-to-date;
NEW SPACING option
930309 - 1.1 - increased mask size to 4 MegaWord; implemented
OVERLAP ?, OVERLAP ORIGIN, OVERLAP EXTENT,
OVERLAP SYMM_OP, OVERLAP NCS_RT, OVERLAP RESET_NCS;
implemented OVERLAP TRIM; removed options
OVERLAP ORIGIN and EXTENT again since they are
not needed (YET !); implemented OVERLAP ERASE;
none of these documented yet !
930310 - 1.2 - tried to program general overlap case (> 2 NCS);
re-implemented OVERLAP ORIGIN and EXTENT;
implemented SIMILARITY, ODL, BORDER_CHECK,
ATOM_FIT, EZD, OVERLAP EZD, ISLAND_ERASE
930311 - 1.3 - debugged INTRPL (also in ES_AVERAGE); removed
some other bugs; implemented on DEC ALPHA (4 to 8
times faster than VGX or Indigo); cleaned up the
code a bit; worked example for the manual
930312 - 1.4 - tried to program NEW UNIT_CELL (seems to work okay);
included use of RT-operator here; implemented
NEW RESET_RT_OPERATOR; introduced cutoff factor
in OVERLAP TRIM and ERASE plus the option to
produce an EZD file with these commands as well
930313 - 2.0 - updated manual completely; added LABEL option
930315 - 2.1 - corrected manual; include various volumes in LIST
option; NEW UNIT_CELL now does its utmost to keep
the VOLUME of the actual mask as constant as
possible !
930416 - 2.2 - minor bug fixes; implemented MACRO facility;
made index for manual
930507 - 2.3 - bug fixes in NEW BONES; new option NEW OLDBONES
for BONES files without radii
930510 - 2.4 - new option NEW BALL (spherical mask)
930602 - 2.5 - added more hints to manual; print solvent content
in overlap calculations; made smaller version for
ESVs (only 4 masks in memory); print program
dimensioning with "?" option; NEW CUBE option;
OVERLAP ASU option
930608 - 2.6 - added $ option to issue shell commands
930614 - 2.7 - debugged handling of "O" datablock files
930616 - 3.0 - new production version; new format types (see 2.59);
made definition of asymm. unit for OVERLAP options
more liberal (see 2.51)
930624 - 3.1 - new overlap algorithm (set with OV MODE; see 2.49.i);
new option TRanslate (see 2.18.i); minor bug fixes;
increased some counter arrays (for the virus
people)
931119 - 3.2 - cleaned up (for) manual; drastically shortened
941223 - 3.3 - COMpressed mark format now default for WRite
950207 -3.3.1- removed minor bug in LIst command
950711 - 3.4 - new BLob_erase and DOt_odl options
951022 - 3.5 - made sensitive to OSYM
951030 - 3.6 - enable reading of many NCS operators from one file
for the OVerlap NCs command
951106 - 3.7 - removed long-standing bug from NEw UNitcell command
(in figuring out fractional mask bottom and top)
960415 -3.7.1- minor bug fixes
960425 -3.7.2- increase max number of atoms in PDB file to 100,000
960517 - 3.8 - implemented simple symbol mechanism
960629 -3.8.1- default mask output format changed to OMASK
961126 - 4.0 - implemented dynamic memory allocation
970626 - 4.1 - support initialisation macro (setenv GKMAMA macrofile)
970627 - 4.2 - changed ATom_fit command to include HETATMs, and to
optionally produce two new PDB files, one with all
atoms inside the mask, and one with those outside;
made the ouput of the OVerlap TRim command a bit
clearer when it checks to see if you specified an
asymmetric unit plus 1, 2 or 3 points on all sides
970722 - 5.0 - implemented VRML commands
970724 -5.0.1- added VRml CEll and VRml BOx
970922 -5.0.2- fixed a little bug so that the NEw BAll command now
actually generates a sphere rather than a cube ;-)
971204 - 5.1 - debugged NEw UNit_cell command; better error checks
for NEw COpy command
970409 -5.1.1- added NEw ENcompass command
970714 - 5.2 - added new OVerlap UNit_cell command
980901 - 5.3 - NEw BOnes will now check if reasonable atomic radii
are used (if not, probably the NEw OLd_bones command
should have been used instead of the NEw BOnes command);
new INvert_ncs command to invert O-style operators
(Cartesian space only !)
980929 - 5.4 - new ZP_restart command to re-start the program with
different memory allocation
981021 -5.4.1- new ECho command to echo command-line input (useful
in scripts)
981022 - 5.5 - implemented command history (# command)
990301 - 5.6 - the SMooth, CUt, EXpand and COntract commands now have
as an extra (optional; default = 1) parameter the number
of times the operation should be carried out. So instead
of issuing the "expand m1" command five times, you can
use "expa m1 5". Also sped up the ISland_erase command
(typically, by a factor of 5-10).
990319 -5.6.1- changed maximum number of masks allowed to 100
001130 -5.6.2- minor bug fix; new VRml CLose_file command
010122 - 6.0 - use C routines to do dynamic memory allocation
and port to Linux
010704 -6.0.1- SImilarity command provides a bit more information
010806 - X - added some example figures to demonstrate some of
the options that produce plots
011025 -6.0.2- minor changes
011130 -6.0.3- minor bug fix
020513 -6.0.4- max number of (bones) atoms to generate masks around
increased from 100000 to 500000
030227 - X - added information about the various formats
030915 - 6.1 - new GTranslate command
040701 -6.1.1- changed checks of dynamic memory allocation to allow
for pointers with negative values as returned by
some recent Linux versions
050331 -6.1.2- added fudge margins to the OVerlap ASu_mask command;
added section to manual on how to generate masks for
solvent flattening
050428 - X - minor changes to the manual (description of getting
a solvent-flattening mask)
070508 -6.1.3- changed DOt_odl command so it can produce a file of
spheres instead of dots
070626 -6.1.4- the LIst command now also prints the centre-of-gravity
of a mask (in orthogonal coordinates)
071122 -6.1.5- increased maximum number of atoms to 1,500,000
071123 -6.1.6- print warning if HETATM cards (skipped!) in PDB file
071129 -6.1.7- BLob_erase command now has an optional parameter to
impose an upper limit on the size of blobs you want
to keep
071130 -6.1.8- minor bug fix
080625 -6.1.9- suppress error messages if more than 10 of them
From version 4.1 on, MAMA 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 GKMAMA to point to a MAMA macro file, e.g.:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- setenv GKMAMA /home/gerard/mama.init ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
From version 4.0 onward, MAMA allocates memory for masks dynamically. This means that you can increase the size and number of masks that the program can handle on the fly:
1 - through the environment variables MASKSIZE and NUMMASKS (must be in capital letters !), for example put the following in your .cshrc file:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- setenv MASKSIZE 5000000 setenv NUMMASKS 4 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
2 - by using command-line arguments MASKSIZE and NUMMASKS (need not be in capitals), for example:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- run mama masksize 20000000 nummasks 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 mask which is bigger than that, you can use the command-line argument(s).
From version 5.4 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.
MAMA needs space for NUMMASKS + 2 masks.
If you're tired of editing masks, don't call for your mother, but use MAMA ! MAMA is to masks what MOLEMAN is to PDB files.
With MAMA you can fill the voids that PDB_MASK and BONES_MASK leave in your masks, you can slightly extend your mask when you are putting in side chains in your poly-Ala search model or when X-PLOR has moved them around for you, you can take away parts of the mask which overlap with a neighbour molecule, etc. etc.
In addition, MAMA contains all the functionality of Alwyn's programs PDB_MASK, BONES_MASK, and MASK_NEW_GRID as well as options to remove overlap due to (NCS-) symmetry and to copy a mask from one space group to another.
The overlap tools can also be used to investigate close contacts between various molecules in the asymmetric unit due to (non-) crystallographic symmetry.
As a bonus, you are able to emulate Delaney's cavity-finding program (using "cellular logic methods"; see the example below).
MAMA allows you to work with upto EIGHT masks simultaneously ! You may either manipulate one mask or combine two of them. The wild-card character "*" can be used for most single-mask options if you want to carry out an operation for all masks in memory.
When you read a mask, 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 masks ! MAMA checks that you don't use duplicate mask names.
MAMA 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. MAMA will prompt you for the values of any parameters that were not supplied in this way.
MAMA runs in interactive mode by default. This means that if
(a) an input file can not be opened, MAMA will ask you what to do
(b) if you delete a mask which has unsaved changes, MAMA will
ask you if you're absolutely sure
(c) if you quit and there are masks with unsaved changes, MAMA
will ask you if you really want to quit
You may run MAMA in batch mode by supplying the command line option -b (or -batch). In that case, MAMA will crash if she can't open an input file and any unsaved changes (with QUIT or DELETE) are lost forever. You may want to use this mode if you run MAMA in batch (using an input script).
NOTE: all output files are opened as "UNKNOWN", which means that any existing files will be overwritten !
NOTE: this program is sensitive to the environment variable OSYM.
It should point to your local copy of $ODAT/symm, the directory
which contains the spacegroup symmetry operators in O format.
When asked for a file with spacegroup operators in O format,
you may either provide a filename, or the name of a sapcegroup
(including blanks if you like, case doesn't matter). The program
will try to open the following files, assuming that STRING is the
what you input:
(1) open a file called STRING
(2) if this fails, check if OSYM is defined and open $OSYM/STRING
(3) if this fails, open $OSYM/string.sym
(4) if this fails, open $OSYM/string.o
Hint: if you make soft links in the OSYM directory, you can also type
spacegroup numbers (e.g.: \ln -s p212121.sym 19.sym).
MAMA supports a number of different formats for both reading and writing masks. Upon reading, MAMA will recognise the type of format automatically. Upon writing, you can supply the format type as a parameter.
OMASK:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- .MASK_INPUT ! Created by MAMA V. 020513/6.0.4 at Thu Feb 27 18:32:36 2003 for gerard ORIGIN -10 2 35 EXTENT 94 100 117 GRID 80 90 144 CELL 45.0500 51.8500 79.9600 90.0000 90.0000 90.0000 COMPRESSED 106545 106547 106639 106641 106733 106735 [...] ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
COMPRESSED:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- COMPRESSED_MASK -10 2 35 Created by MAMA V. 020513/6.0.4 at Thu Feb 27 18:33:16 2003 for gerard 94 100 117 80 90 144 45.0500 51.8500 79.9600 90.0000 90.0000 90.0000 106545 106547 106639 106641 106733 106735 115850 115854 115944 115948 [...] ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
NEW:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- NEW_MASK ! Created by MAMA V. 020513/6.0.4 at Thu Feb 27 18:31:08 2003 for gerard ORIGIN -10 2 35 EXTENT 94 100 117 GRID 80 90 144 CELL 45.0500 51.8500 79.9600 90.0000 90.0000 90.0000 MAP 00000000000000000000000000000000000000000000000000000000000000000000000000000000 00000000000000000000000000000000000000000000000000000000000000000000000000000000 00000000000000000000000000000000000000000000000000000000000000000000000000000000 [...] ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
OEXPLICIT:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- .MASK_INPUT ! Created by MAMA V. 020513/6.0.4 at Thu Feb 27 18:32:54 2003 for gerard ORIGIN -10 2 35 EXTENT 94 100 117 GRID 80 90 144 CELL 45.0500 51.8500 79.9600 90.0000 90.0000 90.0000 EXPLICIT 00000000000000000000000000000000000000000000000000000000000000000000000000000000 00000000000000000000000000000000000000000000000000000000000000000000000000000000 00000000000000000000000000000000000000000000000000000000000000000000000000000000 [...] ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
OLD:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- -10 2 35 Created by MAMA V. 020513/6.0.4 at Thu Feb 27 18:33:28 2003 for gerard 94 100 117 80 90 144 45.0500 51.8500 79.9600 90.0000 90.0000 90.0000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 [...] ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The major difference between these formats is the size of the mask files produced and the time it takes to read or write them. For example, in one case:
- OLD format, 2227275 bytes, 2.5 CPU seconds
- OEX format, 1113831 bytes, 2.3 CPU seconds
- NEW format, 1113823 bytes, 2.3 CPU seconds
- COM format, 88816 bytes, < 1 CPU second
- OMA format, 88909 bytes, < 1 CPU second
When you start MAMA, she welcomes you with a list of available commands and options:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- *** MAMA *** MAMA *** MAMA *** MAMA *** MAMA *** MAMA *** MAMA *** MAMA ***Version - 070508/6.1.3 (c) 1992-2006 Gerard J. Kleywegt & T. Alwyn Jones, BMC, Uppsala (SE) 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 - Tue May 8 14:49:31 2007 User - gerard Mode - interactive Host - sarek (Irix/SGI) ProcID - 20390 Tty - /dev/ttyq17
*** MAMA *** MAMA *** MAMA *** MAMA *** MAMA *** MAMA *** MAMA *** MAMA ***
Reference(s) for this program:
* 1 * 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.
* 2 * G.J. Kleywegt & T.A. Jones (1993). Masks Made Easy. CCP4/ESF-EACBM Newsletter on Protein Crystallography 28, May 1993, pp. 56-59. [http://xray.bmc.uu.se/usf/factory_1.html]
* 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 & 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]
* 5 * 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]
* 6 * G.J. Kleywegt (1999). Experimental assessment of differences between related protein crystal structures. Acta Cryst. D55, 1878-1857. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=10531486&dopt=Citation] [http://scripts.iucr.org/cgi-bin/paper?se0283]
* 7 * 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.
* 8 * 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.
==> For manuals and up-to-date references, visit: ==> http://xray.bmc.uu.se/usf ==> For reprints, visit: ==> http://xray.bmc.uu.se/gerard ==> For downloading up-to-date versions, visit: ==> ftp://xray.bmc.uu.se/pub/gerard
*** MAMA *** MAMA *** MAMA *** MAMA *** MAMA *** MAMA *** MAMA *** MAMA ***
Allocate masks of size : ( 3000000) Max number of masks : ( 5)
Max nr of masks in memory : 5 Max nr of points in mask : 3000000 Max nr of symmetry operators : 180 Max nr of NCS RT operators : 180
Initialising : (XVRML - 20051205/0.8) Nr of predefined colours : ( 411)
Symbol START_TIME : (Tue May 8 14:49:31 2007) Symbol USERNAME : (gerard)
MAMA's options :
? (list options) ! (comment) @ macrofile QUit & symbol value & ? (list symbols) $ shell_command ZP_restart masksize nummasks ECho on_off # parameter(s) (command history)
REad maskname filename WRite maskname filename [how] DElete maskname LIst [maskname] DUplicate newmask oldmask NBr_count maskname UNite newmask mask1 mask2 SImilarity mask1 mask2 ODl maskname filename BOrder_check maskname DOt_odl maskname filename [radius] EZd maskname ezdfile LAbel mask text TRanslate mask tx ty tz GTranslate gx gy gz ATom_fit maskname pdbfile [pdb_inside] [pdb_outside] INvert_ncs infile outfile
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 maskname NEw RAdius value NEw RT_operator filename NEw FActor value NEw PAd p1 p2 p3 NEw SPacing value NEw REset_rt_operator NEw ENcompass oldmask
NEw PDb maskname pdbfile NEw BOnes maskname bonesfile NEw COpy mask oldmask NEw MAke maskname NEw UNit_cell mask oldmask NEw OLdbones maskname bonesfile NEw BAll mask x y z rad NEw CUbe mask x y z extent
FIll_voids maskname ISland_erase maskname EXpand maskname [cycles] SMooth maskname factor [cycles] COntract maskname [cycles] CUt maskname factor [cycles] NOt maskname BLob_erase maskname min_size
ANd mask1 mask2 OR mask1 mask2 BUtnot mask1 mask2 XOr mask1 mask2
OVerlap ? (list status) OVerlap SYmm_op filename OVerlap ORigin o1 o2 o3 OVerlap EXtent e1 e2 e3 OVerlap NCs_rt filename OVerlap REset_ncs OVerlap MOde mode_type OVerlap UNit_cell mask factor trim nextra [ezdf] OVerlap TRim mask factor [ezdf] OVerlap ERase mask factor [ezdf] OVerlap EZd mask ezdfile OVerlap ASu_mask newmask oldmask [f1 f2 f3]
VRml SEtup central_atom max_dist backgr_col default_col VRml INit [filename] VRml COlour_list VRml DOt_surface mask [colour] VRml TRace pdb_file [colour] VRml CEll mask [colour] [line_solid] [x_offset] [y_offset] [z_offset] VRml BOx mask [colour] [line_solid] VRml CLose_file
Max nr of masks in memory : 5 Max nr of points in mask : 3000000 Max nr of symmetry operators : 180 Max nr of NCS RT operators : 180
Execute initialisation macro : (/home/gerard/mama.init) ... Opened macro file : (/home/gerard/mama.init) ... On unit : ( 61) Command > (! MAMA initialisation macro) Command > (echo on) 1 @ /home/gerard/mama.init 2 ! MAMA initialisation macro 3 echo on ... End of macro file ... Control returned to terminal ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAMA > $ xterm & MAMA > $ 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 -----
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 ----- MAMA > & ? Nr of defined symbols : ( 4) Symbol PROGRAM : (MAMA) Symbol VERSION : (960517/3.8) Symbol START_TIME : (Fri May 17 20:21:40 1996) Symbol USERNAME : (gerard) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The symbol mechanism is fairly simplistic and has some limitations:
- max length of a symbol name is 20 characters
- max length of a symbol value is 256 characters
- max number of symbols is 100
- symbols can not be deleted, but they can be redefined
- symbol values are accessed by supplying $SYMBOL_NAME as an
argument on the command line; the line that you type on the terminal
(or in a macro) is parsed once; if there are additional parameters
which the program prompts you for, you cannot use symbols for those
- only one substitution per argument (e.g., "$file1 $file2" will
lead to a substituion of the entire argument by the value of
symbol FILE1 only !)
- command names (first argument on any command line) cannot be
replaced by a symbol (e.g.: "$command $arg1 $arg2" is not valid)
- symbols may be equated to each other, e.g. "& file2 $file1" will
give FILE2 the same value as FILE1
- symbol substitution is not recursive (e.g., if you set the value
of FILE2 to be "$file1", any reference to $FILE2 will be replaced
by "$file1", not by the value of FILE1
- symbols on comment lines (starting with "!") are not expanded
- symbols on system command lines (starting with "$") are not expanded
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAMA > wr m1 test.mask com Writing mask (compressed format) Grid points : ( 360594) Stretches : ( 1458) Mask points : ( 30854) Mask write OK ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAMA > re m2 cavity_2.mask [...] MAMA > dot m2 cav2s.odl 0.1 Sphere radius (A): ( 0.100) ODL file written Nr of mask points : ( 986) Nr of surface dots : ( 456) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
An ODL file with dots looks like this:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- begin mdot colour magenta dot 11.900 20.300 21.700 dot 11.900 20.300 22.400 [...] dot 18.900 25.200 22.400 dot 18.900 25.200 23.100 end_object ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
An ODL file with spheres looks like this:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- begin sdot colour cyan sphere_xyz 11.900 20.300 21.700 0.100 sphere_xyz 11.900 20.300 22.400 0.100 [...] sphere_xyz 18.900 25.200 22.400 0.100 sphere_xyz 18.900 25.200 23.100 0.100 end_object ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAMA > delet m1 WARNING - unsaved changes to mask M1 !!! Really DELETE this mask (Y/N) ? (N) y Deleted : (M1) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAMA > li m6 Nr of masks in memory : ( 1)Mask 1 = M6 File = tomcat.mask Grid = 100 100 100 Origin = 0 0 0 Extent = 99 99 99 Cell = 50.000 50.000 50.000 90.000 90.000 90.000 Nr of points = 970299 Set = 91154 ( 9.39 %) Cell volume = 1.250E+05 Voxel = 1.250E-01 Grid volume = 1.213E+05 Mask = 1.139E+04 Centre-of-gravity (A) = 26.755 25.000 25.831 Spacing = 0.500 0.500 0.500 Top = 98 98 98 Changes = F Label = Read from tomcat.mask ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
From version 6.0.1 on, this command prints some more information.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAMA > si m2 m3 Command > (si m2 m3) Similarity Mask : (M2) Similarity Mask : (M3) Lower limits common volume : ( 23 35 -1) Upper limits common volume : ( 86 105 75) Limits first mask : ( 13 76 13 83 12 88) Limits second mask : ( 1 64 1 71 1 77) Number of common mask points : ( 349888) Nr of points in common grid : ( 349888) Nr of points set in mask 1 = N1 : ( 88991) Nr of points set in mask 2 = N2 : ( 30250) Nr of points set in both = N12 : ( 30250)Tanimoto index = N12 / (N1+N2-N12) : ( 0.340) Similarity index = N12 / SQRT(N1*N2) : ( 0.583) Sim index 2 = 2*N12 / (N1+N2) : ( 0.507) Fraction common mask 1 = N12 / N1 : ( 0.340) Fraction common mask 2 = N12 / N2 : ( 1.000)
AND mask1 mask2 = N12 : ( 30250) OR mask1 mask2 = N1+N2-N12 : ( 88991) BUTNOT mask1 mask2 = N1-N12 : ( 58741) BUTNOT mask2 mask1 = N2-N12 : ( 0) XOR mask1 mask2 = N1+N2-2*N12 : ( 58741) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
From version 4.2 onward, this command checks both ATOM and HETATM atoms. In addition, there are two new optional parameters, namely a PDB file for all atoms inside the mask, and a PDB file for all atoms outside the mask. You could use this to find all internal water molecules in your model, for example.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAMA > at m1 1cbs.pdb inside.pdb outside.pdb Checking atoms with radius : ( 2.000) ERROR - C1 REA 200 not covered by the mask ERROR - C2 REA 200 not covered by the mask ERROR - C3 REA 200 not covered by the mask ERROR - C16 REA 200 not covered by the mask ERROR - O HOH 304 not covered by the mask ERROR - O HOH 311 not covered by the mask ERROR - O HOH 315 not covered by the mask ERROR - O HOH 316 not covered by the mask ERROR - O HOH 318 not covered by the mask ... ERROR - O HOH 398 not covered by the mask ERROR - O HOH 399 not covered by the mask Nr of atoms read : ( 1213) Nr covered by the mask : ( 1141) Below lower grid bounds : ( 0) Above upper grid bounds : ( 0) Nr not covered by mask : ( 72) ERROR --- Mask too tight ! CPU total/user/sys : 1.4 1.4 0.0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAMA > tr m1 Old origin : ( 21 34 -1) Grid : ( 100 110 64) Nr of unit cells translation in X ? (0) 1 Nr of unit cells translation in Y ? (0) -1 Nr of unit cells translation in Z ? (0) 2 New origin : ( 121 -76 127) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAMA > 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 mask and your model/data. Only use this option if you understand this and know what you are doing ...
Old origin : ( 121 -76 127) Grid : ( 100 110 64) Nr of GRID POINTs translation in X ? (0) -21 Nr of GRID POINTs translation in Y ? (0) 76 Nr of GRID POINTs translation in Z ? (0) -127 New origin : ( 100 0 0) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAMA > inv Input NCS file ? ( ) ab.rt Output NCS file ? ( ) inv.rt==> Read NCS operator : (.LSQ_RT_M1_TO_M1)
...
Nr of NCS operators to invert : ( 1)
***** Operator nr 1 *****
Nr of RT operators : 1
RT-OP 1 = 0.3884420 0.0835182 0.9176806 -16.778 0.1145766 0.9837781 -0.1380325 25.467 -0.9143222 0.1587623 0.3725714 66.911 Determinant of rotation matrix 1.000000 Column-vector products (12,13,23) 0.000000 0.000000 0.000000 Crowther Alpha Beta Gamma 171.446 -68.126 -170.149 Spherical polars Omega Phi Chi 89.041 80.798 68.137 Direction cosines of rotation axis 0.159898 0.986992 0.016733 Dave Smith -159.671 -156.110 167.866 X-PLOR polars Phi Psi Kappa 174.026 170.748 68.137 Lattmann Theta+ Theta2 Theta- -1.297 68.126 -198.405 Rotation angle 68.137
***** INVERSE Operator nr 1 *****
Nr of RT operators : 1
RT-OP 1 = 0.3884419 0.1145766 -0.9143222 64.778 0.0835182 0.9837780 0.1587623 -34.276 0.9176804 -0.1380325 0.3725714 -6.017 Determinant of rotation matrix 1.000000 Column-vector products (12,13,23) 0.000000 0.000000 0.000000 Crowther Alpha Beta Gamma 170.149 68.126 -171.446 Spherical polars Omega Phi Chi 90.959 -99.202 68.137 Direction cosines of rotation axis -0.159898 -0.986992 -0.016733 Dave Smith -23.080 23.411 -16.434 X-PLOR polars Phi Psi Kappa -5.974 -170.748 68.137 Lattmann Theta+ Theta2 Theta- 1.297 68.126 161.595 Rotation angle 68.137
Nr of NCS operators written : ( 1) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
MAMA > new rt rt_error_imp.o
NEW RT-operator : ( 0.392 0.082 0.916 0.113 0.984
-0.137 -0.913 0.158 0.377 64.649 -34.211 -6.153)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAMA > new same m1 MAMA > new enc m2 Current NEw ORigin : ( 4 38 -16) Current NEw EXtent : ( 43 54 49) Current mask origin : ( -4 32 -27) Current mask extent : ( 60 67 74) New origin : ( -4 32 -27) New extent : ( 60 67 74) MAMA > new make New mask ? (M3) m9 Nr of points set : ( 0) CPU total/user/sys : 1.6 1.6 0.0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAMA > new spa 0.8 NEW grid : ( 146 153 103) MAMA > new grid 144 156 104 NEW grid : ( 144 156 104) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
As of version 6.1.7, there is an optional parameter to impose an upper limit on the size of blobs you want to keep as well.
These options combine two masks, but they alter only one.
If you combine two masks, both must have unit cell constants
which are identical to within 0.01 A and 0.01 degrees ! Also,
both must be on the SAME grid and they must have a non-zero overlap.
Only points inside the common volume are compared; the others
(if any) are NOT affected !
Furthermore, MASK1 and MASK2 may not be identical.
In all cases, the result of the operation is stored in MASK1 !
Use the SIMILARITY option first if you want to get an idea of
what will happen to your mask when you use one of these options.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAMA > and m1 m7 ERROR --- Masks have different cell constants MAMA > and m1 m4 Mask : (M1) And Mask : (M4) Nr of points set before : ( 30854) Lower limits common volume : ( 31 45 8) Upper limits common volume : ( 78 97 68) Limits first mask : ( 11 58 12 64 10 70) Limits second mask : ( 1 48 1 53 1 61) Number of common mask points : ( 155184) Nr of points set after : ( 27761) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
When used while your brain is active, these options are very powerful. They allow you to trim your mask in places where it overlaps with (non-) crystallographically related mates or to visualise places in the structure where a molecule might interact with a (NCS-) symmetry-related partner. See the HINTS at the end of this manual for clever tricks that help you find such contacts !
The overlap commands require careful input ! In particular, you should define the asymmetric unit of your unit cell very accurately !
The overlap option works as follows:
- it creates an "overlap map" the size of your asymmetric unit
- each point in the mask is subjected to ALL the NCS operators
and forced into the asymmetric unit (by applying the symmetry
operators of your space group); the point it ends up on is
marked in the overlap map
- the overlap map is then processed so that it contains a
count of the number of times a mask point ended up at a
particular place in the asymmetric unit
- this new overlap map is "averaged" inside the mask, except that
the counts are ADDED instead of averaged; this means, that
if you have three molecules in the asymmetric unit, points
without overlap will get a value of round about three (this
is "round about" since the operators lead to non-integer
grid points which have to be interpolated)
- if you do OVERLAP ERASE, all mask points which have a count
higher than the value you supply will be removed from the
mask. This value MUST be larger than the number of NCS
operators; we recommend this number plus one.
- if you are wise, you don't use the ERASE option but rather
the TRIM option ! If there is overlap, this means that
two different parts of the mask end up in the same place
after applying the NCS and/or symmetry operators and BOTH
places will be "flagged" as giving rise to overlap. Using
ERASE removes both parts but this will usually be too much.
It is better to remove only points at the mask SURFACE which
have overlap since this may be sufficient to get rid of (most
of) the overlap ! This is exactly what TRIM does for you !
It is recommended that you use TRIM two or three times in
succession to remove all of the overlap without cutting too
much off your mask.
Note: from version 5.2 on, there is a new command, OVerlap UNit_cell, which is easier to use than OV TRim and OV ERase, and which should be spacegroup-general.
If you want to make an informed decision, here are the algorithms:
*1* in both cases, all NCS operators are applied to each of the mask points. The resulting point will in general be non-integral; therefore the eight nearest points are flagged as follows:
2A* in LABEL mode, each point is OR-ed with 2**N, where N is the number of the NCS operator (modulo 32, since we use 4-byte integers for the overlap map). Thus, this option counts for each point in the asymmetric unit WHICH operators give rise to this point, BUT NOT how often they do that, AND NOT if the number of NCS operators is greater than 31 !!! As a consequence, if you have only one NCS operator (e.g., a tetramer in the asymmetric unit for which you want to use proper symmetry), this option is useless, since each flagged point will obviously be considered to arise from operator number 1, but it is impossible to figure out HOW OFTEN a mask point gave rise to this point, i.e. to detect overlap. In general, any overlap between the mask under operator N and itself will go undetected !! On the other hand, if you have more than 31 operators, the ultimate count MAY be an underestimation of the actual overlap.
2B* in COUNT mode, for each "hit" point in the asymmetric unit a simple counter is incremented. Since each mask point, under each NCS operator, will give rise to the flagging of EIGHT points in the asymmetric unit, you would expect that a normal, non-overlapping point would be flagged around eight times. For this reason, the accumulated counters are divided by eight afterwards, so as to get numbers comparable to those obtained with the LABEL algorithm.
*3* for the ezd, trim and erase options, the asymmetric unit in which each point contains a counter (LABEL: an estimate of the number of NCS operators that "hit" that point; COUNT: the number of times that point is "hit", divided by eight) is projected back onto the mask, but rather than "averaging", the counters (obtained after interpolation) are accumulated. At the end of that, each well-behaved mask point would be expected to contain an overlap count close to the number of NCS operators (this can be used to decide on a proper cut-off to use for the trim and erase options).
NOTE: from version 3.0 onward, you may add ONE, TWO or THREE points on all sides (must be the same number of extra points for each direction !). This turns out to be necessary for "pathetic" spacegroups such as R23 where the asymmetric unit runs from 0-1/3, 0-1/3, 0-1/2.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAMA > ov sym symop.o Nr of symmetry operators : ( 4) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAMA > ov reset_ncs Nr of NCS RT operators : ( 0) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAMA > ov ncs rt_unit.o New NCS RT operator : ( 1) MAMA > ov ncs rt_error_imp.o New NCS RT operator : ( 2) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAMA > ov ncs allncs.o==> Read NCS operator : (.LSQ_RT_M9A_TO_A)
Nr of NCS operators : 1
NCSOP 1 = 1.0000000 0.0000000 0.0000000 0.000 ... Rotation angle 0.000000
==> Read NCS operator : (.LSQ_RT_M9A_TO_B)
Nr of NCS operators : 1 ... Rotation angle 179.490646
==> Read NCS operator : (.LSQ_RT_M9A_TO_C)
Nr of NCS operators : 1 ... Rotation angle 179.362045
==> Read NCS operator : (.LSQ_RT_M9A_TO_D)
Nr of NCS operators : 1 ... Nr of NCS operators now : ( 4) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
NOTE: in the output of OVERLAP EZD, TRIM and ERASE there are
some checks as to whether or not you have picked a
proper asymmetric unit. First, there's the number of
grid points: the number of points in your asymmetric
unit TIMES the number of crystallographic symmetry
operators MUST be equal to the calculated number of
grid points in your unit cell. (Don't worry, MAMA
knows that you have added an extra point in all three
directions !)
Second, the routine that calculates the overlap map
prints something like:
Nr of errors in FRC2V : ( 0)
This is a count of the number of points which could not
be brought into your asymmetric unit by applying your
symmetry operators. If this number is not zero, you
either have a wrong asymmetric unit, or a wrong set of
symmetry operators.
Similarly, the "averaging" routine prints:
Severe FRCSYM errors : ( 0)
Again, if this number is non-zero, you made an error.
See the example for the OVERLAP TRIM option.
Finally, MAMA prints which part of the unit cell will
be checked:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Checking the following part of the unit cell :
Start in fractional coordinates : ( 0.000 0.000 0.000)
End in fractional coordinates : ( 0.500 0.500 1.000)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Naturally, these limits should coincide with those of the asymmetric unit you had in mind (check the International Tables when in doubt).
NOTE: the origin of the new mask will be the same as that of the asymmetric unit; its extent will normally be that of the asymmetric unit minus 1, 2 or 3 points in all three directions. However, if your solvent-flattening software complains that your mask doesn't cover an entire asymmetric unit, you can add 0 or 1 points in any or all directions with the fudge margin parameters (default is 0 for all three). For instance, for P212121 in CCP4, the asymmetric unit is 0-1, 0-1, 0-1/4. In order for the OVerlap ASu_mask option to give a proper asymmetric unit, you must use fudge margins of 0, 0, 1.
NOTE: since the asymmetric-unit mask is generally not a continous "blob", you should NOT use the regular "clean-up" commands such as COntract, ISland_erase and EXpand on it !!!
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAMA > over asu m2 m1 0 0 1 ASU Mask : (M2) Fudge margins : ( 0 0 1) Assume margin (extra points) : ( 1) Nr of points in unit cell : ( 704000) Nr in your asymmetric unit : ( 176000) Nr of symmetry operators : ( 4) Asymm. unit * symm. opers. : ( 704000) Extra points at all sides : ( 1) Creating overlap map (mode COUNT) ... Nr of symmetry operators : ( 4) Nr of NCS RT operators : ( 3) Checking the following part of the unit cell : Start in fractional coordinates : ( 0.000 0.000 0.000) End in fractional coordinates : ( 1.000 1.000 0.250) ... Busy ... Expanding mask ... Nr of errors in FRC2V : ( 0) Counting ... Counts for asymmetric unit : Nr of points set 0 to 1 times : 45378 Nr of points set 1 to 2 times : 66977 Nr of points set 2 to 3 times : 59 Nr of suspect points : 59 Nr of points in solvent areas .......... 78173 Solvent areas as %-age of asymm. unit .. 41.02 ASU extent : ( 100 110 17) Nr of points set : ( 98046) CPU total/user/sys : 10.1 10.1 0.0 MAMA > li m2 Nr of masks in memory : ( 2)Mask 2 = M2 File = not_defined Grid = 100 110 64 Origin = 0 0 0 Extent = 100 110 17 Cell = 91.800 99.500 56.500 90.000 90.000 90.000 Nr of points = 187000 Set = 98046 ( 52.43 %) Cell volume = 5.161E+05 Voxel = 7.331E-01 Grid volume = 1.371E+05 Mask = 7.187E+04 Spacing = 0.918 0.905 0.883 Top = 99 109 16 Changes = T Label = No comment ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This command ignores the OV ORigin and OV EXtent settings, instead using a fixed origin of (0,0,0), and calculating the extent of your unit cell from the grid of the mask on which you work. The OV MOde is used however, so you can still use LABEL and COUNT modes. Also, the NCS and symmetry operators must still be provided.
The OVerlap UNit_cell command has the following parameters:
- mask = name of the mask for which you want to remove overlap
- factor = the overlap cutting factor (same as for the OV ERase
and OV TRim commands)
- trim = the surface cutting factor: only overlapping mask points
with at least "trim" non-mask neighbours (0 to 26) will be removed
from the mask. In the OV TRim command, this number is always fixed
at 1, in the OV ERase command, it is always 0. Here, you can set
it yourself, enabling you to emulate both the TRim and ERase
behaviours, but allowing more flexibility by letting you set the
precise number yourself. (Note: this "trim" parameter is the same
as the "factor" parameter of the CUt command.)
- nextra = number of extra points that will be added on all sides
of the unit cell (sometimes necessary; a value of 1 or 2 is
recommended)
- ezdfile = optional; see the OV TRim and ERase commands
At present, the easy way to remove overlap is as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! read the mask re m1 coma_okay.mask li m1 ! define spacegroup symmetry ov sym p212121 ! define all NCS operators ov ncs rt_unit.o ov ncs rt_a_to_b.o ov ncs rt_a_to_c.o ! list settings ov ? ! remove overlap (three cycles) ov un m1 4.0 5 2 ov un m1 4.0 5 2 ov un m1 4.0 5 2 ! clean up the mask a bit contract m1 island m1 expand m1 ! save the new mask wr m1 coma_ovtrim.mask ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAMA > ov un m1 4.0 5 2 Unit-cell-based overlap removal for mask : (M1) Nr of points set before : ( 29669) Unit cell origin : ( 0 0 0) Unit cell grid : ( 100 110 64) Unit cell extent : ( 102 112 66) Unit cell spacing (A) : ( 0.918 0.905 0.883) Nr of points in unit cell : ( 704000) Nr of extra points for grid : ( 2) Nr of unit cell grid points : ( 753984) Creating overlap map (mode COUNT) ... Nr of symmetry operators : ( 4) Nr of NCS RT operators : ( 3) Checking the following part of the unit cell : Start in fractional coordinates : ( 0.000 0.000 0.000) End in fractional coordinates : ( 1.010 1.009 1.016) ... Busy ... Expanding mask ... Nr of errors in FRC2V : ( 0) Counting ... Counts for asymmetric unit : Nr of points set 0 to 1 times : 156667 Nr of points set 1 to 2 times : 241448 Nr of points set 2 to 3 times : 1688 Nr of suspect points : 1688 Nr of points in solvent areas .......... 354181 Solvent areas as %-age of asymm. unit .. 46.97 "Averaging" overlap map ... Map Cell : ( 91.800 99.500 56.500 90.000 90.000 90.000) Spacing : ( 0.918 0.905 0.883) Map origin : ( 0 0 0) Map extent : ( 102 112 66) Mask origin : ( 25 39 -8) Mask extent : ( 78 63 79) FORGN : ( 0.000 0.000 0.000) FEXT : ( 1.010 1.009 1.016) GEXT : ( 1.000 1.000 1.000) ... Busy ... Nr of boundary points : ( 0) Severe FRCSYM errors : ( 0) Counting neighbours ... Removing overlapping mask points ... Min count for removal : ( 4.000) Min nr of nbrs outside mask : ( 5) Points with count 0 - 1 = 31 Points with count 1 - 2 = 1681 Points with count 2 - 3 = 14356 Points with count 3 - 4 = 12728 Points with count 4 - 5 = 659 Points with count 5 - 6 = 213 Points with count 6 - 7 = 1 Total nr of mask points : ( 29669) Suspicious mask points : ( 873) Percentage suspicious : ( 2.942) Nr of mask points removed : ( 172) Percentage removed : ( 0.580) Nr of points set after : ( 29497) CPU total/user/sys : 16.6 16.5 0.1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
From version 5.0 on, MAMA 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 MAMA, 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 DOt mask
- VRml TRace pdbfile
- VRml CEll mask
- VRml BOx mask
- VRml CLose_file
The VRML interface was written for two purposes:
- quick inspection of masks and models (much quicker than
first writing them, then reading them into O, etc.; also,
not all MAMA users have access to O); since you can write
any number of masks and molecules to a VRML file you can
quickly see the results of mask improvement operations,
you can compare different masks, etc.
- creating files with masks 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 !)
The options have been kept simple and fast. For fancier pictures of molecules you should use dedicated software (e.g., all-atom ball-and-stick models). Masks are drawn as hollow sets of points (i.e., dot surfaces).
Example of a VRML display generated with MAMA.
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 ----- MAMA > vr set " CA " 4.5 white "0.35 0.87 1.0" Central atom type : ( CA) Max central atom distance : ( 4.500) Background colour : (1.000000 1.000000 1.000000) Default colour : (0.3500000 0.8700000 1.000000) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAMA > vr se Central atom type ? ( CA) Central atom type : ( CA) Max central atom distance ? ( 4.500000) Max central atom distance : ( 4.500) Background colour ? (1.000000 1.000000 1.000000) grey Background colour : (0.5000000 0.5000000 0.5000000) Default colour ? (0.3500000 0.8700000 1.000000) red Default colour : (1.000000 0.0000000E+00 0.0000000E+00) ----- 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 DOt and VRml TRace commands
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAMA > vr in Open VRML file : (mama.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 ----- MAMA > vr close Command > (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 ----- MAMA > vr co 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 mask you select to the current VRML file in the colour you indicate (if any). Only the surface points are written (to keep the files small).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAMA > vr ini Closed VRML file Open VRML file : (mama.wrl) Opened VRML file MAMA > vr do m2 green VRML - Dot surface for mask M2 Nr of points written : ( 13227) CPU total/user/sys : 2.1 2.0 0.0 ----- 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 ----- MAMA > vr tr /nfs/pdb/full/1cbs.pdb yellow VRML - Trace of CA atoms for PDB file /nfs/pdb/full/1cbs.pdb Nr of atoms written : ( 137) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Adds a unit cell. You must supply the mask 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 ----- MAMA > vr cel m1 green line -1 1 0 VRML - Cell for mask M1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Adds the box of a selected mask. This can be helpful to see if the mask extends close to the borders of its grid.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- MAMA > vr box m1 purple VRML - Box for mask M1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The following options accept the wildcard character "*", i.e.,
if you type an asterisk instead of a maskname, the operation
will be carried out for ALL masks in memory:
LIST, DELETE, FILL_VOIDS, ISLAND_ERASE, NBR_COUNT, BORDER_CHECK,
SMOOTH, EXPAND, CUT, CONTRACT and NOT.
Fortran code for reading/writing masks is available from the O ftp-server (directory pub/gerard/extras/fortran).
Generating a mask for solvent flattening is quite different from generating a mask for averaging. In the former case, the mask should cover one or more asymmetric units, and depending on the distribution of the molecules, it will usually be discontinous (different parts of your molecule will be in different places in the asymmetric unit). In the latter case, the mask is continuous and thus tools that assume this can be used (e.g., EXpand, COntract and ISland_erase).
If you don't have an atomic model yet, but you do have a mask from averaging (e.g., from COMA), you can generate a solvent-flattening mask by expanding the mask (under non-crystallographic and crystallographic symmetry) to fill an asymmetric unit.
If you do have an atomic model, you can proceed in two different ways:
- first symmetry-expand the model, then generate the mask (this has the advantage that it can also be used to generate a mask around an entire unit cell). For this you will need the USF programs MAMA (version 6.1.2 or later) and XPAND (version 1.7.1 or later)
- first generate the mask from the model, then symmetry-expand it (this has the advantage that you can improve the mask before you expand it with COntract etc.). For this you will need MAMA (version 6.1.2 or later)
Whichever method you use, you must begin by establishing the precise definition of the asymmetric unit that the programs you will be using expect. For instance, in P212121 the CCP4 programs insist you select your asymmetric unit as 0-1, 0-1, 0-1/4 (and not as 0-1/2, 0-1/2, 0-1, which is an equally valid choice purely crystallographically).
Next, you need to decide or find out what grid you are going to use, and from that calculate the extent of your asymmetric unit in grid points.
In the following, we shall discuss the two cases (first mask, then expansion, versus first expansion, then mask) separately.
Thanks to Erik Vogan and Venki Ramakrishnan for useful comments.
Venki Ramakrishnan suggested a third method which is to generate a model map (e.g., with SFALL if you use CCP4) and to convert that into a mask. Perhaps this is the easiest way to do it :-) For more details, see the manual of the CCP4 program MAPMASK.
If you have a mask, either from earlier round of NCS averaging, or generated from an atomic model (e.g., an initial model you built, or a molecular replacement solution), then you can simply expand it under (non-)crystallographic symmetry with MAMA to get a mask that covers the asymmetric unit.
In the following example, we use the P2 myelin data that are distributed with RAVE and O. This is what we have:
- cell = 91.8 99.5 56.5 90 90 90
- spacegroup = P212121
- grid 100 110 64
In this case, we have a mask around one molecule (in a file called p2.mask) and three-fold NCS (with NCS operators in O format in files called rt_unit.o, rt_a_to_b.o and rt_a_to_c.o). If you don't have NCS, all you need is the unit operator which looks like this:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
unit_operator R 12 (3f15.7)
1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
0.0000000 0.0000000 0.0000000
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
In spacegroup P212121, CCP4 wants the asymmetric unit to be 0-1, 0-1, 0-1/4, i.e. if the origin is 0, 0, 0 then the extent of the asymmetric unit in grid points is 100 110 16. In fact, CCP4 wants an extra point in the C direction, so this should be 17 instead of 16.
The following MAMA recipe will generate our asymmetric unit mask (make sure to check the write-up for each command elsewhere in this manual !):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! read the "molecular mask" read m1 p2.mask ! choose overlap mode "count" ov mode count ! origin of ASU is 0 0 0 ov origin 0 0 0 ! the extent should be 100 110 16 PLUS 1, 2, or 3 points added ! in each direction ov ext 101 111 17 ! spacegroup operators ov sym p212121 ! reset NCS operators ov reset ! read all NCS operators (they could also be in one file); ! if you don't have NCS, supply the unit operator ov ncs rt_unit.o ov ncs rt_a_to_b.o ov ncs rt_a_to_c.o ! now generate the asymmetric-unit mask. we need to fudge the ! extent of this mask by 1 point along C for CCP4 over asu m2 m1 0 0 1 ! check that the mask is okay li m2 ! save it wr m2 p2_asu.mask ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
At this stage, you probably want to check the mask in O. When you're happy, convert it to CCP4 format and perhaps expand it to cover an entire unit cell:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- mama2ccp4 maskin p2_asu.mask maskout mama_ccp4.msk mapmask mskin mama_ccp4.msk mskout mama_ccp4_cell.msk << EOF SYMM P212121 XYZLIM CELL END EOF ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
If you have an appropriate atomic model (i.e., you shouldn't be missing any domains or loops in this model, or the corresponding areas in the map will be flattened during the solvent flattening !), you can first expand that into slightly more than an asymmetric unit or unit cell. The reason why we need to cover slightly more than the asymmetric unit or unit cell is that atoms that lie just outside it will still contribute to the mask (if you use a masking radius of 3 Å, you will need a margin of at least that much on all sides - divide by the cell axis lengths to find out how much that is in fractional coordinates, and err on the side of caution).
For the expansion we will use the XPAND program (option "F"):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Task ? (N) d Input PDB file ? (in.pdb) 1pmp.pdbReading PDB file ... CRYST1 card found : (CRYST1 91.800 99.500 56.500 90.00 90.00 90.00 P 21 21 21 12 1PMP 178) Cell axes (A) : ( 91.800 99.500 56.500) Cell angles (deg) : ( 90.000 90.000 90.000) Spacegroup name : (P 21 21 21) SGS operator file : (p212121.sym)
Task ? (D) f Input PDB file ? (1pmp.pdb) Output PDB file ? (out.pdb) asu.pdb SGS operator file ? (p212121.sym) OSYM : (/home/gerard/oinfo/symm/) Opened file : (/home/gerard/oinfo/symm/p212121.sym) Opening O datablock : (/home/gerard/oinfo/symm/p212121.sym) O-style symm-ops for spacegroup P212121 19 4 4 P212121 PG222 ORTHORHOMBIC 'P 21 21 21' Datablock : (.SPACE_GROUP_OPERATORS) Data type : (R) Number : (48) Format : ((3F15.6)) Nr of SGS operators : ( 4)
Nr of spacegroup symmetry operators : 4
[...]
Cell constants ? ( 91.800 99.500 56.500 90.000 90.000 90.000) Select option: M = apply to the Molecule as a whole A = apply to each Atom individually Option (M/A) ? (M) a Max allowed fractional range [-1,+2> Fractional lower limits ? ( 0.000 0.000 0.000) -0.1 -0.1 -0.1 Fractional upper limits ? ( 1.000 1.000 1.000) 1.1 1.1 0.35
Reading PDB file ...
Nr of lines read : ( 3440) Nr of atoms read : ( 3192)
Nr of atoms written : ( 8367) Nr of lines written : ( 8615)
Off-spring counts : Nr of atoms with 6 off-spring = 59 Nr of atoms with 5 off-spring = 87 Nr of atoms with 4 off-spring = 375 Nr of atoms with 3 off-spring = 1084 Nr of atoms with 2 off-spring = 1239 Nr of atoms with 1 off-spring = 348 Nr of atoms with 0 off-spring = 0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
So now we have a PDB file that contains all atoms in the range -0.1 -> +1.1, -0.1 -> +1.1, -0.1 -> +0.35 (in fractional coordinates). The next step is to generate a mask around these atoms, and then to carve out precisely one asymmetric unit. This we do with MAMA, and the recipe is:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! define the cell constants new cell 91.8 99.5 56.5 90 90 90 ! define the grid new grid 100 110 64 ! define the masking radius around the atoms new rad 3.0 new ? ! generate the mask from the (more than one) asymmetric unit ! full of atoms generated with XPAND new pdb m1 asu.pdb li m1 ! define the origin of the asymmetric unit new origin 0 0 0 ! define the extent of the asymmetric unit that your solvent-flattening ! software expects (here: 0-1, 0-1, 0-1/4 + 1 point for CCP4 P212121) new extent 100 110 17 ! copy the corresponding part of the first mask we generated new copy m2 m1 li m2 wr m2 p2_xpa.mask ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
At this stage, you probably want to check the mask in O. When you're happy, convert it to CCP4 format and perhaps expand it to cover an entire unit cell:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- mama2ccp4 maskin p2_xpa.mask maskout mama_ccp4.msk mapmask mskin mama_ccp4.msk mskout mama_ccp4_cell.msk << EOF SYMM P212121 XYZLIM CELL END EOF ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
(1) Overlap removal doesn't work with pathetic asymmetric units which have borders defined as "y<x" etc.
(2) There is no provision for overlap removal when multiple domain masks are used.
Created at Thu Jun 26 11:57:38 2008
by MAN2HTML version 070111/2.0.8 . This manual
describes MAMA, a program of the Uppsala
Software Factory (USF), written and maintained by Gerard Kleywegt. © 1992-2007.