Program : MASKIT
Version : 990126
Author : Gerard J. Kleywegt & T. Alwyn Jones,
Dept. of Cell and Molecular Biology,
Uppsala University, Biomedical Centre, Box 590,
SE-751 24 Uppsala, SWEDEN
E-mail : gerard@xray.bmc.uu.se
Purpose : calculate cross-crystal correlation map to define a mask
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 (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.
* 3 * 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]
* 4 * G.J. Kleywegt & T.A. Jones (2037 ?). Convenient single and multiple crystal real-space averaging. To be published ???
* 5 * G.J. Kleywegt & T.A. Jones (1998 ?). Software for handling macromolecular envelopes. To be published.
* 6 * G.J. Kleywegt (1998 ?). Local density correlation and ... To be published.
* 7 * G.J. Kleywegt & T.A. Jones (1999 ?). Chapter 25.2.6. O and associated programs. Int. Tables for Crystallography, Volume F. To be published.
971222 - 0.1 - first version
980710 - 0.3 - first working version
990126 - 0.4 - FRCSYM and interpolation errors are no longer listed
(only their total number if any occured)
MASKIT is a program that calculates a correlation map between the densities of a molecule as found in two different crystal forms. It can be used if you want to define a mask for cross-crystal averaging.
MASKIT is *very* similar to COMA (which calculates correlation maps for NCS-related molecules), and for details of the algorithm and application of you are referred to the COMA manual.
You will need MASKIT (in addition to COMA) if you want to do electron-density averaging between different crystal forms, and one or more of these crystal forms does not contain NCS. In all other cases, COMA will do all you need (in combination with O, MAPMAN, and MAMA).
For example: if you have one crystal form with two molecules
and one with only one molecule, then:
- use COMA to define an NCS-based mask for the first crystal
form
- use MASKIT to define a mask based on the density of one
molecule in each crystal form
- use MAMA to combine the two masks into one that is valid
both for NCS (in the first crystal form) and for cross-crystal
averaging (between the two crystal forms).
If *all* your crystal forms contain NCS, you do not need MASKIT
(although it doesn't hurt and doesn't cost more than some
CPU time). For instance: if crystal form one has two-fold
NCS, and crystal form 2 has three-fold NCS, then:
- use COMA to define an NCS mask for crystal form 1
- use COMA to define an NCS mask for crystal form 2
- use the RT-operator between the two crystal forms to
transform one mask on top of the other (using the
NEw UNit_cell command in MAMA)
- use the tools in MAMA to combine the two masks into one
MASKIT is a quick-and-dirty program, in that it ignores any NCS that may be present in any of the crystal forms. Also, it will only work for two crystal forms at a time. If you have three or more, you will have to run MASKIT once for every additional crystal form.
In order to run MASKIT, you will need:
- CCP4 map of the unit cell (or asymmetric unit) of each
crystal form
- O-style symmetry operators for each crystal form
- the Cartesian operator that transforms the molecule
in crystal form 1 (your "reference molecule" for cross-crystal
averaging) on to the molecule in crystal form 2
- values for a few input parameters (see COMA manual)
The cross-crystal RT-operator can be obtained, e.g. from molecular replacement (e.g. using density from one of the crystal forms), or by superimposing partial models in the two crystal forms. Such operators can be improved with the program MAVE, if you like.
The output will be a local cross-crystal density correlation map that can be contoured in O (hint: correlation coefficients lie between -1.0 and +1.0; if you mappage the map, multiply it by 100 first), to find a good cut-off value. The map can then be converted into a mask with MAPMAN, and touched up (and combined with other masks) with MAMA.
Like COMA, MASKIT uses the algorithm of Randy Read as described in:
FMDAP Vellieux, JF Hunt, S, Roy & RJ Read, "DEMON/ANGEL: a suite of programs to carry out density modification", J. Appl. Cryst. 28, 347-351 (1995).
The following example uses data from two crystal forms of Candida antarctica lipase B (Uppenberg et al.), one monoclinic (P21) with two molecules per asymmetric unit, and one orthorhombic (P212121) with one molecule per asymmetric unit.
For details concerning the input, see the COMA manual !
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----...
*** MASKIT *** MASKIT *** MASKIT *** MASKIT *** MASKIT *** MASKIT ***
Allocate maps of size : ( 5000000) Allocate masks of size : ( 5000000) Allocate mini maps/masks of size : ( 500000)
Crystal form 1 - CCP4 map file ? ( ) ../p21_start.E Crystal form 1 - CCP4 map file : (../p21_start.E) Read header
...
Grid spacing (A): ( 0.957 1.052 0.985)
Crystal form 1 - Spacegroup symm-ops ? (symop.o) p21 Crystal form 1 - Spacegroup symm-ops : (p21) Try to open as : (p21)
...
SYMOP 2 = -1.0000 0.0000 0.0000 0.000 0.0000 1.0000 0.0000 0.500 0.0000 0.0000 -1.0000 0.000 Determinant of rotation matrix = 1.000000 Rotation angle = 180.000000
Crystal form 2 - CCP4 map file ? ( ) ../p212121_start.E Crystal form 2 - CCP4 map file : (../p212121_start.E) Read header
...
Origin (pts) : ( 0 0 0) Extent (pts) : ( 60 48 90)
Crystal form 2 - Spacegroup symm-ops ? (symop.o) p212121 Crystal form 2 - Spacegroup symm-ops : (p212121) Try to open as : (p212121)
...
SYMOP 4 = 1.0000 0.0000 0.0000 0.500 0.0000 -1.0000 0.0000 0.500 0.0000 0.0000 -1.0000 0.000 Determinant of rotation matrix = 1.000000 Rotation angle = 180.000000
Define the area where you expect your "reference" molecule to be in terms of fractional coordinates (applies to crystal form 1 !). Fractional search range A ? ( 0.000 0.500) -0.2 0.6 Fractional search range B ? ( 0.000 0.500) -0.4 0.9 Fractional search range C ? ( 0.000 0.500) 0 0.8 Fractional search range A : ( -0.200 0.600) Fractional search range B : ( -0.400 0.900) Fractional search range C : ( 0.000 0.800)
File with RT-operator FROM xtal 1 TO xtal 2 ? (or2or.rt) ../p21_to_p212121.o File with RT-operator FROM xtal 1 TO xtal 2 : (../p21_to_p212121.o) Opening O datablock : (../p21_to_p212121.o) Datablock : (.SPACE_GROUP_OPERATORS) Data type : (R) Number : (12) Format : ((3F15.6)) Operator : ( -0.113 0.677 0.727 -0.420 0.631 -0.652 - 0.900 -0.380 0.213 26.850 18.667 8.592)
Sphere radius ~ 1.5 * resolution of trusted phases Sphere radius (A) ? ( 4.300) 4.5 Sphere radius (A) : ( 4.500)
Output CCP4 correlation map file ? (maskit.E) Output CCP4 correlation map file : (maskit.E)
Output map grid : ( 45 34 58) Spacing (A) : ( 1.489 1.485 1.495)
Origin : ( -10 -14 -1) Extent : ( 39 46 49) Calculated output map size : ( 87906) Nr of mask points in sphere : ( 113) Progress (%) : ( 5.000) Progress (%) : ( 9.999) Progress (%) : ( 14.999) ERROR --- Serious FRCSYM error Mask point in reference : ( 11 8 9) ERROR --- Serious FRCSYM error Mask point in reference : ( 11 8 8) Progress (%) : ( 19.999)
...
Progress (%) : ( 94.994) Progress (%) : ( 99.993) Nr of points : ( 87906)
CRYSTAL FORM #1 --------------- Cell volume (A**3) : ( 2.888E+05) Voxel volume (A**3) : ( 3.254E+00) Bin 37 ... CC >= 0.85 Nr 54 Cum 54 Cum Vol 1.7574E+02 Solv Cont (%) 100 Bin 36 ... CC >= 0.80 Nr 370 Cum 424 Cum Vol 1.3799E+03 Solv Cont (%) 99 Bin 35 ... CC >= 0.75 Nr 1136 Cum 1560 Cum Vol 5.0770E+03 Solv Cont (%) 96 Bin 34 ... CC >= 0.70 Nr 1869 Cum 3429 Cum Vol 1.1160E+04 Solv Cont (%) 92 Bin 33 ... CC >= 0.65 Nr 2213 Cum 5642 Cum Vol 1.8362E+04 Solv Cont (%) 87 Bin 32 ... CC >= 0.60 Nr 2190 Cum 7832 Cum Vol 2.5489E+04 Solv Cont (%) 82 Bin 31 ... CC >= 0.55 Nr 1882 Cum 9714 Cum Vol 3.1614E+04 Solv Cont (%) 78 Bin 30 ... CC >= 0.50 Nr 1513 Cum 11227 Cum Vol 3.6538E+04 Solv Cont (%) 75 Bin 29 ... CC >= 0.45 Nr 1401 Cum 12628 Cum Vol 4.1098E+04 Solv Cont (%) 72 Bin 28 ... CC >= 0.40 Nr 1481 Cum 14109 Cum Vol 4.5918E+04 Solv Cont (%) 68 Bin 27 ... CC >= 0.35 Nr 1805 Cum 15914 Cum Vol 5.1792E+04 Solv Cont (%) 64 Bin 26 ... CC >= 0.30 Nr 2726 Cum 18640 Cum Vol 6.0664E+04 Solv Cont (%) 58 Bin 25 ... CC >= 0.25 Nr 3908 Cum 22548 Cum Vol 7.3382E+04 Solv Cont (%) 49 Bin 24 ... CC >= 0.20 Nr 5751 Cum 28299 Cum Vol 9.2099E+04 Solv Cont (%) 36
...
Bin 10 ... CC >= -0.50 Nr 11 Cum 87906 Cum Vol 2.8609E+05 Solv Cont (%) -98
CRYSTAL FORM #2 --------------- Cell volume (A**3) : ( 2.671E+05) Bin 37 ... CC >= 0.85 Nr 54 Cum 54 Cum Vol 1.7574E+02 Solv Cont (%) 100 Bin 36 ... CC >= 0.80 Nr 370 Cum 424 Cum Vol 1.3799E+03 Solv Cont (%) 98 Bin 35 ... CC >= 0.75 Nr 1136 Cum 1560 Cum Vol 5.0770E+03 Solv Cont (%) 92 Bin 34 ... CC >= 0.70 Nr 1869 Cum 3429 Cum Vol 1.1160E+04 Solv Cont (%) 83 Bin 33 ... CC >= 0.65 Nr 2213 Cum 5642 Cum Vol 1.8362E+04 Solv Cont (%) 73 Bin 32 ... CC >= 0.60 Nr 2190 Cum 7832 Cum Vol 2.5489E+04 Solv Cont (%) 62 Bin 31 ... CC >= 0.55 Nr 1882 Cum 9714 Cum Vol 3.1614E+04 Solv Cont (%) 53 Bin 30 ... CC >= 0.50 Nr 1513 Cum 11227 Cum Vol 3.6538E+04 Solv Cont (%) 45 Bin 29 ... CC >= 0.45 Nr 1401 Cum 12628 Cum Vol 4.1098E+04 Solv Cont (%) 38 Bin 28 ... CC >= 0.40 Nr 1481 Cum 14109 Cum Vol 4.5918E+04 Solv Cont (%) 31 Bin 27 ... CC >= 0.35 Nr 1805 Cum 15914 Cum Vol 5.1792E+04 Solv Cont (%) 22 Bin 26 ... CC >= 0.30 Nr 2726 Cum 18640 Cum Vol 6.0664E+04 Solv Cont (%) 9 Bin 25 ... CC >= 0.25 Nr 3908 Cum 22548 Cum Vol 7.3382E+04 Solv Cont (%) -10 Bin 24 ... CC >= 0.20 Nr 5751 Cum 28299 Cum Vol 9.2099E+04 Solv Cont (%) -38
...
Bin 11 ... CC >= -0.45 Nr 21 Cum 87895 Cum Vol 2.8605E+05 Solv Cont (%) -328 Bin 10 ... CC >= -0.50 Nr 11 Cum 87906 Cum Vol 2.8609E+05 Solv Cont (%) -328
"Cumul Vol" ignores any mask overlap ! "Solv Cont" ignores overlap, assumes one domain, no NCS, and all SymmOps used here !
Stamp : (Created by MASKIT V. 980710/0.3 at Fri Jul 10 18:47:15 1998 for user gerard) STOP ... Toodle pip ... statement executed (Q)QOPEN allocated # 1 User: gerard Logical Name: maskit.E Status: UNKNOWN Filename: maskit.E
File name for output map file on unit 10 : maskit.E logical name maskit.E
Minimum density in map = -0.54059 Maximum density = 0.84817 Mean density = 0.10594 Rms deviation from mean = 0.24391
Map written out
*** MASKIT *** MASKIT *** MASKIT *** MASKIT *** MASKIT *** MASKIT ***
Version - 980710/0.3 Started - Fri Jul 10 18:32:33 1998 Stopped - Fri Jul 10 18:47:15 1998
CPU-time taken : User - 659.6 Sys - 0.8 Total - 660.4
*** MASKIT *** MASKIT *** MASKIT *** MASKIT *** MASKIT *** MASKIT ***
>>>>>> This program: (C) 1992-98, GJ Kleywegt & TA Jones <<<<<< >>>> E-mail: gerard@xray.bmc.uu.se or alwyn@xray.bmc.uu.se <<<< >>>>>>>>>>>>>>>>> http://alpha2.bmc.uu.se/usf <<<<<<<&l
*** MASKIT *** MASKIT *** MASKIT *** MASKIT *** MASKIT *** MASKIT ***
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
In this particular case, a cut-off of the correlation map somewhere in the range of ~0.30 to ~0.50 produces a mask that (after some fiddling with MAMA) compares very well to that generated from the PDB file of the final model !
MASKIT allocates memory for maps and masks dynamically. This means that you can increase the size of maps and masks that the program can handle on the fly:
1 - through the environment variables MAPSIZE and MASKSIZE (must be in capital letters !), for example put the following in your .cshrc file:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- setenv MAPSIZE 8000000 setenv MASKSIZE 3000000 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
2 - by using command-line arguments MAPSIZE and MASKSIZE (need not be in capitals), for example:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- run coma -b mapsize 10000000 masksize 5000000 ----- 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 and/or mask which is bigger than that, you can use the command-line argument(s).
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.
MASKIT needs space for 3 maps and 0.3 masks (actually, 2 maps and one mask, each with 1/10-th the size of a "normal" mask).
None, at present.
Created at Sat Jan 30 02:51:12 1999
by MAN2HTML version 971024/1.6