Program : COMDEM
Version : 961122
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 : combine multiple-domain expanded maps
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 (1999 ?). Chapter 25.2.6. O and associated programs. Int. Tables for Crystallography, Volume F. To be published.
931213 - 0.1 - first version
931216 - 0.2 - tested and debugged
931217 - 1.0 - first production version
940113 -1.0.1- check that at least two maps entered
950118 - 1.1 - sensitive to environment variable CCP4_OPEN
960412 - 1.2 - echo all input to help debug scripts
961122 - 2.0 - dynamic memory allocation
From version 2.0 onward, COMDEM allocates memory for its maps dynamically. This means that you can increase the size that the program can handle on the fly:
1 - through the environment variable MAPSIZE (must be in capital letters !), for example put the following in your .cshrc file or your script:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- setenv MAPSIZE 8000000 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
2 - by using command-line argument MAPSIZE (need not be in capitals), for example in your script:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- run comdem mapsize 10000000 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Note that command-line argument takes precedence over the environment variable. So you can set the environment variable in your .cshrc file to a "typical" value, and if you have to deal with maps which are bigger than that, you can use the command-line argument.
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.
COMDEM needs space for 3 maps.
NOTE: this program is now 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 abort execution on startup. To fix this, put the following line in your .login or .cshrc file: setenv CCP4_OPEN UNKNOWN
If you want to use multiple-domain averaging, you should average and expand your map for each domain separately (i.e., with its own mask and set of NCS operators). Make sure that you keep a zero background in the expansion step.
Then, use this program to combine the individual expanded maps and to calculate and set the background level for all points not covered by any mask after the maps have been combined.
You may apply different weights to each of the maps, but I don't think this is normally necessary (since each map is derived from one and the same "master map"), i.e. use weights equal to one.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ... Max size of maps : ( 4194304)First domain map ? ( ) tempm1_zero.E Read header ... Map read OK Cell axes (A) : ( 110.600 110.600 160.300) Cell angles (d) : ( 90.000 90.000 90.000) Grid axes (pts) : ( 160 160 240) Origin (pts) : ( 0 0 0) Extent (pts) : ( 162 162 32) Map nr 1 Size 839808 ED min, max, total -6.4655E+01 9.7743E+01 2.4085E+05 ED ave, var, stdev 2.8679E-01 6.0887E+01 7.8030E+00
Weight ? ( 1.000) 1.0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Now give the name of the second file and its weight:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Map nr : ( 2) Domain map file name ? ( ) tempm2_zero.E Read header ... Map read OK Cell axes (A) : ( 110.600 110.600 160.300) Cell angles (d) : ( 90.000 90.000 90.000) Grid axes (pts) : ( 160 160 240) Origin (pts) : ( 0 0 0) Extent (pts) : ( 162 162 32) Map nr 2 Size 839808 ED min, max, total -5.1632E+01 6.7189E+01 6.6272E+04 ED ave, var, stdev 7.8914E-02 1.2725E+01 3.5672E+00Weight ? ( 1.000) RMSD map A / B : ( 8.579E+00) R-factor (A) : ( 1.234E+00) Ditto, B scaled : ( 1.997E+00) Scale for B : ( 4.230E+00) R-factor (B) : ( 5.221E+00) Ditto, A scaled : ( 1.997E+00) Scale for A : ( 2.364E-01) Corr coeff : ( 0.001) Shape similarity : ( 0.002) Busy ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Note that several statistics are printed: minimum, maximum and integrated electron density, the average density, the variance (used for scaling) and the standard deviation (the square root of the variance).
In addition, the RMS difference between this map and the first one is printed, as is the "shape similarity index" (values from -1 to +1; +1 means that the two maps have identical shapes, irrespective of the scales they are on).
NOTE that the correlation coefficient between each of the maps MUST be essentially ZERO, since they are supposed to cover DISJOINT areas in space !!
If you want to combine more masks, just keep supplying file names to the program. Hit [RETURN] to indicate that there are no more maps to be added.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Map nr : ( 3) Domain map file name ? ( ) No more maps to addSum of weights / Nr of maps : ( 1.000E+00) Dividing by this number ... Calculating background density ... Nr of points set : ( 266836) Nr of background points : ( 572972) Sum of density set : ( 3.071E+05) Average density in masks : ( 1.151E+00) Average background level : ( -5.360E-01) Setting background density ... Map nr 0 Size 839808 ED min, max, total -7.8140E+01 9.7743E+01 -1.3083E+01 ED ave, var, stdev -1.5578E-05 7.3830E+01 8.5924E+00 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
After all maps have been added, statistics for the combined map are printed and you are asked to supply the name of the output file:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- New summed CCP4 map ? ( ) zero.E ... Map written out ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Note that the "Minimum density in map" is lower than the minimum of the two maps. This is because their masks have a minute overlap, and apparently one of the overlapping points gets two negative contributions.
If you want other ways of combining maps (e.g., MAX(map1,map2,...)), let me know (or use MAPMAN).
None, at present.
Created at Fri Dec 18 19:42:07 1998
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