Program : COMAP
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 maps for multiple-crystal averaging of
electron-density 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.
930316 - 0.1 - initial version from map_add.f
930615 - 1.0 - new production version
931217 - 1.1 - minor changes
940113 -1.1.1- check that at least two maps entered
950118 - 1.2 - sensitive to environment variable CCP4_OPEN
960412 - 1.3 - echo all input to help debug scripts
961122 - 2.0 - dynamic memory allocation
From version 2.0 onward, COMAP 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 comap 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.
COMAP 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
With COMAP you can combine and scale various maps to produce a weighted, averaged map. COMAP is a more general version of Alwyn's map_add program.
COMAP allows you to combine ANY number of maps, provided all have the same grid, origin, extent and unit cells (within 0.01 A or degree). The final map contains the following density:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Ecombi (x,y,z) = W * SUM (weight(i)*scale(i)*map(i)(x,y,z))
i=1,
NMAP
- weight (i) = weight for map nr I, defined by the user
/ 1.0, if I = 1
- scale (i) =
\ VAR(1)/VAR(I), if I > 1 (VAR = variance of the map)
- W = 1.0 / (SUM (weight(i)*scale(i)))
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Note that by clever choices of the weights, COMAP can be used to add or subtract maps. The scale factors are computed by the program and will ensure that (if the Fobs used to produce the maps have been scaled appropriately) the individual maps are scaled together properly.
The following example shows how to add two maps with weights 1.0 and 2.0:
Start the program and provide the name of the first map and its weight:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ... Reference map : av_0.E ... Map nr 1 Size 352000 ED min, max, total -6.2134E+01 9.3133E+01 2.6856E+00 ED ave, var, stdev 7.6294E-06 1.9540E+02 1.3978E+01Scale : ( 1.000) Weight ? ( 1.000) 1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Now give the name of the second file and its weight:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Map nr : ( 2) Map b: scr.E Read header. ... Map nr 2 Size 352000 ED min, max, total -3.6909E+02 5.0000E+02 2.4826E-02 ED ave, var, stdev 7.0529E-08 6.0782E+03 7.7963E+01Scale : ( 0.032) Weight ? ( 1.000) 2.0 Multiplier : ( 6.429E-02) RMSD map A / B : ( 6.676E+01) Shape similarity A / B : ( 0.834) 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).
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.
Note that COMAP actually checks if the maps are on the same grid etc. as the first one:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Map nr : ( 3) Map b: av_2x.E Read header. ... Map read OK. Grid : ( 100 110 64) Origin : ( 31 45 8) Extent : ( 48 53 61) Cell : ( 91.800 99.500 56.500 90.000 90.000 90.000) ERROR --- Different origin, extent, grid, cell ERROR --- This map will NOT be addedMap nr : ( 3) Map b: ----- 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 ----- Map nr : ( 3) Map b: No more maps to addSum of weights and scales : ( 1.064E+00) Map nr 0 Size 352000 ED min, max, total -7.7514E+01 1.1771E+02 9.8195E-01 ED ave, var, stdev 2.7896E-06 2.9797E+02 1.7262E+01
New summed CCP4 map: sum.E ... Map written out. ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
None, at present.
Created at Fri Dec 18 19:42:07 1998
by MAN2HTML version 971024/1.6