OMIT (CCP4: Supported Program)
NAMEomit - program to calculate omit-maps according to Bhat procedure
SYNOPSISomit HKLIN foo_in.mtz MAPOUT foo_out.map
DESCRIPTIONThe present program has combined the original conglomerate of separate programs, all needed to calculate an omit-map, into one single automatic procedure. The user is strongly advised to read the paper "CALCULATION OF AN OMIT MAP" by T.N. BHAT, J. Appl. Cryst. (1988) 21, 279-281.
Note: Memory requirements are governed by a parameter MAXREF set in the program, and this may need to be increased for large problems. If this is the case, the program will hopefully exit gracefully and let you know. Change it as necessary (top of the program source code) and recompile. Increasing MAXREF increases the record lengths for some scratch files, and this can cause problems on some VMS systems. These scratch files are also large in total, which may also cause problems.
INPUT AND OUTPUT FILES
LABIN <program label>=<file label>...(Compulsory.)
Program labels are:
SCALE <scale_fobs> <scale_fcalc>(Compulsory.)
<scale_fobs> and <scale_fcalc> are scale factors for Fobs and Fcalc respectively. For example, <scale_fobs> = 2.0 and <scale_fcalc> = -1.0 allows one to calculate a 2FO-FC omit-map.
RESOLUTION <resmin> <resmax>Resolution limits, either 4(sin theta/lambda)**2 or d in Angstrom (either order). If this card isn't given, resolution range will be read from HKLIN.
TRUNCATEInclude this card to truncate initial map, so that the density values fall between -1.0*RMSMAP and 20.0*RMSMAP (ITRUNC=1). Default is ITRUNC= 0 (recommended).
HISTOGRAMInclude this card to apply HISTOGRAM MAPPING to the omit map, so that the histogram of densities of the omit map equals that of the starting map (IHIST =1). Default is IHIST = 0 (recommended).
DLIMIT <dstlmt>Points in the electron density map within <dstlmt> of a symmetry related grid point are set to -RMS density value of the map. Set <dstlmt> = 0.0 for no modification of input map; 3.0-3.5 Angstrom seems a good value otherwise. [Default 3.0]
GRID <nx> <ny> <nz>Number of sampling divisions along each unit cell edge for the output map. The number of points along each axis should be even, and a product of the factors 2, 3, 4 or 5 (each of which may appear any number of times). There is also a maximum value for the number of points set in the program. If any of <nx> <ny> and <nz> do not satisfy these conditions, then they will be reset appropriately. If this keyword is omitted, then the program will choose appropriate values automatically.
MFFOUTPUTOutput omit map in MFF format (Groningen Master Fourier File format). The default is to output the omit map in CCP4 format.
TITLE <title><title> will be written to MAPOUT.
ENDEnd input and run program.
PROGRAM FUNCTIONInternal settings of the program:
Unix example script found in $CEXAM/unix/runnable/
VMS example script found in $CEXAM/vms/
AUTHORProgram written by Bauke Dijkstra (April 1994). email@example.com
Modified by Fred. Vellieux to include histogram mapping and the option of skipping the map truncation step (Feb. 1996).firstname.lastname@example.org
CCP4 modifications made by Martyn Winn (July 1997).email@example.com