OMIT (CCP4: Supported Program)


omit - program to calculate omit-maps according to Bhat procedure


omit HKLIN foo_in.mtz MAPOUT
[Key-worded input]


The 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 data in MTZ format. This file should contain observed and/or calculated structure factor amplitudes, and phases from some source.


Output binary omit-map. By default, this is in CCP4 format, but if the keyword MFFOUTPUT is specified then it will be output in MFF format (Groningen Master Fourier File format). The fast, medium and slow axes are set to be Z, X and Y respectively. An output CCP4 map can be manipulated by the programs MAPMASK or MAPROT if required.


LABIN <program label>=<file label>...


Program labels are:

Observed structure factor amplitudes, Fobs.
Calculated structure factor amplitudes, Fcalc.
Phases, Phi.

SCALE <scale_fobs> <scale_fcalc>


<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.


Include 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).


Include 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.


Output 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.


End input and run program.


Internal settings of the program:
  • The neutral volume (see Bhat's article!) has been fixed to a volume of two (2!) gridpoints around the phased volumne.
  • In contrast to what Bhat mentions (step J of his procedure), in the current version of the program, structure factors are obtained by Fourier transformation of a map in which the density values in the phased and neutral volumes have been set to 0.0.
  • Before starting the OMIT procedure, the electron density map may be truncated such that the density values are between -1.0*RMSMAP and 20.0*RMSMAP.


Unix example script found in $CEXAM/unix/runnable/

VMS example script found in $CEXAM/vms/


  1. T.N. Bhat, "CALCULATION OF AN OMIT MAP", J. Appl. Cryst., 21, 279-281 (1988)
  2. F.M.D.Vellieux and B.W.Dijkstra, "Computation of Bhat's OMIT maps with different coefficients", J. Appl. Cryst., 30, 396-399 (1997)


Program written by Bauke Dijkstra (April 1994).

Modified by Fred. Vellieux to include histogram mapping and the option of skipping the map truncation step (Feb. 1996).

CCP4 modifications made by Martyn Winn (July 1997).