OMIT (CCP4: Supported Program)
- program to calculate omit-maps according to Bhat procedure
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 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
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
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 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).
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.
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
Output omit map in MFF format (Groningen Master Fourier File format).
The default is to output the omit map in CCP4 format.
<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 volume.
- 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/
T.N. Bhat, "CALCULATION OF AN OMIT MAP", J. Appl. Cryst.,
21, 279-281 (1988)
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).