COMIT (CCP4: Supported Program)

NAME

comit - Composite omit maps

SYNOPSIS

ccomit -pdbin filename -mtzin filename -mtzout filename -mapout filename -prefix filename -colin-fo colpath -colin-fc colpath -colout colpath -nomit number of spheres -pad-radius radius/A -verbose verbosity -stdin
[Keyworded input]

DESCRIPTION

'comit' Calculates composite omit maps by omitting spheres of density from the assymetric unit and reconsructing those spheres using sigma-a weighted maps.

'comit' can use one of two methods. A fast calculation using the output from refmac can generate a very good approximation to the full composite omit map with the correct choice of input MTZ columns. A slow calculation involves re-running refmac on mutliple versions of the model with a few atom occupancies set to zero in each case. In slow mode the program is run twice, once to generate the input models for refmac, and once to assemple the output maps from refmac.

HOW TO RUN COMIT

Examples

Fast method:

comit --mtzin my.mtz --colin-fo FP,SIGFP --colin-fc FC_ALL,PHIC_ALL --mtzout omit.mtz

Slow method:

~/clipper21/brigantine/comit --pdbin my.pdb --prefix omit

foreach name ( omit_0*.pdb )

refmac5 XYZIN $name XYZOUT refmac.pdb HKLIN /home/cowtan/test/ejd/gg_scaleit2.mtz HKLOUT $name:r.mtz << eof
refi type REST resi MLKF meth CGMAT bref ISOT
ncyc 10
solvent YES
weight AUTO
labin  FP=FP SIGFP=SIGFP FREE=FreeR_flag
eof

end

~/clipper21/brigantine/comit --prefix omit --mtzout omit.mtz

INPUT/OUTPUT FILES

Note: Fast or slow mode are determined by the absence or presence of the 'prefix' keyword. In slow mode, the first and second runs are determined by the presence or absence of the 'pdbin' keyword.

Fast mode

-mtzin: MTZ file from refmac.
-mtzout: [Optional] MTZ file with added omit map coefficients.
-mapout: [Optional] Omit map.

Slow mode

-pdbin: Atomic model. A series of models will be created for refinement in refmac with some atom occupancies set to zero.
-prefix: Prefix for output models (pre-refmac) or input mtz files (post-refmac).
-mtzout: [Optional] MTZ file with added omit map coefficients.
-mapout: [Optional] Omit map.

KEYWORDED INPUT

See Note on keyword input.

-colin-fo colpath

[Fast mode] Observed F and sigma for work structure. See Note on column paths.

-colin-fc colpath

[Fast mode] Map coefficients for work structure. These should normally be set to FC_ALL,PHICALL after refmac. Use of FWT,PHWT is generally inadvisable, leading to a much more biased map, however for very poor models this may be better than nothing. See Note on column paths.

-nomit number of spheres

Approximate number of regions to omit. Default = 20

-pad-radius radius/A

Padding radius to separate included and excluded density. Default = 3A

-verbose verbosity

Note on column paths:

When using the command line, MTZ columns are described as groups using a comma separated format. A more specific form includes the crystal and dataset name sparated by slashes, and enclosing any column labels in square brackets. If your data was generated by another column-group using program, you can just specify the name of the group. e.g.
FP,SIGFP /*/*/[FP,SIGFP] /native/peak/Fobs (The last case expands to two column names: Fobs.F_phi.F and Fobs.F_phi.phi)

Note on keyword input:

Keywords may appear on the command line, or by specifying the '-stdin' flag, on standard input. In the latter case, one keyword is given per line and the '-' is optional, and the rest of the line is the argument of that keyword if required, so quoting is not used in this case.

Reading the Ouput:

Problems:

AUTHOR

Kevin Cowtan, York.