MAPCUT (CCP4: Supported Program)


mapcut - Prepare MR density search


mapcut -mtzin filename -pdbin filename -mapin filename -mskin filename -colin-fc colpath -mtzout filename -mapout filename -colout-hl colpath -colout-fc colpath -mask-radius radius/A -cell-multiplier multiplier -resolution resolution -offset-to-origin -pad-resolution -verbose verbosity -stdin
[Keyworded input]


'Mapcut' is a tool for preparing a electron-density search model for molecular replacement. Sometimes it is desirable to search using electron density rather than atomic coordinates - most commonly in the case of determining a cross-crystal averaging operator. This tool takes an electron density map (usually specified as an MTZ file containing map coefficients, although a map file may also be used), and a mask (usually described as a set of atomic coordinates defining the region of interest, although a mask file may also be used). The masked density is cut out and placed in an artificual unit cell several times larger than the masked region. The results are output as an MTZ file of map coefficients (although a map file may also be output).


Input MTZ file. This contains the map coefficients (F,PHI) for the electron density to be used. (If FOM weighting is required, map coefficients are generated from F/PHI/FOM or HL coeffs with chltofom).
-mapin may be specified instead.
Input PDB file containing atom giving the location of the density to be cut. A mask will be generated covering the atoms and extending to a given radius beyond them.
-mskin may be specified instead.
Output MTZ file. This will contain the new map coefficients.
-mapout may be specified instead.


See Note on keyword input.

-colin-wrk-fc colpath

Map coefficients F and phi for the electron density. See Note on column paths.

-mask-radius radius/A

[Optional] Radius used when generating a mask to cover the atoms (default 5A).

-cell-multiplier resolution/A

[Optional] Number of times bigger the output cell should be than the cut density (default 2.5x).


[Optional] Move the density to the origin. May be required for older MR programs, however output translations from the MR calcualtion will need adjusting.


[Optional] Pad the resolution of the output data by a single reciprocal lattice box - this may improve the results of the MR calculation.

-verbose verbosity

Note on column paths:

When using the command line, MTZ columns are described as groups using a slash separated format including the crystal and dataset name. If your data was generated by another column-group using program, you can just specify the name of the group, for example '/native/peak/Fobs'. You can wildcard the crystal and dataset if the file does not contain any duplicate labels, e.g. '/*/*/Fobs'. You can also access individual non-grouped columns from existing files by giving a comma-separated list of names in square brackets, e.g. '/*/*/[FP,SIGFP]'.

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:



Kevin Cowtan, York.