CMAKEREFERENCE (CCP4: Supported Program)


cmakereference - Generate reference structure for pirate/buccaneer.


cmakereference -pdbid accession-code -pdbin filename -cifin filename -colin-fo colpath -mtzout filename -pdbout filename -resolution reso/A [-stdin]
[Keyworded input]


'cmakereference' is used to generate reference structures for use by the programs pirate/buccaneer. Three standard reference structures are now provided as part of the distribution (based on 1AJR, 1JZ8 and 1TQW). These are selected automatically by pirate/buccaneer, and are suitable for common light-atom protein structures with varying solvent content and resolution up to 1.85A. For exotic cases and high resolution cases you will have to provide your own reference structures using cmakereference.

The accession code is compulsory. If no -pdbin / -cifin for the deposited structure are given, they are fetched by ftp if possible.


Input PDB file containing the deposited coordinates. makereference accepts either .ent or .ent.Z files. If you download a .ent.gz file, then you will need to gunzip it first.
Input mmCIF or MTZ file containing the deposited reflections. For mmCIF reflection files, makereference accepts either .ent or .ent.Z files. If you download a .ent.gz file, then you will need to gunzip it first. If the (uncompressed) file extension is not .ent, then makereference will try to open it as an MTZ file, in which case you will probably need to specify -colin-fo as well.
Output MTZ file containing the data for the reference structure. The columns are F, sigF, and a set of Hendrickson-Lattman (HL) coefficients describing the calculated phases from the final model. This becomes -mtzin-ref for Pirate/Buccaneer.
Output PDB file containing the final model for the reference structure. This becomes -pdbin-ref for Buccaneer.


See Note on keyword input.

-colin-fo colpath

If cifin is an MTZ file, then specify the columns with this keyword. For example: -colin-fo '/*/*/[FP,SIGFP]'

-resolution reso

Default: taken from cifin
Resolution to truncate the data at.

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. End input with <Ctrl-D> (END is not recognised).


Kevin Cowtan, York.


pirate, buccaneer, cif2mtz