cmakereference - Generate reference structure for pirate/buccaneer.
'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.
If cifin is an MTZ file, then specify the columns with this keyword. For example: -colin-fo '/*/*/[FP,SIGFP]'
Default: taken from cifin
Resolution to truncate the data at.
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