PROCHECK Operating Manual

2. How to run PROCHECK

To run PROCHECK, type the following:-

setup procheck (or source /sgi/local/setup/procheck.set)
procheck coordinate_file [chain-ID] resolution

where:

coordinate_file is the name of the file containing your protein structure and should include the full path unless the file is in the default directory. The file must be in Brookhaven format (see Appendix B).
[chain-ID] is an optional parameter used for multiple chain files when only one of the chains is to be analysed. If all chains are required, or the file only contains a single chain, you omit this parameter. Otherwise enter the single-letter chain ID of the chain to be analysed.
resolution is the resolution at which the structure has been determined. If the resolution is unknown or not relevant (eg for structures solved by NMR) enter any resolution (eg 2.0).

For example, to run the check on the Brookhaven file 1abc, which was solved to 2.4Å you might enter:

procheck 1abc.pdb 2.4

Running just the plotting programs

The PROPLOT script runs just the plotting programs that generate the output PostScript files. It skips the programs that calculate the data, and so is much faster than running PROCHECK all over again. (Of course, the calculation programs need to have been run at least once so that all the required data files are present). The script is particularly useful if you want to regenerate some, or all, of the plots, perhaps with different plot parameters in the procheck.prm file (see Customizing the PROCHECK plots).

To run PROPLOT, enter:

setup procheck (or source /sgi/local/setup/procheck.set)
proplot coordinate_file [chain-ID] resolution

where the parameters are the same as before.