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2. How to run PROCHECK

To run PROCHECK, type the following:-

    procheck coordinate_file [chain-ID] resolution
  • 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 /data/pdb/p1abc.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:

    proplot coordinate_file [chain-ID] resolution

where the parameters are the same as before.

Running in batch-mode on a VAX

On VAX computers, you can submit the entire process to a batch queue by entering:-

    prosub coordinate_file [chain-ID] resolution queue-name default-directory
where the first three parameters are as before, and:
  • queue-name is the name of the batch-queue to which you want the job submitted.

  • default-directory is the directory to which the files created by PROCHECK are to be written. Note, this need not be the same directory as the one containing the structure file, but it must be one to which you have write access.

If you just type prosub you will be prompted for each of these 5 parameters in turn. If you do not want to specify a chain ID, leave this entry blank.

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