PROCHECK Operating Manual

4. PROCHECK outputs

• PostScript files (see Sample plots)

  The output PostScript files all have an extension of .ps, their names being:

        filename_01.ps  }
        filename_02.ps  }
        filename_03.ps  } One PostScript file per plot
          ...
        filename_10.ps  }
  

  where filename is the root name of the original PDB file.

  You can make these filenames more self-descriptive by opting to add File-handles to the names. The output filename become:-

        filename_01_ramachand.ps - Ramchandran plot
        filename_02_ramglypro.ps - Gly & Pro Ramchandran plot
          ...  etc.
  

  The full list of descriptors is given in File-handles.

  The plots show each of the different PROCHECK analyses generated by the run. They can be sent directly to a PostScript printer or viewed on a graphics or X Windows terminal.

  Examples of all the plots produced by PROCHECK are given in Sample plots.

• Residue-by-residue listing (see Appendix D)

  The residue-by-residue listing has a .out extension and lists all the computed stereochemical properties, by residue, in a printable ASCII text file. It is described in detail in Appendix D.

• Other output files

  The other files output by PROCHECK have the following extensions:-

        .lan    Main-chain bond lengths and bond angles used by the plotting programs
        .nb     List of atom-pairs making near-neighbour contacts
        .new    "Cleaned-up" version of the original coordinates file
        .pln    Coordinates of atoms in planar groups
        .rin    Residue information used by the plotting programs
        .sco    Main-chain and side-chain properties
        .sdh    Residue-by-residue G-factors
        .sum    PROCHECK summary results
  

  Most of these files are used internally by the PROCHECK suite and are unlikely to be of much use to you. The more informative ones are the following:-

  • .new file The .new file holds the `cleaned-up' version of the original PDB file, with any wrong atom-labels corrected in accordance with the IUPAC naming conventions (IUPAC-IUB Commission of Biochemical Nomenclature, 1970).

  • .sum file The .sum file gives a short summary of the overall PROCHECK RESULTS.

• Log files

  Each program in the suite also produces its own log file. Should the PROCHECK suite crash, or give strange-looking results, these log files should be the first place you look for a reason for the problem. The 7 files are:

       anglen.log   clean.log    pplot.log    tplot.log
       bplot.log    nb.log       secstr.log
  

PROCHECK Operating Manual