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PROCHECK Operating Manual
4. PROCHECK outputs
PROCHECK generates a number of output files in the default directory
which have the same name as the original PDB file, but with
different extensions.
-
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
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