PLCC_Commandline

PLCC command line options

You can use the following command to access the built-in help on command line options:

java -jar plcc.jar --help

Depending on the version you use, you will see something more or less similar to this:

[======================== plcc -- Protein-Ligand Contact Calculation ========================]
Init... (Version 0.4)
  Loaded 65 settings from properties file '/home/ts/.plcc_settings'.
Copyright Tim Schaefer -- http://www.bioinformatik.uni-frankfurt.de

USAGE: java -jar plcc.jar <pdbid> [OPTIONS]
       java -jar plcc.jar --help
valid OPTIONS are: 
-a | --include-coils       : convert the SSE type of all ignored residues to C (coil) and include coils in the graphs
-b | --draw-plcc-fgs <f>   : read graph in plcc format from file <f> and draw it and all its folding graphs, then exit (pdbid will be ignored)
-c | --dont-calc-graphs    : do not calculate SSEs contact graphs
-D | --debug <level>       : set debug level (0: off, 1: normal debug output. >=2: detailed debug output)
-d | --dsspfile <dsspfile> : use DSSP file <dsspfile> (instead of '<pdbid>.dssp')
-f | --folding-graphs      : also handle foldings graphs [req. -c]
-g | --sse-graphtypes <l>  : compute only the SSE graphs in list <l>, e.g. 'abcdef' = alpha, beta, alhpabeta, alphalig, betalig and alphabetalig.
-h | --help                : show this help message and exit
-i | --ignoreligands       : ignore ligand contacts, do NOT print them to the output file
-l | --draw-plcc-graph <f> : read graph in plcc format from file <f> and draw it to <f>.png, then exit (pdbid will be ignored)
-n | --textfiles           : write meta data, debug info and interim results like residue contacts to text files (slower)
-m | --image-format <f>    : write output images in format <f>, which can be 'PNG' for PNG bitmap format or 'SVG' for SVG vector format.
-o | --outputdir <dir>     : write output files to directory <dir> (instead of '.', the current directory)
-p | --pdbfile <pdbfile>   : use PDB file <pdbfile> (instead of '<pdbid>.pdb')
-q | --fg-notations <list> : draw only the folding graph notations in <list>, e.g. 'kars' = KEY, ADJ, RED and SEQ.
-r | --recreate-tables     : drop and recreate DB statistics tables, then exit (see -u).
-s | --showonscreen        : show an overview of the residue contact results on stdout (slower)
-t | --draw-tgf-graph <f>  : read graph in TGF format from file <f> and draw it to <f>.png, then exit (pdbid will be ignored)
-u | --use-database        : write SSE contact data to database [req. -c and credentials in cfg file]
-w | --dont-write-images   : don not draw the SSE graphs and write them to PNG files
-x | --check-rescts <f>    : compare the computed residue level contacts to those in <pdbid>.geo format file <f> and print differences
-y | --write-geodat        : write the computed SSE level contacts in geo.dat format to a file (file name: <pdbid>_<chain>.geodat)
-z | --ramaplot            : draw a ramachandran plot of each chain to the file '<pdbid>_<chain>_plot.svg'

EXAMPLES: java -jar plcc.jar 8icd
          java -jar plcc.jar 8icd -D 2 -d /tmp/dssp/8icd.dssp -p /tmp/pdb/8icd.pdb
          java -jar plcc.jar 8icd -o /tmp
          java -jar plcc.jar IGNORED -l prot_graph_3kmf_A.plg

REQUIRED INPUT FILES: This program requires the PDB file and the DSSP file of a protein.
                      This does not apply to options that don't use it (-l, -t, -r), of course.
                      A PDBID still has to be given as first argument, it will be ignored though.

NOTES: 
       -The DSSP program assumes that the input PDB file only has a single model.
        You have to split PDB files with multiple models up BEFORE running DSSP (use 'splitpdb').
        If you don't do this, the broken DSSP file will get this program into trouble.
       -See the config file '.plcc_settings' in your userhome to set advanced options.
       -If all the parameters above scare you try 'java -jar plcc.jar <PDBID>' for a start.

We suggest you read the documentation provided with the release for up-to-date information.