Documentation

vplg (9)
Tim Schäfer

This page gives a general overview of the VPLG software package. You should read the pages for the different programs for help on a specific tool: [PLCC] [SplitPDB]

Installing the VPLG software package

To install the VPLG software package, the following steps are required:

  1. Download an archive with the current version of the software from our Downloads section
  2. Unzip the package to a directory of your choice, preserving paths.
  3. Optional but recommended: Download and install the DSSP program (Kabsch & Sander 1983). Put the dsspcmbi executable into a directory of your choice and make sure it is executable.

Note: If you omit Step 3) you will have to manually download DSSP files for each PDB file you want to process later. See the section on Using the VPLG software for details.

WARNING: If you copy the JAR files out of the original folder tree and execute them elsewhere, you have to copy the lib/ directory there as well! The programs require the libraries and will NOT work if they are missing!

Running the VPLG software package

The recommended way to use VPLG is to start the PLCC tool from the command line:

java -jar plcc.jar

Detailed information on this is available here: [PLCC_Commandline]

Alternatively, you can use the VPG graphical user interface to access basic features of PLCC:

java -jar vpg.jar

See Using the software below for details.

Using the VPLG software package

The recommended way to use VPLG is as follows:

  1. Download a PDB file from the RCSB PDB website (or use your own private file)
  2. Use the [SplitPDB] tool to extract data of a specific model and write it to a new PDB file. Not required (but won't hurt) if the file does not contain models. (Usually PDB files from NMR experiments contain multiple models (often up to 20) while PDB files from other experiments don't.) Then run dsspcmbi (Kabsch & Sander 1983, see Installation instructions) to generate the DSSP file from the new PDB file.
  3. Run [PLCC] with proper command line to generate and visualize the protein graph.

NOTE: If you don't use a private PDB file, you can replace step 2. in the list above with the following alternative step:

Download the DSSP file from one of the servers linked on the DSSP website, e.g., MRS.


Related

Wiki: Home
Wiki: PLCC
Wiki: PLCC_Commandline
Wiki: SplitPDB