SplitPDB_Readme

This is the README for the splitpdb program (splitpdb.jar), which is part of VPLG (Visualization of Protein Ligand Graphs).

Description

The splitpdb program is used to prepare PDB that contain several models for dsspcmbi. It parses the PDB file, extracts data on a specific model from the file, and writes the data to a new PDB file. If the input PDB file does not contain any models, the output file is a copy of the input file. By default, the first model is used, but this can be configured (see below).

Installation and System Requirements

The splitpdb program is written in Java and requires an JRE 1.6, which is available at http://java.sun.com free of charge for many platforms.

Running the program

This is a command line program. The dpg frontend can be used to run this program and automatically generate the command line, but not all options are available from within dpg.

To extract the first model from the PDB file 1tst.pdb and have splitpdb write the resulting PDB output file to 1tst.pdb.split, use the following command line:

java -jar splitpdb.jar 1tst.pdb

You can specify the model and the output file name on the command line. Run the following command for details:

java -jar splitpdb.jar --help

Setup and Configuration

This program does not have a config file and there is no need to configure anything. All options have to be set on the command line.

Author

The splitpdb program was written by Tim Schaefer. See http://www.bioinformatik.uni-frankfurt.de/about_us.html for contact information.

The official VPLG website is at http://vplg.sourceforge.net/.

TS