PDB_EXTRACT

Description

The PDB_EXTRACT program suite contains tools and examples for extracting mmCIF data from structure determination applications.

Distribution

current version (RCSB web site)

If you wish to install and use this software you should always download the most up-to-date version from the above Web site. The links below are to the copies on this CD-ROM, which are suitable for browsing or for use if the Web site is not available. However, they may be out of date and lack the full functionality of the latest version.

Status

PDB_EXTRACT is under constant development as a tool to allow the creation of mmCIF files from a variety of current macromolecular structure determination packages. The version distributed here is version 1.600 of February 2005. Users are recommended to obtain the latest release from the Rutgers site of the Research Collaboratory for Structural Bioinformatics (RCSB) if at all possible. Comments should be directed to [email protected].

Language and platform

The software is written in C++ and should run on versions of Unix with suitable C++ compilers. Binary distributions are provided for Linux, SGI, Sun, OSF and Mac OS X platforms. The binary distributions also include the structure checking module PROCHECK.

Documentation

Installation from source distribution: For Unix-type installations, copy the gzipped tar file pdb-extract-v1.600-prod-src.tar.gz into an empty directory; gunzip and extract files using the Unix tar utility. Set appropriate environment variables (see detailed installation notes); build the application using the make utility; create binary data files. E.g.
```
   cp pdb-extract-v1.600-prod-src.tar.gz /p/q/r; cd /p/q/r
   cat pdb-extract-v1.600-prod-src.tar.gz | gunzip | tar xvf -
   cd /p/q/r/pdb-extract-v1.600-prod-src
   RCSBROOT=/p/q/r/pdb-extract-v1.600-prod-src; export RCSBROOT
   PATH="$RCSBROOT/bin:"$PATH; export PATH
   make
   make binary 
```
If gzip or tar are unavailable, individual source files may be saved to the build directory.
For more details see the Installation Notes
Installation from binary distribution: For Unix-type installations, copy the relevant gzipped tar file pdb-extract-v1.600-prod-bin-xxx.tar.gz into an empty directory; gunzip and extract files using the Unix tar utility. Set appropriate environment variables (see detailed installation notes); create binary data files. E.g.
```
   cp pdb-extract-v1.600-prod-bin-xxx.tar.gz /p/q/r; cd /p/q/r
   cat pdb-extract-v1.600-prod-bin-xxx.tar.gz | gunzip | tar xvf -
   cd /p/q/r/pdb-extract-v1.600-prod-bin-xxx
   RCSBROOT=/p/q/r/pdb-extract-v1.600-prod-bin-xxx; export RCSBROOT
   PATH="$RCSBROOT/bin:"$PATH; export PATH
   cd etc
   ./binary.sh 
```
For more details see the Installation Notes
Documentation and examples for the stand-alone PDB_EXTRACT ( HTML | PDF format )
Documentation on installing the example files: ( text format )

Terms and conditions of use

The software is distributed here under licence from the Protein Data Bank/RCSB. Use of the software is governed by the PDB software licence. Queries concerning any other use should be directed to [email protected].