
Title

PDBHighlight: A RasMol script database.



Introduction

The aim of pdbHighlight is to maintain a searchable database of RasMol
script files, designed to 'highlight' various features of the protein
molecules whose structures are available in the Protein Data Bank (PDB
[1]).

Currently the only script available highlights PDB files according to
the domain definitions of the Structural Classification of Proteins
(SCOP [2]) database.



Using pdbHighlight

The 'ras_script' command line utility is called with the following
syntax;

  ras_script < pdb-code >


First, 'ras_script' calls the 'scopHighlight_using_flat_file.plx' Perl
[3] script that creates a RasMol [4] script file to highlight the PDB
file according to its SCOP domain annotation.

Next, 'ras_script' creates a temporary file which combines the PDB
file with the script file, and invokes RasMol over this new file.

The 'scopHighlight_using_flat_file.plx' script requires the SCOP
parsable files [5], which can be downloaded using the
'wget_domain_data.plx' utility. Please check

http://scop.mrc-lmb.cam.ac.uk/scop/index.html


for the latest version of the data.



Installing

All three Perl scripts require various configuration options which
should be obvious. All three could be improved by making this more
obvious. Copy the right files into the right places and everything
should work nicely. The current major limitation is that a local copy
of the PDB is expected. It would be easy to include a 'wget' step to
grab the PDB from a remote location.



References

[1] Bernstein FC, Koetzle TF, Williams GJ, Meyer EF Jr, Brice MD,
Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. (1977).  The Protein
Data Bank: a computer-based archival file for macromolecular
structures.  J. Mol. Biol. 112, 535-542

[2] Murzin AG, Brenner SE, Hubbard T, Chothia C. (1995).  SCOP: a
structural classification of proteins database for the investigation
of sequences and structures.  J. Mol. Biol. 247, 536-540
http://scop.mrc-lmb.cam.ac.uk/scop/ref/1995-jmb-scop.pdf

[3] Perl

[4] RasMol

[5] Lo Conte L, Brenner SE, Hubbard TJP, Chothia C, Murzin A. (2002).
SCOP database in 2002: refinements accommodate structural genomics.
Nucl. Acid Res. 30, 264-267
http://scop.mrc-lmb.cam.ac.uk/scop/ref/nar2002.pdf
