Title

PDBHighlight: A Rasmol script database.


Introduction

The ultimate 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 in the 
Protein Data Bank (PDB [1]).

Currently the only scripts available are for highlighting PDB 
files according to the domain definitions of the Structural 
Classification of Proteins (SCOP [2]) database. 


Using pdbHighlight

The ras_script utility is called with the following syntax

ras_script < pdb-code >

It calls the scopHighlight_using_flat_file.plx perl script 
which dumps a RasMol script to highlight the PDB file according
to its SCOP domain annotation. 

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

The scopHighlight_using_flat_file.plx script requires the SCOP 
parsable files [3] which can be downloaded using the 
wget_domain_data.plx utility script. Please check 

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

for the latest version of the data.


All three perl scripts require various configuration options
which should be obvious. All three could be improved by making
this more obvious


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] 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

