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Revision: 1.1
Committed: Tue Apr 10 09:34:09 2007 UTC (9 years ago) by dmb
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tiny change; http://www.bioinformatics.org/pdbHighlight/index.php

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1 <br><br>
2 Title <br><br>
3 <a href="http://www.bioinformatics.org/pdbHighlight/index.php">PDBHighlight</a>: A <a href="http://en.wikipedia.org/wiki/RasMol">RasMol</a> script database. <br><br>
4 <br><br>
5 <br><br>
6 Introduction <br><br>
7 The aim of pdbHighlight is to maintain a searchable database of <a href="http://en.wikipedia.org/wiki/RasMol">RasMol</a> script files, designed to 'highlight' various features of the protein molecules whose structures are available in the <a href="http://en.wikipedia.org/wiki/Protein Data Bank">Protein Data Bank</a> (PDB [1]). <br><br>
8 Currently the only script available highlights PDB files according to the domain definitions of the <a href="http://en.wikipedia.org/wiki/Structural Classification of Proteins">Structural Classification of Proteins</a> (SCOP [2]) database. <br><br>
9 <br><br>
10 <br><br>
11 Using pdbHighlight <br><br>
12 The 'ras_script' command line utility is called with the following syntax; <br><br>
13 ras_script < pdb-code > <br><br>
14 <br><br>
15 First, 'ras_script' calls the 'scopHighlight_using_flat_file.plx' <a href="http://en.wikipedia.org/wiki/Perl">Perl</a> [3] script that creates a <a href="http://en.wikipedia.org/wiki/RasMol">RasMol</a> [4] script file to highlight the PDB file according to its SCOP domain annotation. <br><br>
16 Next, 'ras_script' creates a temporary file which combines the PDB file with the script file, and invokes <a href="http://en.wikipedia.org/wiki/RasMol">RasMol</a> over this new file. <br><br>
17 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 <br><br>
18 <a href="http://scop.mrc-lmb.cam.ac.uk/scop/index.html">http://scop.mrc-lmb.cam.ac.uk/scop/index.html</a> <br><br>
19 <br><br>
20 for the latest version of the data. <br><br>
21 <br><br>
22 <br><br>
23 Installing <br><br>
24 All three <a href="http://en.wikipedia.org/wiki/Perl">Perl</a> 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. <br><br>
25 <br><br>
26 <br><br>
27 References <br><br>
28 [1] Bernstein FC, Koetzle TF, Williams GJ, Meyer EF Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. (1977). The <a href="http://en.wikipedia.org/wiki/Protein Data Bank">Protein Data Bank</a>: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542 <br><br>
29 [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 <a href="http://scop.mrc-lmb.cam.ac.uk/scop/ref/1995-jmb-scop.pdf">http://scop.mrc-lmb.cam.ac.uk/scop/ref/1995-jmb-scop.pdf</a> <br><br>
30 [3] <a href="http://en.wikipedia.org/wiki/Perl">Perl</a> <br><br>
31 [4] <a href="http://en.wikipedia.org/wiki/RasMol">RasMol</a> <br><br>
32 [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 <a href="http://scop.mrc-lmb.cam.ac.uk/scop/ref/nar2002.pdf">http://scop.mrc-lmb.cam.ac.uk/scop/ref/nar2002.pdf</a>