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Revision: 1.2
Committed: Tue Apr 10 09:16:48 2007 UTC (9 years, 8 months ago) by dmb
Branch: MAIN
CVS Tags: HEAD
Changes since 1.1: +49 -35 lines
Log Message:
Slug fix.

Don't forget to visit http://www.bioinformatics.org/pdbHighlight/

Line File contents
1
2 Title
3
4 PDBHighlight: A RasMol script database.
5
6
7
8 Introduction
9
10 The aim of pdbHighlight is to maintain a searchable database of RasMol
11 script files, designed to 'highlight' various features of the protein
12 molecules whose structures are available in the Protein Data Bank (PDB
13 [1]).
14
15 Currently the only script available highlights PDB files according to
16 the domain definitions of the Structural Classification of Proteins
17 (SCOP [2]) database.
18
19
20
21 Using pdbHighlight
22
23 The 'ras_script' command line utility is called with the following
24 syntax;
25
26 ras_script < pdb-code >
27
28
29 First, 'ras_script' calls the 'scopHighlight_using_flat_file.plx' Perl
30 [3] script that creates a RasMol [4] script file to highlight the PDB
31 file according to its SCOP domain annotation.
32
33 Next, 'ras_script' creates a temporary file which combines the PDB
34 file with the script file, and invokes RasMol over this new file.
35
36 The 'scopHighlight_using_flat_file.plx' script requires the SCOP
37 parsable files [5], which can be downloaded using the
38 'wget_domain_data.plx' utility. Please check
39
40 http://scop.mrc-lmb.cam.ac.uk/scop/index.html
41
42
43 for the latest version of the data.
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45
46
47 Installing
48
49 All three Perl scripts require various configuration options which
50 should be obvious. All three could be improved by making this more
51 obvious. Copy the right files into the right places and everything
52 should work nicely. The current major limitation is that a local copy
53 of the PDB is expected. It would be easy to include a 'wget' step to
54 grab the PDB from a remote location.
55
56
57
58 References
59
60 [1] Bernstein FC, Koetzle TF, Williams GJ, Meyer EF Jr, Brice MD,
61 Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. (1977). The Protein
62 Data Bank: a computer-based archival file for macromolecular
63 structures. J. Mol. Biol. 112, 535-542
64
65 [2] Murzin AG, Brenner SE, Hubbard T, Chothia C. (1995). SCOP: a
66 structural classification of proteins database for the investigation
67 of sequences and structures. J. Mol. Biol. 247, 536-540
68 http://scop.mrc-lmb.cam.ac.uk/scop/ref/1995-jmb-scop.pdf
69
70 [3] Perl
71
72 [4] RasMol
73
74 [5] Lo Conte L, Brenner SE, Hubbard TJP, Chothia C, Murzin A. (2002).
75 SCOP database in 2002: refinements accommodate structural genomics.
76 Nucl. Acid Res. 30, 264-267
77 http://scop.mrc-lmb.cam.ac.uk/scop/ref/nar2002.pdf