[BioPython] filtering PDB files by resolution
Peter
biopython at maubp.freeserve.co.uk
Tue Jul 10 12:33:08 UTC 2007
Link to the "Top 500" PDB page,
http://kinemage.biochem.duke.edu/databases/top500.php
Peter wrote:
> Alternatively maybe you could take the list of PDB identifiers and your
> 1.00 Angstroms, and put these into the www.pdb.org web query interface.
Anyway, using the web interface, here are twenty structures from the 494
unique PDB IDs on the "Richardson group's Top 500" list done by X-Ray
crystallography with a resolution under 1.0 Angstroms:
1A6M 1.0
1AHO 1.0
1B0Y 0.9
1BXO 0.9
1BYI 1.0
1C75 1.0
1CEX 1.0
1EJG 0.5
1ETN 0.9
1GCI 0.8
1IXH 1.0
1LKK 1.0
1NLS 0.9
1RB9 0.9
2ERL 1.0
2FDN 0.9
2PVB 0.9
3PYP 0.9
4LZT 0.9
7A3H 0.9
I just pasted in the 494 unique PDB IDs (comma separated) and specified
the x-ray resolution to be between 0.0 and 1.0
Note 1A1Y (resolution 1.05 angstroms) is now obsolete, and does not
appear in the search results even if you relax the resolution limit.
Also watch out for the fact that some of the PDB IDs on the Top 500 list
have been replaced:
1TAX -> 1GOK
1GDO -> 1XFF
5ICB -> 1IG5
2MYR -> 1E70
Finally, I can't see how to use the web query to search for resolutions
from other experimental techniques - but it looks like all of the "Top
500" were done by x-ray anyway. Do check this!
Peter
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