I also would welcome such a feature. "3 Search all of PDB, for that spatial arrangement of residues"I think the EBI's Tempura does something similar or identical:
Tempura is a server that allows for specific templates to be generated from a submitted structure. These templates can then be scanned against a non-redundant subset of the PDB, a list of PDBcodes or an individual structure. http://www.ebi.ac.uk/thornton-srv/databases/tempura/ *Tempura* is a server designed to allow a user to specify the amino acids to be selected for searching using the "reverse template" approach previously published as part of the ProFunc suite Best, Eran On Thu, Apr 2, 2009 at 5:57 PM, Thomas Stout <[email protected]> wrote: > > As more of an "implementor" and end-user than a developer I would > agree that yes, this would be strongly welcomed! CCSDs ReLiBase does > this, but again that is far from user friendly or open source (and > ReLiBase+ is exorbitantly priced) > > Good luck, > Tom > > On Apr 2, 2009, at 7:23 AM, Chris Larsen <[email protected]> wrote: > > > All, > > > > I am attempting to write up a structure biology proposal for the > > NIH...and just trying to establish JMol capabilities here. > > > > Would you al agree that the following function does not exist in Jmol? > > > > 1 Select residues in a protein's catalytic group > > 2 Note positions relative to each other > > 3 Search all of PDB, for that spatial arrangement of residues > > 4 Return back list of of PDB IDs with rms deviation, as a table > > > > This is basically blast but for structure. I've gotten some static > > from review about this but I think a plug in would be really welcomed. > > Its sequence agnostic. What do you think? If we could get funding for > > this, it would add to the developer squad already on the team. Let me > > know please. I'm not talking about SYBYL, I'd like something for the > > masses to use easily...Highlight three things and press a button to > > launch. > > > > Further I'd like the spirit of this request to remain open source > > please, but the idea is mentioned in straight up confidence to this > > group and is already written up, so no poaching eh? We all have a lot > > on our plates but JMol is a really good effort I'd like to support. > > > > Cheers, > > > > Chris Larsen > > > > > > -- > > ** Vecna's Maryland office moved 11/6/08. > > My new phone, fax, and address are below.** > > > > Christopher Larsen, Ph.D. > > Sr. Scientist / Grants Manager > > Vecna Technologies > > 6404 Ivy Lane #500 > > Greenbelt, MD 20740 > > Phone: (240) 965-4525 > > Fax: (240) 965-4507 > > 240-737-1625 > > > > > > --- > > --- > > --- > > --------------------------------------------------------------------- > > _______________________________________________ > > Jmol-users mailing list > > [email protected] > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > ------------------------------------------------------------------------------ > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users >
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