Frieda Reichsman wrote: > > On Oct 15, 2007, at 11:45 AM, Angel Herraez wrote: > >> SITE 1 CAT 3 SER A 200 GLU A 327 HIS A 440 >> >> would give e.g. >> >> define site_CAT SER200:A, GLU327:A, HIS440:A >> >> right? >> >> then, you could >> select site_CAT >> >> >> That must be done within the pdb reader, I guess. >> >> For sure the Master can take care of this in a snap :-) > > This would be a powerful piece of code for Jmol. Eric Martz implemented > a similar thing in Protein Explorer (see the "Features of the Molecule" > control panel in PE) and it is wicked cool, not to mention incredibly > useful. > > There can be more than one "site" defined in a pdb file, for example > catalytic as opposed to ligand-binding, and there can be more than one > of each, of course. I don't know how much that would complicate things. > At present, a minority of pdb file define sites, but still, a very > useful feature when the definitions are there. >
We also implemented a "site" selection mechanism in the "JenaLib Jmol Viewer" (e.g.: http://www.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=1deh&VIEW=site). Since we are scanning the whole PDB for site information it might be helpful to share our observations: 1) Until now all site identifiers are unique inside each PDB file. This means that each site is present only once. If there are several sites of the same type the identifiers are usually numbered, e.g. ZA1, ZA2. 2) Unlike Eran seems to think there is no defined site number, only the siteID . (see PDB format description at "http://www.wwpdb.org/documentation/format23/sect7.html";) 3) There are about 100 PDB entries with site documentation but without a residue list. 4) There are currently 26 site IDs with special characters not compatible with Jmol set definitions: +--------+---------+ | PDB_id | site_id | +--------+---------+ | 1a03 | L2' | | 1a03 | LI' | | 1a4u | ND' | | 1aqp | C-I | | 1cbf | P-4 | | 1gqv | P-1 | | 1ies | 1' | | 1ies | 2' | | 1nlk | E-P | | 1rne | S1' | | 1rne | S2' | | 1sbn | S1' | | 1sbn | S2' | | 1sbn | S3' | | 1sbn | S4' | | 1sib | S1' | | 1sib | S2' | | 1sib | S3' | | 1srx | S-S | | 1ums | S1' | | 1ums | S2' | | 1ums | S3' | | 1umt | S1' | | 1umt | S2' | | 1umt | S3' | | 2dlf | H-1 | +--------+---------+ 5) You have to be careful with hetero component residue names. They might clash with reserved words in Jmol. Therefore we avoid including the residue name in the set definition. Regards, Rolf ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
