Thank you immensely for that list, Rolf. OK, so I have it set now to replace non alphanumeric digits with "_" in the variable name site_XXX. Not a perfect solution, but a serviceable one, I think.
Bob Rolf Huehne wrote: >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 > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------- 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
