Eran, it's a great idea. I've added this capability to Jmol. The next version of Jmol, 11.3.33, will have this support.
Eran Hodis wrote: >Hello, > >I'd like to select sites that have been defined in a pdb file but >have been unable to do so. > >As an example I point to the file 2ace.pdb which includes the >following lines in its PDB file: > >REMARK 800 SITE >REMARK 800 SITE_IDENTIFIER: CAT >REMARK 800 SITE_DESCRIPTION: CATALYTIC TRIAD. > >SITE 1 CAT 3 SER A 200 GLU A 327 HIS A 440 > > >I'd like to be able to issue a command in Jmol that selects a site >either by site number of by site_identifier. How can I do this? It >seems like it is possible from the documentation, but I have so far >not succeeded. > > > The command will be in this case: select site_cat or select site_1 And the Jmol variable site_cat will be assigned the list of groups corresponding to this site: print site_cat > [SER]200:A > [GLU]327:A > [HIS]440:A Multiple sites will be defined, as for 1hf4, and each time a file is loaded, the site list will be reset. To see the site list for any loaded protein, use show site_list or print site_list site_list can then be programmatically used to make lists of the sites: script inline "select " + site_list[1] --Bob >Thank you, >Eran Hodis > >------------------------------------------------------------------------- >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
