Rolf Huehne wrote: >Bob Hanson wrote: > > >>Great work, Rolf. Here are three important questions: >> >>1) Currently Jmol identifies a protein residue as a group that contains >>N, CA, and C and either O or O1. >> >>Q: Is this still viable with the remediated set? >> >> >> >I scanned all remediated PDB files for residues that match this >condition and added full names for the residue names from the "chemical >Components Dictionary" (if available) to the resulting list >(temporarily) available at >"http://www.fli-leibniz.de/ImgLibPDB/tmp/scan_pdb_for-N_C_CA-and-O_or_O1-residues-2007_10_19-with_names.txt"; > >The list will only help to identify false positives but not help to >identify false negatives. > > > This could be valuable. I forgot to mention that this is just the preliminary filter. Jmol also checks the ATTACHMENT of these groups -- there has to be a sequence: N-CA-C-O, which I think the vast majority of items on this list would fail. Anyway, I'm not sure I want to do a full-fledged analysis of this. Basically it sounds like there's no significant change here.
>Q: What about protein structures with only alpha carbon atoms? > > > That's easy -- only CA. >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
