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. Q: What about protein structures with only alpha carbon atoms? 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
