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 am still working on this... > > It would be good to have specific examples of the following changes, and > to know how many structures show these changes: > > C C1 > C C2 > C CA > C CB > > CA C1 > CA C2 > CA CH3 > > N N6 > N OXT > > O C > O CA > O CB > O H1 > O N > O O8 > O OXT > O1 OD > > 3HH3 C > O C > UNK C > C CA > O CA > UNK CA > > N1 N > NT N > O N > UNK N > > > OT1 O > OXT O > UNK O > > A list is (temporarily) available at "http://www.fli-leibniz.de/ImgLibPDB/tmp/atom_name_change_examples-2007_10_19.txt";. > > 2) Currently Jmol identifies a nucleic acid residue as a group > containing O5' or O5*. > > Q: Is this valid with the remediated set? > I scanned all remediated PDB files for atom names containing "O5'" or "O5*" 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/pdb-O5_check-2007_10_19-unique_residues-with_names.txt";. > It would be good to know what files show the following changes: > > O5* OP3 > They are included in the first list mentioned above. > > 3) In addition, Jmol attempts to determine backbone atoms from a list of > known backbone atoms. These atoms currently include: > > 1H,1H2',1H5',1HA,2H,2H2',2H5',2HA,2HO',3H, > C,C1',C2',C3',C4',C5',CA,H,H1',H3',H3T,H4',H5T,HA, > N,O,O1,O1P,O2',O2P,O3',O4',O5',O5T,OP1,OP2,OXT,P > > (where ' may be *) > > Q: Is this valid? (Was it ever?) > I am not a chemist and don't feel competent enough to judge this. 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
