Here's my two cents: On 18 Oct 2007 at 13:36, 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 think YES, and suspect O1 is not needed for remediated files (but we must leave it for the old ones) > It would be good to have specific examples of the following changes, and > to know how many structures show these changes: In my opinion, thee desn't seem to be a problem with any of the 20 amino acids; changes in names affect only hydrogen or deuterium (the others are fixes of wrongly identified atoms). > 2) Currently Jmol identifies a nucleic acid residue as a group > containing O5' or O5*. > > Q: Is this valid with the remediated set? I think YES Only O5 is checked? > It would be good to know what files show the following changes: > > O5* OP3 Worrying, yes > 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?) Well, I guess it was since all of us were selecting backbone all the time. The only significant changes I've detected for proteins (details sent to Bob off-list) are terminal amino hydrogens and glycine alpha hydrogens. For nucleics, I reported yesterday. Hope it helps and we'll have a shiny 11.4 fully PDB v2- and v3-compatible. I'm still amazed at how the wwPDB people have done the remediation and there is no such thing as a document listing atom name changes. The "dictionary" is unworkable (has molecules, or residues, not atoms). Or I'm being very dense. ------------------------------------------------------------------------- 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
