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? 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 2) Currently Jmol identifies a nucleic acid residue as a group containing O5' or O5*. Q: Is this valid with the remediated set? It would be good to know what files show the following changes: O5* OP3 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?) Bob Rolf Huehne wrote: >Bob Hanson wrote: > >>Rolf, three questions: >> >>1) Can you run the same analysis, restricting your search to ATOM >>records? I'm guessing (hoping) that a lot of these are HETATM. >> > >There are now additionally new versions available based only on "ATOM" >records of pre-remediated files: > >1) Unique atom name changes (580 entries, 5 KB) >http://www.fli-leibniz.de/ImgLibPDB/tmp/pdb_remediation-atom_name_changes-atom_records-unique.txt > >2) Residue specific atom name changes (2714 entries, 43 KB) >http://www.fli-leibniz.de/ImgLibPDB/tmp/pdb_remediation-atom_name_changes-atom_records-residue_specific.txt > >3) All atom name changes (8682747 entries, compressed, 86 MB) >http://www.fli-leibniz.de/ImgLibPDB/tmp/pdb_remediation-atom_name_changes-atom_records-full.zip > > >>2) Is there a way to detect that a file is remediated? For example, in a >>remark? >> >> >It is indicated in "REMARK 4" described generally in >"http://www.wwpdb.org/documentation/format23/remarks1.html#REMARK4"; and >specifically for remediation in >"http://www.wwpdb.org/documentation/format3.0.1-dif.pdf";. > > > > >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
