It seems that one of the consequences of latest version of PDB (called "remediated" data or wwPDB) is that oxygen atoms in phosphate in nucleic acids have changed name, from O1P, O2P to OP1, OP2
If needed, I can do further research into this and confirm it is in fact a general change of rules in PDB, but with this file the change is indeed so: 1bna.pdb (new, from http://www.pdb.org/pdb/download/downloadFile.do?fileFormat=pdb&compres sion=NO&structureId=1BNA pdb1bna.ent (old, from ftp://ftp-original- v2.rcsb.org/pub/pdb/data/structures/all/pdb/pdb1bna.ent.Z As a result, Jmol (11.2.14 and 11.3.32) puts those atoms into the "bases" set, not the "backbone" set. Some update is needed in predefined sets definition to account for this. http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/vi ewer/JmolConstants.java?view=markup lines 2118 and 2119 ------------------------------------------------------------------------- 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
