Subject: RE: [PyMOL] Possible hydrogen addition bug Hi all,
I believe this would be as a result of the "pdb" file not containing the hybridisation information. When you manually change that bond to be double (using the builder module) and then add hydrogens it is correct. This is not an uncommon issue with small molecules from the pdb. Bob, as an aside, which viewers do read cif files as coordinates? I know Mercury does. Cheers Joel -----Original Message----- From: Matthew Baumgartner [mailto:mp...@pitt.edu] Sent: Friday, 7 June 2013 8:51 a.m. To: pymol-users Subject: [PyMOL] Possible hydrogen addition bug Hi, I may have found a bug in the way pymol interprets connectivity of atoms. I noticed this in one pdb structure that I am working with 1RV1. Steps to reproduce: fetch 1RV1 #extract one of the ligands to it's own object extract 'lig', /1RV1//A/110 #add hydrogens h_add lig Now look at atom C2 on the ligand and notice that pymol added a hydrogen almost along an existing bond to another ring. I am running pymol 1.5.0.1 on Ubuntu 13.04. I'm not sure if this has been reported before and has been fixed already in 1.6. I haven't gotten around to upgrading yet, but I am willing to. Thanks, Matt -- ------------------------------------------------------------------------------ How ServiceNow helps IT people transform IT departments: 1. A cloud service to automate IT design, transition and operations 2. Dashboards that offer high-level views of enterprise services 3. A single system of record for all IT processes http://p.sf.net/sfu/servicenow-d2d-j _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net ------------------------------------------------------------------------------ How ServiceNow helps IT people transform IT departments: 1. A cloud service to automate IT design, transition and operations 2. Dashboards that offer high-level views of enterprise services 3. A single system of record for all IT processes http://p.sf.net/sfu/servicenow-d2d-j _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
