Actually, upon closer look, the residue wasn't defined using the proscribed PDB alternate location identifiers, so in fact, PyMOL itself is unable to avoid misconnecting the atoms. Thus, you'll need to use "unbond" either way.
_____ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of DeLano Scientific Sent: Thursday, September 06, 2007 11:24 AM To: 'Mark A Saper'; 'Pymol' Subject: Re: [PyMOL] PDB changed CONNECT records Mark, set connect_mode = 0 is the default, and this uses both distance-based and explicit (CONECT-based) connectivity. set connect_mode = 1 uses only explicity connectivity we don't have a connect_mode = 2 yet (forcing use of distance-based connectivity only), so instead, you'll need to remove the errant CONECT records from the "new & improved" pdb file or simple unbond the mis-connected residues. unbond ARA`307/, ARB`308/ Cheers, Warren _____ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Mark A Saper Sent: Thursday, September 06, 2007 10:48 AM To: Pymol Subject: [PyMOL] PDB changed CONNECT records This was previously discussed in an archived email but I can't find it right now. Does the setting connect_mode=0 use the CONECT records in the PDB file or not? I think it does. Apparently in pdb code 1ABE, the CONECT records were changed in a 2005 revision. Two alternate sugar conformations are now interconnected when using the current 1ABE. The old 1ABE (from 1993) seems fine. Should setting connect_mode to 0 before loading PDB fix it? I don't think it does. Thanks, Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics, University of Michigan 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. sa...@umich.edu (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html
