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
