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/

From: [] 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.



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. (734) 764-3353 fax (734) 764-3323