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: [] 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

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

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