AFAIK setting connect_mode=1 strictly uses the CONECT records from pdb file to draw bonds.

On 9/6/07, Mark A Saper <> wrote:
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


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