Petro,
 
I am not sure this works in older versions, but
 
set connect_mode,1
 
Should force current versions of PyMOL to only use connectivity information explicitly provided in the PDB file.
 
Cheers,
Warren

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From: pymol-users-bounces@lists.sourceforge.net [mailto:pymol-users-bounces@lists.sourceforge.net] On Behalf Of Piter_
Sent: Monday, July 14, 2008 12:28 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] How to disable automatic atom connection?

Hi all.
How can I disable automatic atom connection in pymol.
I want Pymol to make bonds only using connect field in pdb file.
Thanks.
Petro.