Tom,

 

set valence

 

edit_mode

 

Ctrl-right-click on the bond

 

Ctrl-W

 

seems to do the trick.  Perhaps there’s a problem with the version of PyMOL you’re using?

 

Cheers,

Warren

 


From: Thomas S. Leyh, Ph. D. [mailto:leyh@aecom.yu.edu]
Sent: Thursday, May 14, 2009 10:13 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] create double bonds in small molecules

 

Hi,

 

    I've been trying to get PyMOL to display a double bond at the position of the vinyl in the attached, small-moleculePDB for some time.  The PDB was generated by converting a smiles representation of isopentenly diphosphate (obtained from PubChem) using Corina.  The number of attached atoms at the vinyl group is correct, but PyMOL doesn't display the double bond.  Cycling the bond valence produces a single-bond version (with added protons), but stops there - it won't cycle through triple, double, single.  Downloaded a PDB of fumarate that does display double bonds in response to Set Valence - so, my version of PyMOL (1.1beta2, Vista environment) seems fine.

 

    Thoughts?

 

    Thanks,

 

    Tom