Re: [PyMOL] create double bonds in small molecules

[Warren D. <wa...@de...>]

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:le...@ae...] 
Sent: Thursday, May 14, 2009 10:13 AM
To: pym...@li...
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