The easiest thing would be to convert your small molecule to an SDF, MOL, or MOL2 format before loading it into PyMOL.

Short of that, you'd have to select each bond independently (ctrl-right-click while in editing mode) and use Ctrl-W to set the valences.


-----Original Message-----
From: pymol-users-admin@lists.sourceforge.net on behalf of Wulf Blankenfeldt
Sent: Mon 3/6/2006 6:22 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Displaying/defining double bonds in a ligand molecule

Hello pymolers,

I'd like to display double bonds in a small molecule ligand bound to the
active centre of a protein. Of course, the ligand is non-standard, i.e.
pymol doesn't know about its chemical nature. Googling a bit, I found
that I can

set valence, 0.1

but this only display double bonds in the protein, which I don't want.

How do I teach pymol to display double bonds in my ligand?

Thanks for your help,


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