RE: [PyMOL] Displaying/defining double bonds in a ligand molecule

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

Wulf,

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.

Cheers,
Warren


-----Original Message-----
From: pym...@li... on behalf of Wulf =
Blankenfeldt
Sent: Mon 3/6/2006 6:22 AM
To: pym...@li...
Subject: [PyMOL] Displaying/defining double bonds in a ligand molecule
=20
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.=20
pymol doesn't know about its chemical nature. Googling a bit, I found=20
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,




Wulf



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