By default, PyMOL creates single bonds when joining fragments. To
change a bond valence, CTRL-right click on the bond to select it. You
should see a "ring" about the bond. Then press CTRL-W to cycle through
the possible bond valences: single, double, triple.
Note that it is essentially impossible right now to build complex
molecules in PyMOL without using some external molecular minimization
and mechanics program, since the "molecular sculpting" feature can only
maintain pre-existing atomic geometries. =20
For coarse modeling of protein-ligand interactions, I tend to use PyMOL
to draw the initial covalent structures, use MacroModel to perform
energy minimization, and then return the structure to PyMOL for purposes
modeling the complex.
Warren L. DeLano, Ph.D.
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
> -----Original Message-----
> From: Guillaume Michaud [mailto:r1ck5p@...]
> Sent: Monday, March 11, 2002 12:43 PM
> To: pymol-users@...
> Subject: [PyMOL] Create a double bond
> PLEASE WRITE BACK TO=20
> I was just wondering how to create a=20
> double bond between two atoms (for=20
> example between a carbon and an oxygen=20
> or C=3DC).
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