Molecular sculpting works like a real-time energy minimizer, except that it
isn't minimizing the energy. Instead, its just trying to return local atomic
geometries (bonds, angles, chirality, planarity) to the configuration the
molecules possess when they were first loaded into PyMOL.
To actually use this feature:
1. load a PDB file
2. configure the mouse for editing (Mouse menu)
or click in the mouse/key matrix box
3. select auto-sculpting from the Sculpting menu
4. select Sculpting from the Wizard menu
5. ctrl-middle-click on any atom in your protein to activate sculpting
the green part will be free to move
the cyan part will be a fixed cushion to provide context
the grey part will be excluded
6. now perform any conformational editing operation in the green region
ctrl-left-click-and-drag on an atom
ctrl-right-click on a bond, then ctrl-left-click-and-drag about that
You can adjust the radius and cushion using the blue pop-up menus.
Right now I'm not sure the sculpting feature is more than entertainment, but my
expectation is that it will become part of PyMOL's crystallographic model
building system in the future.
Warren L. DeLano, Ph.D.
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
From: patricia.a.elk...@gsk.com [mailto:patricia.a.elk...@gsk.com]
Sent: Thursday, July 18, 2002 4:04 AM
Subject: [PyMOL] molecular sculpting
I would like to understand the molecular sculpting possibilities of pymol
but haven't been able to figure it out yet. When using the wizard, the
first request is to click and atom but how to proceed from there?
I have used the bit of script provided on the web page and deformed
the benzene ring but have not been clever enough to see the possibilities
Could anyone provide just enough of a step-by-step push-this, click-that lead
molecular sculpting to get me started?