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 such as: ctrl-left-click-and-drag on an atom ctrl-right-click on a bond, then ctrl-left-click-and-drag about that bond 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 -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. Informatics Manager Sunesis Pharmaceuticals, Inc. 341 Oyster Point Blvd. S. San Francisco, CA 94080 (650)-266-3606 FAX:(650)-266-3501 -----Original Message----- From: patricia.a.elk...@gsk.com [mailto:patricia.a.elk...@gsk.com] Sent: Thursday, July 18, 2002 4:04 AM To: firstname.lastname@example.org 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 from that. Could anyone provide just enough of a step-by-step push-this, click-that lead into the molecular sculpting to get me started? Thanks! Trissa