From: Lieven B. <li...@ul...> - 2002-07-18 15:18:13
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Pat...@gs... wrote: > 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? I don't know about the script or the wizard (yet), but I did try the sculpting demo in the Demo menu. You can then just drag atoms by left-clicking them while holding down the control key. The dragged atom moves, everything it is connected to is dragged along, and the structure tries to minimize its energy. Great fun! -- Lieven Buts Department of Ultrastructure Brussels Free University |
From: DeLano, W. <wa...@su...> - 2002-07-18 16:39:30
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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. =20 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:=20 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 --=20 mailto:wa...@su...=20 Warren L. DeLano, Ph.D.=20 Informatics Manager=20 Sunesis Pharmaceuticals, Inc.=20 341 Oyster Point Blvd.=20 S. San Francisco, CA 94080=20 (650)-266-3606 FAX:(650)-266-3501=20 -----Original Message----- From: Pat...@gs... [mailto:Pat...@gs...] Sent: Thursday, July 18, 2002 4:04 AM To: pym...@li... Subject: [PyMOL] molecular sculpting I would like to understand the molecular sculpting possibilities of = pymol=20 but haven't been able to figure it out yet. When using the wizard, the=20 first request is to click and atom but how to proceed from there?=20 I have used the bit of script provided on the web page and deformed=20 the benzene ring but have not been clever enough to see the = possibilities=20 from that.=20 Could anyone provide just enough of a step-by-step push-this, click-that = lead into the=20 molecular sculpting to get me started? Thanks!=20 Trissa |
From: Lieven B. <li...@ul...> - 2002-07-19 08:14:11
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"DeLano, Warren" wrote: > 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. I agree. I think it has great potential there, as it allows for a more "physical" or "intuitive" way of manipulating the model than moving individual atoms or turning torsion angles. -- Lieven Buts Brussels Free University |