Jim, (we discussed this at ACS, but just for the mailing list record).
PyMOL does not yet support real-space refinement internally. However, I suspect one could use cctbx to accomplish this with PyMOL. Perhaps someone familiar with both open-source projects would like to take a stab at it? Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: Jim Nettles [mailto:jnet...@emory.edu] > Sent: Tuesday, August 30, 2005 6:00 AM > To: Warren DeLano > Cc: pymol-users@lists.sourceforge.net; Mathieu Coincon > Subject: Re: [PyMOL] Refinement in auto_sculpt > > Hello all, > > > Perhaps I'm awaking from hibernation or something, > but the communication below came as a surprise to me. > > > Do I read this correctly that Pymol does real space > refining into electron density using the sculpting function? > If so, that is great! I apologize if this has been discussed > before and I missed it. Could someone please clue me in as to > how to best use this function? > > > Thanks, > > > Jim Nettles > > > On Aug 30, 2005, at 8:33 AM, Warren DeLano wrote: > > > Mathieu, > > > > Deselect Sculpting from the builder menu or "unset sculpting" > > > > Note that if you're doing this a lot, then create some custom > on/off function keys as follows: > > > > # F1 to turn on sculpting > > cmd.set_key('F1',lambda > :(cmd.set("sculpting"),cmd.set("auto_sculpt"))) > > > > # F2 to turn off sculpting > > cmd.set_key('F2',lambda > :(cmd.unset("sculpting"),cmd.unset("auto_sculpt"))) > > > > Cheers, > > Warren > > > From: pymol-users-ad...@lists.sourceforge.net on behalf of > Mathieu Coincon > > Sent: Mon 8/29/2005 8:26 AM > > To: pymol-users@lists.sourceforge.net > > Subject: [PyMOL] Refinement in auto_sculpt > > > > > > Hi, > > i'm usinig pymol for modelling my protein in electron density. > > I like it very much but there is one thing I would like to > understand. > > Is there a way to stop the refinement of the geometry: > > I'm using auto_sculpt and I protect/deprotect the protein > but sometimes the > > refinemt run during a long time I would like to stop it ? i > played with the > > number of cycles and other parameters but it didn't work. > > > > > > > ------------------------------------------------------- > > SF.Net email is Sponsored by the Better Software Conference & EXPO > > September 19-22, 2005 * San Francisco, CA * Development > Lifecycle Practices > > Agile & Plan-Driven Development * Managing Projects & Teams * > Testing & QA > > Security * Process Improvement & Measurement * > http://www.sqe.com/bsce5sf > > _______________________________________________ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > >
