[PyMOL] abalone
hi all: i have came across the sowftware abalone for molecular simulations, where they have mentioned we can do simulations of proetin molecule by stating specific force fields and at specified temperature. could i create mutations in pymol and open the same file in abalone?? how useful is abalone?? is their any other sowftware that will serve the same porpose (where i can do simulations to get stable protein - enzyme). kindly suggest me about this sowftware and its applications. thanks, mohan. -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] pymol dies when minimizing
I had once a problem with pymol that itr would not open from a terminal window. After a long battle with it, the problem was solved after I upgraded my OS. Robin Emig wrote: Does anyone else have the problem where pymol dies, or wont update the display after minimizing on windows? Is there a way to fix this? -Robin -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] pymol dies when minimizing
Hi, Yeah I have a similar issue and have been meaning to post it. On windows 7 following minimization, the viewer doesn't update when you open it again, no menus either. Using PyMOL 1.2r2 Looking forward to a solution J _ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 From: Robin Emig [mailto:re...@pacificbiosciences.com] Sent: Wednesday, 2 June 2010 7:34 a.m. To: pymol-users@lists.sourceforge.net Subject: [PyMOL] pymol dies when minimizing Does anyone else have the problem where pymol dies, or wont update the display after minimizing on windows? Is there a way to fix this? -Robin -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] convert surface from pymol into a CCP4 map
I have a nice cavity surface that I've made in PyMOL. I'd like to convert it to some type of envelope in CCP4 map format, for input into Coot. I know that surfaces can be saved in .wrl format. I've also tried using Voidoo to prepare a pseudo-map representing the cavity, but it doesn't look as good as the one from PyMOL. Any other approaches to this? -Mark _ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry University of Michigan Biophysics, 3040 Chemistry Building 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. sa...@umich.edu phone (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/?q=saper http://www.strucbio.umich.edu/ -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
[PyMOL] Fwd: abalone
hello all: any abalone users -- Forwarded message -- From: mohan raj mohanrajdec2...@gmail.com Date: Wed, Jun 2, 2010 at 11:41 AM Subject: abalone To: PyMOL-users@lists.sourceforge.net hi all: i have came across the sowftware abalone for molecular simulations, where they have mentioned we can do simulations of proetin molecule by stating specific force fields and at specified temperature. could i create mutations in pymol and open the same file in abalone?? how useful is abalone?? is their any other sowftware that will serve the same porpose (where i can do simulations to get stable protein - enzyme). kindly suggest me about this sowftware and its applications. thanks, mohan. -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
