From: Jed G. <jgo...@wh...> - 2017-04-04 15:35:37
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Try using remove not alt +A to remove alternative conformations. Jed On Mon, Apr 3, 2017 at 11:47 AM, Vivien Schoonenberg < viv...@gm...> wrote: > Hi there, > > > > I’m saving the sequences from each chain of the PDB via pymol with > > >>save something.fasta, chain A > > > > This is the same sequence that is shown in pymol and seems to correspond > to the structure I am looking at. > > However, when I loaded new B-factors in my structure, I noticed something > funny happened. The list which I made corresponding to the sequence I saved > earlier was too short. > > I found out by iterating that some residues repeated themselves(>>iterate > (chain A and n. CA), print resn). They carry the same residue number, and > are not shown in the sequence. However, when I load my B-factors my list > shifts because of these repeats, making it too short for the complete chain > and loading the wrong value onto residues. > > > > Does anyone know why this happens and how I can fix this? > > > > Thank you, > > Vivien > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- ------------------------- Jed Goldstone, PhD Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS #32 Woods Hole, MA 02543 http://www.whoi.edu/hpb/Site.do?id=481 (508) 685-2253 (cell/home) (508) 289-4823 (work/WHOI) |
From: Vivien S. <viv...@gm...> - 2017-04-04 15:44:49
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This worked! Thank you Leandro and Jed! From: je...@gm... [mailto:je...@gm...] On Behalf Of Jed Goldstone Sent: Tuesday, April 4, 2017 11:35 To: Vivien Schoonenberg <viv...@gm...> Cc: pym...@li... Subject: Re: [PyMOL] (no subject) Try using remove not alt +A to remove alternative conformations. Jed On Mon, Apr 3, 2017 at 11:47 AM, Vivien Schoonenberg <viv...@gm... <mailto:viv...@gm...> > wrote: Hi there, I’m saving the sequences from each chain of the PDB via pymol with >>save something.fasta, chain A This is the same sequence that is shown in pymol and seems to correspond to the structure I am looking at. However, when I loaded new B-factors in my structure, I noticed something funny happened. The list which I made corresponding to the sequence I saved earlier was too short. I found out by iterating that some residues repeated themselves(>>iterate (chain A and n. CA), print resn). They carry the same residue number, and are not shown in the sequence. However, when I load my B-factors my list shifts because of these repeats, making it too short for the complete chain and loading the wrong value onto residues. Does anyone know why this happens and how I can fix this? Thank you, Vivien ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ PyMOL-users mailing list (PyM...@li... <mailto:PyM...@li...> ) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... -- ------------------------- Jed Goldstone, PhD Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS #32 Woods Hole, MA 02543 http://www.whoi.edu/hpb/Site.do?id=481 (508) 685-2253 (cell/home) (508) 289-4823 (work/WHOI) |
From: jacky z. <jac...@gm...> - 2017-07-30 03:26:39
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Hi, pymol external gui menus missing, I have compiled pymol in mac os by using brew. Anyone can provide some suggestions? Jacky -- Lei Zhao, Ph.D. & M.D. Associate Professor National Clinical Research Center for Normal Aging and Geriatric National Engineering Research Center for Antibody Medicine The Key Lab of Normal Aging and Geriatric PLA General Hospital Beijing 100853 P.R.China Tel:86-15210661966 |
From: David H. <li...@co...> - 2017-07-31 18:20:03
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For some reason, the people doing brew have decided to stop supporting compiling tcl-tk with X11 support. Not 100% sure, but I'm pretty certain pymol cannot use tcl-tk with aqua. If you already had pymol installed, this seems to eliminate the external gui. If you didn't, new installations of pymol will now crash randomly. Here's how I got to the old version that worked $ cd /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/ $ git checkout 46e1ef94247cd2fb9555b724c05aaaa1e8907996 -- tcl-tk.rb $ cd ../../homebrew-science/ Edit the pymol.rb file so that it depends on "tcl-tk" instead of "homebrew/dupes/tcl-tk" $ brew remove tcl-tk python pymol $ brew install pymol $ brew pin tcl-tk Really, I uninstalled all my homebrew packages and then reinstalled everything because some of their changes over the last 6 months had made things oddly broken. If you want to do the same, you can try this: $ brew list > installed $ <installed xargs brew remove $ brew cleanup $ <installed xargs brew install -David On Sat, Jul 29, 2017 at 11:26 PM, jacky zhao <jac...@gm...> wrote: > Hi, > pymol external gui menus missing, I have compiled pymol in mac os by using > brew. > > Anyone can provide some suggestions? > > Jacky > > -- > Lei Zhao, Ph.D. & M.D. > Associate Professor > National Clinical Research Center for Normal Aging and Geriatric > National Engineering Research Center for Antibody Medicine > The Key Lab of Normal Aging and Geriatric > PLA General Hospital > Beijing 100853 > P.R.China > Tel:86-15210661966 > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
From: ragini s. <rag...@gm...> - 2018-10-07 17:23:10
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Pls unsubscribe me |
From: P D. <pd...@cd...> - 2018-10-12 06:52:29
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Please unsubscribe me |
From: Jose A. S. P. <asa...@ci...> - 2018-10-16 14:54:34
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Please unsubscribe me. -- *Dr. Arturo Sánchez* Full member of the American Society for Virology Full Member of the World Society for Virology Miembro de la Red Mexicana de Virología Miembro del Consejo Consultivo Científico de la CIBIOGEM *Centro de Investigaciones Biológicas del Noroeste S. C. (CIBNOR)* Laboratorio de Referencia, Análisis y Diagnóstico en Sanidad Acuícola Calle Hermosa 101. Col. Los Ángeles. CP 83106. Hermosillo, Sonora. México. Tel. +52 (662) 2-13-15-93. Ext 5004. https://www.cibnor.mx/ E-mail: asa...@ci... Skype: swine.flu3 |
From: Len B. <ban...@um...> - 2019-03-16 20:04:49
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From: Warren L. D. <wa...@su...> - 2001-11-22 20:32:41
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On Thu, 22 Nov 2001, Sona Vasudevan wrote: > Hi! > > Just wondering if there is a way to save a pymol session like in Insight > and setor if I want to get back to it. PyMOL isn't quite as sophisticated as Insight II in this respect, however the logging features can achieve session-like behavior. It works sort-of like Grasp but with log files that are much more straight-forward to edit and modify, since they are written in the PyMOL command language (.pml files) or using PyMOL's Python API (.pym files). Example: Select "Log..." from the file menu immediately after you start PyMOL to start writing a ".pml" or ".pym" log file. Go about your business. When done, press the "Get View" button and quit the program. To resume your "session", launch PyMOL and select "Resume..." from the file menu. Open your log file and *PRESTO* PyMOL should be in the same state as when you left. Any additional actions you then take will be appended on to the log. Note that any "ray", "png", or "save" operations will be repeated when you resume the log file. Thus, you may want to edit the log file and remove these commands with a text editor (Notepad on Windows) before resuming. Perhaps it would be nice to have a setting which ignores this kinds of commands when resuming. Hmm... - Warren PS. There is only bug I know of in the logging feature of 0.68 which affects conformational editing when logging to .pml files. It will be fixed in the next release, but for now just log to .pym files if you are going to edit conformations. |