[PyMOL] Install pymol as module in python in linux
Hi all, I have been trying for a while, but cannot seem to figure out how to install pymol on my unix server so that I can run pymol from within a python script. (So that I can use it with the command ' import pymol'. I did manage to do this on my windows with a wheel, but don't know how to solve it on my unix system) Any tips would be very welcome! Thanks, 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 (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] (no subject)
This worked! Thank you Leandro and Jed! From: jedg...@gmail.com [mailto:jedg...@gmail.com] On Behalf Of Jed Goldstone Sent: Tuesday, April 4, 2017 11:35 To: Vivien Schoonenberg <vivienschoonenb...@gmail.com> Cc: pymol-users@lists.sourceforge.net 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 <vivienschoonenb...@gmail.com <mailto:vivienschoonenb...@gmail.com> > 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 (PyMOL-users@lists.sourceforge.net <mailto: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 -- - 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) -- 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 (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] (no subject)
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 (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] Getting rid of shadows
Hi Rui, Thank you! I also already figured out that if I turn off the depth cue most of my problem is solved as well ( set depth_cue, 0) -Vivien From: Rui Sousa [mailto:rui.so...@univ-nantes.fr] Sent: Thursday, February 23, 2017 10:02 To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Getting rid of shadows Hi Vivian, I'm not sure if I fully understand your question, but if you want to have a picture without shadows, by using "set light_count, 0" (https://pymolwiki.org/index.php/Light_count) you should be able to achieve this. Rui Le 22/02/2017 17:46, Vivien Schoonenberg a écrit : Hi, Im recoloring my protein in different shades of similar colors, but to truly see the difference between them, I want to create a view in pyMOL without any shadows. For this purpose, I want to make a half sphere behind the camera with lights, which all emit the same amount of light. I have a hard time figuring out how to set coordinates and changing the strength of the lights. Do you maybe have a suggestion on how to solve this? Thanks, 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 (PyMOL-users@lists.sourceforge.net <mailto: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 -- 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 (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] Getting rid of shadows
Hi, I'm recoloring my protein in different shades of similar colors, but to truly see the difference between them, I want to create a view in pyMOL without any shadows. For this purpose, I want to make a half sphere behind the camera with lights, which all emit the same amount of light. I have a hard time figuring out how to set coordinates and changing the strength of the lights. Do you maybe have a suggestion on how to solve this? Thanks, 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 (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
