Re: [PyMOL] Odd issue with control and shift keys in pymol

Hi Paul and Adam, I can confirm this. The problem comes with two patches that Fedora applies to freeglut (freeglut_xinput.c). I don't know why they do this, but if I compile freeglut without those, PyMOL works fine. Paul, that 1.4.1 version of PyMOL and also Coot, are those linked to the system g

Re: [PyMOL] Odd issue with control and shift keys in pymol

Hi Thomas, Thanks for the info. I don't have the 1.4 version of Pymol handy at the moment, but Coot does use the system libglut without problems. --p On 07/01/2013 05:36 AM, Thomas Holder wrote: > Hi Paul and Adam, > > I can confirm this. The problem comes with two patches that Fedora > applie

Re: [PyMOL] cut protein in half

Hi Yeping, The technique will differ depending on the structure you have. Can you send me a copy and I can try to put something together for you? If it's a homodimer, usually we can just disable one unit and show the open channel. Also, see http://hollow.sourceforge.net/channel.html and http://ww

Re: [PyMOL] 2013 PyMOL Open Source Fellowship–Request for Applications

Greetings PyMOLers, We have pushed back the deadline for the 2013 PyMOL Open Source Fellowship program to July 8th for those wishing to participate. If you like PyMOL, science, programming, and open-source here's your chance to give back. Students and postdocs are especially welcome to apply. For

[PyMOL] restricting selection to the current frame

Hi, Is it possible to force a selection to only apply to the specific frame rather then across frames? I'm running in to a problem where I have some (~40) frames from an explicit solvent MD that I want to look at. What I want to do is look at water molecules around a specific residue at each fra

Re: [PyMOL] restricting selection to the current frame

I know you have asked for frames, but I assume that each frame is mapped to a state. The selection logic allows for you to specify the state. So if the waters of interest are in state 1,40: python for i in range(1,41): cmd.select("wat_"+i,"byres in within 6 of ",state=i) python end J > 'sel

Re: [PyMOL] Label problems (PyMOL ver. 1.6)

Hi Yoshitaka, did you get the source code from SVN? On June 13 (after 1.6.0.0 release) we pushed a label related fix to SVN, does that fix your issue? Can you also check if it's related to shaders and if yes, tell us what graphics card you have? PyMOL> set use_shaders, 0 PyMOL> set use_shaders,

Re: [PyMOL] restricting selection to the current frame

Yes, sorry, the frames are mapped to states. Ah, yes, that is what I needed, that 'state' keyword argument was not listed in the wiki page. For posterity's sake, a couple of minor modifications were required in the code you provided. python for i in range(1,41): cmd.select("wat_" + str(i),

Re: [PyMOL] restricting selection to the current frame

Matthew Baumgartner wrote, On 07/01/13 21:34: > I removed the byres command because I have more then 1 water > molecules in my system and the residue ID's were rolling over and waters > far from the residue of interest were being selected. > If anyone has a suggestion on this, please let me k

[PyMOL] Accessing progress bar

Hi, My google-fu didn't find anything, but is it possible to access the progress bar in pymol (the one that comes up when ray tracing) in a script? I have a script that is a little long running and it would benefit from giving users feedback on progress. Thanks, Matt -- ---