Re: [PyMOL] Slow Pymol rendering

2016-05-06 Thread Chen Zhao
Dear James, Thank you for your help! I tried versions 364.19, 352.79, 340.96, and none of them worked. Finally, I tried version 304.131 and it worked! (although my graphics card is listed as supported under all versions). Later I realized that command nvidia-detect could check which driver should

Re: [PyMOL] High Resolution Ray Tracing

2016-05-06 Thread David Hall
Feel free to send me the files off list. -David Hall > On May 6, 2016, at 1:54 PM, Stephen Kerry wrote: > > Dear All, > > I have a protein complex scene that I need to create a large, high resolution > (1200 dpi) ray traced image of, but am unable to do so as I always run out of > memory at

[PyMOL] High Resolution Ray Tracing

2016-05-06 Thread Stephen Kerry
Dear All, I have a protein complex scene that I need to create a large, high resolution (1200 dpi) ray traced image of, but am unable to do so as I always run out of memory at the end of the ray tracing process, with the following error: python2.7(972,0x7fff7397f300) malloc: *** mach_vm_map(

Re: [PyMOL] Slow Pymol rendering

2016-05-06 Thread James Kress
The NVIDIA driver for x64 Linux is free and can be downloaded here: http://www.nvidia.com/download/driverResults.aspx/101818/en-us Or you can search here for something different: http://www.nvidia.com/Download/Find.aspx?lang=en-us Jim James Kress Ph.D., President The KressWorks® Foun

Re: [PyMOL] different distance calculated for same atoms

2016-05-06 Thread Julian Heinrich
Hi You're passing more than one atom per selection to the cmd.distance() function, in which case the function returns the average between the measured distances (http://pymolwiki.org/index.php/Distance#PYMOL_API ). On a side note, this could be done much simpler: fetch 2nuz, async=0 h_add resn LE

[PyMOL] Slow Pymol rendering

2016-05-06 Thread Chen Zhao
Dear all, I recently upgraded to Debian 8 and I compiled the source code for pymol 1.8.2.0. However, the graphics is really slow. The information that pymol prints out is as follows: Detected OpenGL version 2.0 or greater. Shaders available. Detected GLSL version 1.30. OpenGL graphics engine:

[PyMOL] different distance calculated for same atoms

2016-05-06 Thread riddhiman sarkar
Hello , I am a new Pymol user. I am trying to calculate all the H-H distances between the methyl protons (CH3) in different Leucine residues in a protein, which are within 5A. For some reason, if I rerun the program with a distance threshold of 2A, I get different values for the same atoms. Here