Re: [PyMOL] regarding APBS tools in PyMOL

2014-04-22 Thread Schubert, Carsten [JRDUS]
Hi Vaheh, my recollection is a bit hazy, but I remember having some issues with the distributed APBS version earlier this year. Try downloading the latest APBS and run the plug-in generated input file using the latest version from the commandline. If that works you may have to swap the APBs bin

[PyMOL] Dynoplot from the command line

2014-04-22 Thread V.V.
Hi, After installing Dynoplot I was able to start it via the plugins menu (which works fine), but when I try starting it via the command line it throws an error (please see the log file). Eventually I'd like to use Dynoplot in combination with "Monitor file continuously" one to visualize the outp

Re: [PyMOL] Detecting Plugins menu

2014-04-22 Thread Spencer Bliven
I just found the pymol._ext_gui property, which seems to be None if X11 is off and a positive number if X11 is present. Seeing as it's a private variable, is it ok to use this to check for X11 presence? -Spencer On Thu, Apr 17, 2014 at 10:21 AM, Spencer Bliven wrote: > Here's what I'm currentl

[PyMOL] regarding APBS tools in PyMOL

2014-04-22 Thread Oganesyan, Vaheh
Colleagues, The latest PyMOL version 1.7.0.3 looks like having issues with molecule size when APBS is being used. I’m loading whole molecule consisting of ~500 aa and APBS plugin after setting up the grid and after starting APBS run few seconds later opens a window with message: APBS stopped wo