Re: [PyMOL] APBS plug in (2.1) with PyMOL v1.7

2014-01-22 Thread Ben Eisenbraun
and .pdb are there. You didn't mention what version of OS X you are using, but the apbs binary included with MacPyMOL doesn't run on versions prior to 10.8. It's relatively straightforward to compile APBS from source and replace the binary in the app bundle. It's at pymol

Re: [PyMOL] Shader issues and automatic disabling (was Re: I just built pymol, comes up but hangs on any attempt...)

2012-10-15 Thread Ben Eisenbraun
follows. infoLog=x PyMOLShader_NewFromFile-Warning: default shader files not found, loading from memory. CShaderPrg_Link-Error: Shader program failed to link name='default'; GL_MAX_VARYING_FLOATS=60 log follows. CShaderPrg_New-Error: vertex shader compilation failed name='volu

Re: [PyMOL] Shader issues and automatic disabling (was Re: I just built pymol, comes up but hangs on any attempt...)

2012-10-05 Thread Ben Eisenbraun
e shaders are actually loaded. In my local test case, the PyMOL directory is hosted on NFS and automounted to/from the same location, so in theory no matter which side is trying the fopen (or whatever), it should be able to find the file on disk at the same path. Thank

Re: [PyMOL] Shader issues and automatic disabling (was Re: I just built pymol, comes up but hangs on any attempt...)

2012-10-05 Thread Ben Eisenbraun
ctually going to break anything? Thanks. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu | -- D

[PyMOL] Shader issues and automatic disabling (was Re: I just built pymol, comes up but hangs on any attempt...)

2012-10-05 Thread Ben Eisenbraun
ed GLSL version 1.20. OpenGL graphics engine: GL_VENDOR: NVIDIA Corporation GL_RENDERER: Quadro 4000/PCIe/SSE2 GL_VERSION: 2.1.2 NVIDIA 304.37 Adapting to Quadro hardware. Detected 24 CPU cores. Enabled multithreaded rendering. -ben -- | Ben Eisenbraun | SBGrid Consortium

Re: [PyMOL] Virtual machines and graphics cards

2011-05-02 Thread Ben Eisenbraun
working." Have fun. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu | -- WhatsUp Gold -

[PyMOL] MacPyMOL 1.4 on OS X 10.5.8 load command error

2011-03-24 Thread Ben Eisenbraun
.html The fix is not entirely clear to me by looking at those sources. It looks like you'll have to experiment a bit if you want to continue to support 10.5 users. -ben -- | Ben Eisenbraun | SBGrid Consortium

Re: [PyMOL] loading plugins from user home directories

2010-07-16 Thread Ben Eisenbraun
On Fri, Jul 16, 2010 at 05:21:44PM -0400, Ben Eisenbraun wrote: > I've been poking through modules/pmg_tk/PMGApp.py, and I easily modified it > to support installing/deleting plugins to the user's directory, but my > python-fu is weak, and I can't seem to figu

[PyMOL] loading plugins from user home directories

2010-07-16 Thread Ben Eisenbraun
willing to push on and try to figure it out, but I'm curious what Jason et al think of the idea, since I don't really want to maintain a separate patch to enable this functionality. Thoughts, Jason, et al? :-) -b -- | Ben Eisenbraun | Software S

Re: [PyMOL] stereo issue on OS X 10.6.3 with PyMOL 1.2r3

2010-06-14 Thread Ben Eisenbraun
; to invoking MacPyMOL This sounds good, but it doesn't work for me. With the menu bar on the CRT, I still have to use -S to get stereo to work. -ben -- | Ben Eisenbraun | Software Sysadmin | | Structural Biology Grid | http://sbgrid.o

Re: [PyMOL] stereo issue on OS X 10.6.3 with PyMOL 1.2r3

2010-06-14 Thread Ben Eisenbraun
n regular MacPyMOL, > selecting the quad-buffered option has no effect). Yes, we had to use the -S to force stereo mode as well. I have an OS X 10.5.8 machine with a Quadro 4500 that works fine with MacPyMOL and PyMOLX11Hybrid once stereo mode is forced. It won't turn on the emitter w

[PyMOL] stereo issue on OS X 10.6.3 with PyMOL 1.2r3

2010-06-10 Thread Ben Eisenbraun
to grab a screenshot, the image comes out without the artifacts, so it's like the screen is not refreshing properly? The other odd thing is that stereo in CCP4mg works fine. Any ideas on how to proceed? Thanks. -ben -- | Ben Eisenbraun | Software Sys

[PyMOL] segmentation fault in 1.2r3pre 64-bit on linux

2010-05-12 Thread Ben Eisenbraun
this? Could it be related to the 3d? I can probably get a core dump, but I don't think the available builds have debugging symbols, so that may not be of much use. Any ideas on how to proceed would be appreciated. Thanks. -ben -- | Ben Eisenbraun | Sof

[PyMOL] DISPLAY issue on OS X 10.5 with PyMOLX11Hybrid 1.1r1

2009-04-17 Thread Ben Eisenbraun
" Detected 2 CPU cores. Enabled multithreaded rendering. Any ideas? I grepped through the PyMOL directories and can see some references to DISPLAY being set, but haven't read the code closely enough to see if there is some failing test that is the culprit here. -ben -- | Ben Eisenbrau

Re: [PyMOL] Command line mode on OS X 10.4 vs 10.5

2009-01-22 Thread Ben Eisenbraun
I believe that my user was using a pure-X11 build circa 0.97 that was also built by David. That ticket was from February 2005, so this was almost 4 years ago now. I'll install the 1.2 betas and try them out. Thanks for your help. -ben -- Ben Eisenbraun Structur

Re: [PyMOL] Command line mode on OS X 10.4 vs 10.5

2009-01-22 Thread Ben Eisenbraun
Application(), FAILED TO establish the default connection to the WindowServer, _CGSDefaultConnection() is NULL. -ben -- Ben Eisenbraun Structural Biology Grid Harvard Medical School http://sbgrid.org http://hms.harvard.edu

Re: [PyMOL] Command line mode on OS X 10.4 vs 10.5

2009-01-22 Thread Ben Eisenbraun
sn't work at all if you're not logged into the console. Is it supposed to? Thanks. -ben -- Ben Eisenbraun Structural Biology Grid Harvard Medical School http://sbgrid.org http://hms.harvard.edu

[PyMOL] Command line mode on OS X 10.4 vs 10.5

2009-01-21 Thread Ben Eisenbraun
CGSWindow 2009-01-21 13:31:53.280 MacPyMOL[38070:807] *** Terminating app due to uncaught exception 'NSInternalInconsistencyException', reason: 'Error (1002) creating CGSWindow' Is this a known issue? Is there a different switch that has to be passed for 10.5? Thanks. -be

[PyMOL] adding python modules for MacPyMOL

2008-12-17 Thread Ben Eisenbraun
multiarray: This Python has API version 1012, module multiarray has version 1013. I poked around in the PyMOLX11Hybrid.app directories, but didn't see an obvious place I could add a module installation. Thanks. -ben -- Ben Eisenbraun Structural Biology Grid Harvard Me

[PyMOL] APBS plugin error

2008-03-06 Thread Ben Eisenbraun
f._raising(r,_self): raise pymol.CmdException CmdException: Thanks! -ben -- Ben Eisenbraun Structural Biology Grid http://sbgrid.org/