VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Tue Jan 19 2010 - 14:21:33 CST

This is what VMD says on startup:

Info) Multithreading available, 4 CPUs detected.
Info) Free system memory: 2658MB (68%)
Info) No CUDA accelerator devices available.
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this optional X server feature.
Info) OpenGL renderer: Quadro NVS 290/PCI/SSE2
Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVF)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (8192x8192), 3-D (2048x2048x2048), Multitexture (4)

Thanks!
Irene

> Date: Tue, 19 Jan 2010 13:50:55 -0600
> From: johns_at_ks.uiuc.edu
> To: einew_at_hotmail.com
> CC: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: visualizing APBS output
>
>
> Irene,
> What graphics card and driver version are you using?
> (what does VMD print to the console when it starts up?)
> To do visualizations of high resolution electrostatic maps using
> the "Color by Volume" feature of VMD, you'll need a GPU that
> has a good amount of video memory, ideally 512MB or more.
> I have a simple electrostatics visualization mini-tutorial
> for VMD available here:
> http://www.ks.uiuc.edu/Research/vmd/minitutorials/colorbypot/
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Jan 19, 2010 at 09:31:08AM -1000, Irene Newhouse wrote:
> > I've been running APBS locally. When I have the results displayed with the
> > top molecule, I see nothing. Displaying in a new window works. I've been
> > trying to follow
> > http://apbs.wustl.edu/MediaWiki/index.php/How_do_I_visualize_the_electrostatic_potential_around_my_biomolecule%3F#Isocontour_visualization?
> > to map the potential to the molecular surface, and I can't get it to work.
> > I can see isosurfaces w/out difficulty, as well as field lines, but I
> > can't display the surface & color by volume. That website dates from an
> > earlier version of VMD. Is there something slightly different in 1.8.7
> > that I'm not aware of?
> >
> > Thanks!
> >
> > Irene Newhouse
> >
> > ----------------------------------------------------------------------
> >
> > Hotmail: Trusted email with Microsoft*s powerful SPAM protection. Sign up
> > now.
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
                                               
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