VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Wed Jan 20 2010 - 12:26:48 CST

Yes, the minitutorial loads correctly from fas2.vmd. So it's not a hardware problem, it's me:-) Off to scratch my head a bit more. Thanks!

Irene

> Date: Tue, 19 Jan 2010 22:07:43 -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,
> Can you try loading the simple example on the tutorial link I gave
> below and let me know if it works for you or not? I actually have an
> NVS 290 at the lab, and I believe it should work for this if everything
> is installed correctly.
>
> Cheers,
> John
>
> On Tue, Jan 19, 2010 at 10:21:33AM -1000, Irene Newhouse wrote:
> > 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
> > > >
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> > > --
> > > 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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> --
> 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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