VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 01 2007 - 17:27:36 CST

Ivana,
  If you see the box, but don't see an isosurface, make sure you've
set the Isosurface mode to "surface", as I've found that some video cards
do a bad job of point rendering, and the non-shaded points surfaces is
the default. Double check that. Loading and displaying the CHARMM PBEQ
is the same process as for an APBS DX file, so you should practice loading
the APBS DX file example from scratch (no saved state) and make sure you
fully understand that process first. Once you've got APBS DX file loading
practiced, then loading the CHARMM PBEQ is the same except that unlike
DX, you need to have the update plugin set correctly installed, as the
original VMD 1.8.5 release didn't include a CHARMM PBEQ plugin, as it
was written much more recently. Let me know if you still need help
getting it displayed. I would also be happy to check your PBEQ file to make
sure that you haven't run across some new variation of PBEQ file that
the existing plugin doesn't understand.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Feb 01, 2007 at 02:42:08PM -0500, ivana adamovic wrote:
> Dear John,
>
> I have put the pbeq plugin in the VMD 1.8.5 and the example file is
> now showing in full color!
>
> I have then tried to load potential (using CHARMM PBEQ Binary
> Potential Map) but it doesn't display anything but empty box:
>
> Info) OpenGL renderer: ATI Radeon X1600 OpenGL Engine
> Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (4096x4096), 3-D (256x256x256), Multitexture (8)
> Found 1 plugins or data handlers in directory
> '/Users/ivana/testplugins/MACOSXX86/molfile'.
> vmd > RCNE SendEventToEventTarget (suom Moved ) failed, -50
> Info) Can't show volumetric data; no filename selected yet
> RCNE SendEventToEventTarget (suom Moved ) failed, -50
> pbeqplugin) box LL origin: -62.4 -46.8 -34.2
> pbeqplugin) box LL origin: -62.4 -46.8 -34.2
> Info) Analyzing Volume...
> Info) Grid size: 209x157x115 (57 MB)
> Info) Total voxels: 3773495
> Info) Min: -3.065859 Max: 2.159204 Range: 5.225063
> Info) Computing volume gradient map for smooth shading
> Info) Added volume data, name=jws.s1.phi.0.6.pbeq : CHARMM PBEQ Potential
> Map
>
> So this looks like a step closer but still something is missing ..
>
> Thanks a lot,
>
> Ivana 

-- 
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