From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 16 2006 - 13:14:20 CDT

Eric,
  Looks like a buggy nVidia driver to me. Can you try the
nVidia Linux driver version 7676, that one works pretty well for us.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, May 16, 2006 at 08:51:14AM +0200, Eric Hajjar wrote:
> John Stone wrote:
>
> >Hi,
> > What does VMD print in the startup messages on your machine when
> >you run it? It's very helpful to know this when reporting bugs, as
> >this will tell me what graphics board, which version of VMD, and what
> >platform you're running on...
> >
> >
>
> Sure,
> the message at startup is :
>
> Info) Multithreading available, 2 CPUs detected.
> Info) OpenGL renderer: GeForce 6800 LE/AGP/SSE2
> Info) Features: STENCIL MSAA(4) RN MDE CVA NPOT PP PS GLSL(OVF)
> Info) OpenGL fragment shader compilation log:
> Info) (160) : warning C7506: OpenGL does not define the global function exp2
> Info) <stdlib>(4596) : warning C7011: implicit cast from "int" to "float"
> Info) OpenGL shader linkage log:
> Info) Fragment info
> Info) -------------
> Info) (160) : warning C7506: OpenGL does not define the global function exp2
> Info) <stdlib>(4596) : warning C7011: implicit cast from "int" to "float"
> Info) <stdlib>(4596) : warning C7011: implicit cast from "int" to "float"
> Info) OpenGL fragment shader compilation log:
> Info) (194) : warning C7506: OpenGL does not define the global function exp2
> Info) OpenGL shader linkage log:
> Info) Fragment info
> Info) -------------
> Info) (194) : warning C7506: OpenGL does not define the global function exp2
> Info) Full GLSL rendering mode is available.
>
>
> Might it be a graphic-card-driver issue ?
> On this machine i have installed the "Gainward GeForce 6800LE 128MB DDR"
>
>
> Thanks for your help/support
>
> Sincerely
>
> Eric
>
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Thu, May 11, 2006 at 08:18:54AM +0200, Eric Hajjar wrote:
> >
> >
> >>John Stone wrote:
> >>
> >>
> >>
> >>>Hi,
> >>>You can view such potential maps either with the volume slice, or with
> >>>the isosurface representation. Most likely you'll find the isosurface
> >>>representation easier to use initially. You can also use the
> >>>"color by volume" feature to display the potential mapped onto your
> >>>graphical representations. You'll most likely need to set the color
> >>>scale
> >>>data range values to something much tighter than the full data range
> >>>in order to get good looking results. (see trajectory tab)
> >>>
> >>>John Stone
> >>>vmd_at_ks.uiuc.edu
> >>>
> >>>
> >>>
> >>>
> >>>
> >>Hi,
> >>thank you so much for your kind reply,
> >>I'm able to visualize the "isosurface" data but nothing appears when i
> >>choose "volume slice".
> >>Also i'm not able to visualize colors that would correspond to the PHI
> >>map successfully loaded, the surface is always in silver, even after
> >>selecting "color by volume" or after changing the "color scale data
> >>range" (traj-tab) to various numbers....
> >>
> >>Maybe this is due to a driver/installation problem ?
> >>
> >>Also is there no way to display the potential as "contour" or "orbitals"
> >>around the atoms with VMD ?
> >>
> >>
> >>Thanks in advance for your help !
> >>
> >>Eric
> >>
> >>
> >>
> >>>On Tue, May 09, 2006 at 12:18:37PM +0200, Eric Hajjar wrote:
> >>>
> >>>
> >>>
> >>>
> >>>>*
> >>>>** i am working with VMD-1.8.3 on a linux machine.*
> >>>>*My problem is that i want to map electrostatic potential (from delphi)
> >>>>to a structure file
> >>>>**I've been browsing the archives but did not find help there; **& New
> >>>>VMD releases brings new questions :
> >>>>
> >>>>In fact i'm able to "load" the ".phi" file into the structural data
> >>>>(pdb file); this gives:
> >>>>
> >>>>*Info) Analyzing Volume...
> >>>>Info) Grid size: 65x65x65 (4 MB)
> >>>>Info) Total voxels: 274625
> >>>>Info) Min: -993.881226 Max: 451.587524 Range: 1445.468750
> >>>>Info) Computing volume gradient map for smooth shading
> >>>>Info) Added volume data, name=complexe.phi : PHIMAP Electron Density Map
> >>>>*
> >>>>Then, if i understand correctly, the only way to "visualize" this data
> >>>>is to use the "Volume Slice" option of drawing ?
> >>>>Well, when i do that i can't see anything !
> >>>>Playing with the "Slice offset" and/or Axis does not help
> >>>>
> >>>>I am missing something: could it be that the potential map generated by
> >>>>delphi **(or the format) **is wrong ?
> >>>>or
> >>>>Could this be hardware related ?
> >>>>
> >>>>I would really appreciate your comments on this If you have experienced
> >>>>something similar
> >>>>and/or if you know how to plot Delphi maps on Pdb files
> >>>>
> >>>>Thanks a lot for your help / advices
> >>>>
> >>>>Sincerely
> >>>>*
> >>>>
> >>>>--
> >>>>-----------------------------
> >>>>Eric Hajjar
> >>>>Phd Student in Molecular Modeling
> >>>>University of Bergen , Computational Biology Unit
> >>>>BCCS, Bergen, NORWAY
> >>>>eric.hajjar_at_bccs.uib.no
> >>>>tel:(+47)55584029
> >>>>mob:(+47)98023282
> >>>>
> >>>>
> >>>>
> >>>>
> >>>
> >>>
> >>>
> >>--
> >>-----------------------------
> >>Eric Hajjar
> >>Phd Student in Molecular Modeling
> >>University of Bergen , Computational Biology Unit
> >>BCCS, Bergen, NORWAY
> >>eric.hajjar_at_bccs.uib.no
> >>tel:(+47)55584029
> >>mob:(+47)98023282
> >>
> >>
> >
> >
> >
>
>
> --
> -----------------------------
> Eric Hajjar
> Phd Student in Molecular Modeling
> University of Bergen , Computational Biology Unit
> BCCS, Bergen, NORWAY
> eric.hajjar_at_bccs.uib.no
> tel:(+47)55584029
> mob:(+47)98023282

-- 
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