From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed May 24 2006 - 13:37:50 CDT

Eric,
  For the "color by volume" method, you'll indeed need to play with the
color scale data range, as some potential maps have values of Inf or other
discontinuities in them, which cause the color range to be HUGE when the
map is initially loaded. By setting the data range to something like
-4 to 4, you should be able to see the potential colors MUCH more easily.
Try that and let me know if you have success. As for the VolumeSlice
representation, I'm not sure, have you tried moving the slide plane into
the middle of the volume (value of 0.5) rather than the edge? At the
extreme edge of the map, the color can sometimes be clamped to black,
depending on the video driver and the map data. If you still have trouble,
I may want to have a copy of the map file just to see if I run into the same
problem or not on my test machine.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, May 24, 2006 at 09:48:31AM +0200, Eric Hajjar wrote:
> John Stone wrote:
>
> >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
> >
> >
> >
>
> Hi,
> I just finished installing this "nVidia Linux driver version 7676" on my
> machine, indeed the "startup message" of VMD is now "clean":
>
> Info) -------------------------------------------------------------
> 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) Full GLSL rendering mode is available.
>
>
> However i stilll have the same problems 1) nothing appears on my screen
> when i select the DrawingMethod: "Volume Slice" ;
> and (worse) 2) No colors can be observed when i Choose "Volume" while in
> the "IsoSurface" DrawingMethod (i can see the Silver-Contour though)
>
> Is there an issue with the delphi maps i'm loading ?
> or Do I have to play with the "parameters" (i tried various "color scale
> data range"...) ?
>
> Again thanks for your kind help/advice
>
> Eric
>
>
>
> PS: (note that i must use the type "grd" to load the ".phi" file
> generated by Delphi)
>
> rePS: (when the .phi file is loaded on top of the pdb molecule: the
> message is ;
> Info) Analyzing Volume...
> Info) Grid size: 65x65x65 (4 MB)
> Info) Total voxels: 274625
> Info) Min: -153.424179 Max: 144.788269 Range: 298.212448
> Info) Computing volume gradient map for smooth shading
> Info) Added volume data, name=example3.phi : PHIMAP Electron Density Map
> )
>
>
> >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
> >>
> >>
> >
> >
> >
>
>
> --
> -----------------------------
> 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

-- 
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