VMD-L Mailing List

From: Eric Hajjar (Eric.Hajjar_at_bccs.uib.no)
Date: Wed May 24 2006 - 02:48:31 CDT

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