VMD-L Mailing List

From: Eric Hajjar (Eric.Hajjar_at_bccs.uib.no)
Date: Tue May 16 2006 - 01:51:14 CDT

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