VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon May 15 2006 - 12:15:11 CDT

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...

  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 

-- 
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