VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon May 15 2006 - 12:29:27 CDT

Eric,
  I missed your second question: the "isosurface" representation is the
one you want if you want to see the 3-D potential surface (I assume that's
what you meant by "contour or orbital").

  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 

-- 
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