VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 09 2006 - 09:25:09 CDT
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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
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
-- 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
- Next message: Guo Zhi: "Re: How to pick up the lost periodic information?"
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- In reply to: Eric Hajjar: "Display the electrostatic character (delphimap) on the structure file"
- Next in thread: Eric Hajjar: "Re: Display the electrostatic character (delphimap) on the structure file"
- Reply: Eric Hajjar: "Re: Display the electrostatic character (delphimap) on the structure file"
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