VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 08 2004 - 16:50:46 CDT

Dara Ara,
  Please email me your PSF and XYZ files and I'll send you the right
atom selection text. Its possible that something weird is happening to
your atom names and that they aren't remaining "Au" inside of VMD.
If you have files for the case with/without water, that'd be useful.

  John

On Wed, Apr 07, 2004 at 02:41:25PM -0600, Kooser, Ara S wrote:
> Hello all,
>
> Thank you very much for your help in the past. I have brought in a
> Au(111) surface into VMD using .psf and .xyz file. An example from each file
> line. The first is the .psf and then .xyz
> PSF
>
> 1 !NTITLE
> REMARKS Au surface 1 1 1
>
> 560 !NATOM
> 1 MAIN 0 UNK Au Au 0.0000000 196.966510
> 0.0000000
>
> 560
> Au box with no waters
> Au 0.0006200 1.0000000 0.695950
>
> My problem is that I want to be able to select just the gold atoms. I load
> the .psf first and then the .xyz. When I type name Au for a representation I
> end up with a blank sceen in my OpenGL display. When I bring in water
> molecules from a .psf and .xyz I don't have this problem. I need to be able
> to select the gold surface and then show all waters within 3 A (this part I
> know how to do). Also I would like to be able to bring in a mixed atom
> surface and look at individual layers. Thanks.
>
> Ara Kooser 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
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