VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 28 2007 - 22:25:26 CDT

Fred,
  I found your problem. Your selections weren't actually the same.
For one you used "name" and for the other you were using "element",
and the PDB/PSF combination you loaded did not define the element type
(old style PDB file), so the elements for all atoms were set to "X".
So, this was nothing to worry about and VMD was doing exactly what it should.

With complex atom selections like the ones you're using, you may find it
easier to make an atom selection "macro" which is a short alias for the
longer selection. You can do this using either the text interface or
the GUI. That can make it MUCH easier to deal with complex atom selections
without worrying so much about typos or other common mistakes.

Cheers,
  John

On Wed, Mar 28, 2007 at 09:11:02AM -0700, Fred Moore wrote:
> John,
>
> Okay, attached are the state file, the first frame of the .pdb and
> the psf file I use.
>
> Thanks, I do appreciate this immensely. I'll look to hear before I
> upload anything.
>
> FM 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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