VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 12 2005 - 16:58:24 CDT

Sam,
  It sounds like VMD doesn't think that your last residue is part of
the selection. If you use the selection "not protein" in VMD before
saving your structure, what do you get? Do you see the residue that's
not being included? I assume you're using VMD 1.8.3, yes?

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Oct 12, 2005 at 05:12:26PM -0400, Samuel Flores wrote:
> Hi Guys,
>
> I have a puzzling error that perhaps someone can help with.
>
> I am trying to read a protein (with solvent) from a pdb file called
> input.pdb and write it, without solvent, to a file called inputp.pdb. I
> tried the following:
>
> mol load pdb input.pdb
> set preprot [atomselect 0 protein]
> $preprot writepdb inputp.pdb
>
> When I go to view inputp.pdb, there is an odd problem: The last residue has
> been truncated! No matter what protein I give it, it always chops off the
> last residue. Why is this happening?
>
> Sam
>
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
> Mingliang Tan
> Sent: Wednesday, October 12, 2005 1:59 PM
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: Show a movie from one static structure to another in VMD?
>
> Dear all,
>
> I would like to know how to show a movie from one static configuration
> (pdb file available) of a protein to another (pdb file available too),
> i.e., is there any way to have a movie showing the intermediate
> structures in VMD?
>
> Thank you very much in advance,
>
> Mingliang
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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