VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Oct 02 2009 - 16:22:26 CDT

Martin,
  Yes, we've observed this too. I believe it is partially the result
of the fact that STRIDE uses the PDB file format, which has relatively
narrow field widths for coordinates, and so coordinates with large
magnitudes can definitely create problems. I don't know of any way
around this limitation of STRIDE. At some point, someone will either
have to revise STRIDE or write a new program to deal with this. If people
know of something competitive with STRIDE that's more modern and has a
similarly open license, let me know.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Oct 02, 2009 at 12:18:41PM -0500, Martin K. Jones wrote:
> I'm using VMD 1.8.6 on Windows XP, and it seems that stride can fail to
> calculate correctly if the coordinates of my molecule are outside of some
> as yet to be determined bounds. The problem is, I have not seen any error
> messages displayed with regard to this failure. In my case, roughly half
> of my molecule gave incorrect results with stride.
>
>
>
> Thanks,
>
> Martin
>
>
>
> _____________
>
>
>
> Martin K Jones
>
> University of Alabama at Birmingham
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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