VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Feb 17 2004 - 10:40:01 CST

Sasidhar,
  I see what you mean. I spent some time playing with this today
and while it appears to work ok for large structures, it does seem to
have some inconsistencies when I use a very small structure such as
the "alanin.pdb" that we provide as an example with VMD. I'll contact
the author of that extension and let him know that there are some bugs
that need fixing there. While some of the extensions are maintained
by the VMD team, others have been developed by people in their limited
free time, this is one of those. I can't make any promise as to when
it'll be fixed since we aren't maintaining it, but I'll see what I can do.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Feb 17, 2004 at 08:06:06AM +0530, Y U Sasidhar wrote:
> There seems to be some problem with 1.8.2 contact map calculation.
> I selected 10 residues for both the axes from same pdb file.
> Along X axis only 6 residues are shown.
> Further the diagonal is not darkest ( corresponding to 0 distance ).
> For example (2,2) is not darkest; rather (2,1) is.
>
> --
> Sasidhar
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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