VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 07 2008 - 13:20:12 CDT
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Hi,
I may be mistaken, but I don't recall MultiSeq having a
pairwise RMSD using STAMP. It may be possible to implement
one, but I don't recall that being a built-in feature. I'm
CCing the main MultiSeq developers in case they wish to
comment on this further.
Cheers,
John Stone
vmd_at_ks.uiuc.edu
On Fri, Oct 03, 2008 at 08:10:16AM -0700, Dong Xu wrote:
> Hi,
>
> How do I calculate pairwise RMSD on a set of PDBs in which the
> proteins have slight different number of atoms? I aligned them using
> MultiSeq Stamp structural alignment, but couldn't figure out the
> pairwise RMSD. I thought it used to be in MultiSeq, but not anymore?
>
> Thanks,
>
> -DX
-- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns_at_ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
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