VMD-L Mailing List
From: Yarrow Madrona (amadrona_at_uci.edu)
Date: Tue Mar 26 2013 - 17:35:44 CDT
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Thanks,
I will take a look at Multiseq.
-Yarrow
> Hi Yarrow,
>
> The fitting routines are trying to find a translation and rotation to
> minimize the RMSD, so actually the problems are related, and are caused
> by how RMSD is calculated. The formula sums over each atom's deviation
> from the reference, and if the number of atoms in the selections isn't
> identical, you run into problems, as there isn't a single reference to
> compare to. You have two options:
>
> -Concoct a selection that does share the number of atoms (if the number
> of protein residues is the same "protein and backbone" should work,
> regardless of a changed sidechains)
>
> -Align your structures using a different metric. Multiseq might be just
> what you need
> (http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node6.html)
>
> -Josh Vermaas
>
> On 03/26/2013 02:10 PM, Yarrow Madrona wrote:
>> Hi,
>>
>> I know this is a basic question but I am having trouble alining two very
>> similar molecules (98% seq homology) based on a heme selection. Each
>> time,
>> I get the following complaint,
>>
>> measure fit: selections must have the same number of atoms
>>
>> A similar result happens when I try to use the RMSD caclulator
>> extension.
>> Any help would be appreciated. Thank you.
>>
>
>
-- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697
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