Re: [Jmol-users] Color structural alignment by deviation "RMSD"?

[Robert H. <ha...@st...>]

On Sun, Feb 28, 2021 at 6:17 AM Angel Herráez <ang...@ua...> wrote:

> Bob, when we load 2 structures and do
>
> compare {2.1} {1.1} subset alpha rotate translate;
>
> is there a residue to residue mapping as a result?
>
>
Yes



>
> somehow but fails when one of
> the chains has a gap or a portion that does not match the other, then the
> match becomes shifted and CA to CA distance is always too high. It may
> work in pairs of proteins that are more similar; not well with the
> examples you
> mentioned.
>
>
That's because Jmol is not doing a sequence alignment, only a 1:1 atom
mapping



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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

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