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

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

precisely my question, Angel.

It's easy enough to color minimum distance, right? (Just like for
isosurfaces.) And matching them up atom for atom is very simple. But
somehow matching residue to residue without a 1:1 mapping of those, that is
another matter entirely.

Bob


On Sat, Feb 27, 2021 at 1:59 PM Angel Herráez <ang...@ua...> wrote:

> Dear Eric
>
> I was about to ask a similar question as Bob:
> I understand from your explanation you do not rely on the 2 proteins
> having
> the same sequence.
> So my question is how do you imagine the distance can be checked, i.e.
> from which atom/residue to which one?  Alpha carbon by order in the chain,
> maybe?
> A loop in JmolScript might be used for this once the intended correlation
> is
> well defined.
>
>
>
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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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