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

[Eric M. <em...@mi...>]

I agree that implementing this is complex for structures with different 
sequences. I just wanted to be sure that I was not missing an existing 
capability of Jmol.

PyMOL apparently does it. I will try importing a .pse file with such 
coloring into Jmol and let you know. Schrödinger has not yet responded 
to my inquiry of whether PyMOL can export a PDB file with structural 
deviations in the temperature field. But its the weekend.

-Eric

On 2/27/21 8:48 PM, Robert Hanson via Jmol-users wrote:
> 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... 
> <mailto: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 
> <http://www.stolaf.edu/people/hansonr>
>
>
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>
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