Re: [Jmol-users] Protein backbone superimposition

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

David, that is great. Right, and of course Jmol allows you to customize
that comparison in exactly this way.

Any thoughts on my question about how incredibly similar the A and B models
are? Really, seeing the individual atoms so directly on top of each other
for whole swaths of chains, including sidechain atoms? Could a refinement
itself actually do that? Are proteins really that way?

Or is this a modeling artifact due to someone using the same model twice
and only then allowing for very minor adjustments?

Am I too skeptical?

Bob


On Thu, Apr 28, 2022 at 4:02 AM David Leader <Dav...@gl...>
wrote:

> Many thanks to Bob for sorting things out for me. After loading the file:
>
> achain = {(4-19,48-63,90-544) and *:A.CA}
> bchain = {(4-19,48-63,90-544) and *:B.CA}
> compare {:A} {:B} atoms {achain} {bchain} translate rotate
> color {:A} yellow
> color {:B} red
>
> worked for me.
>
> I found this definition style easier to follow than that on the Protopedia
> page (although I did get that to work for two different files).
>
> The number of atoms I was trying to specify was correct (my file was from
> the Richardson 8000, so not a download from RCSB) but I had the syntax
> wrong.
>
> I really appreciate this, because although I got a comparison out of the
> RCSB tool, I am familiar with (and like)  the presentation aspects of Jmol
> (and the pngj feature). Now superimposition. Not sure that this current
> work is publishable — a bit of a one trick pony — but the important thing
> for me is to be able to explore it properly and present it clearly, and
> Jmol lets me do that.
>
> David
>
> _______________________________________________________
>
> Dr. David P. Leader (Honorary Senior Research Fellow)
> Boyd Orr Building,
> University of Glasgow, Glasgow G12 8QQ, UK
> Phone: +44 (0)141 330 5905
> http://www.davidleader.net
> _______________________________________________________
>
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>
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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

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

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