Re: [Jmol-users] Protein backbone superimposition

[David L. <Dav...@gl...>]

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

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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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