Re: [Jmol-users] Protein backbone superimposition

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

I had a go at superimposition on Jmol following the instructions at https://proteopedia.org/wiki/index.php/Jmol/superposition as suggested by Karsten (sorry for getting your name wrong way round before).

I got it to work with separate pdb files, and the two subunits of the same pdb file, except in the latter case the alignment was wrong. I tried on RCSB (which I discovered by searching) which pointed out that there were regions in one subunit that couldn’t be determined, explaining the problem. However I don’t seem to be able to zero them out by specifying regions. There must be something wrong with my syntax:

load http://127.0.0.1/proteins/1cr6.pdb  # My local Mac location for files — I use a local web browser and the console for JSmol.
model 0

# Don’t include 20-47 and 64-89 — missing from subunit A

define ~
 1.1 and (4-19,48-63,90-544) and *:A.CA
define ~Bchain 2.1 and (4-19,48-63,90-544) and *:B.CA

compare {2.1} {1.1} ATOMS {~Achain} {~Bchain} ROTATE TRANSLATE

…but all I get is: RMSD NaN --> NaN Angstroms


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<http://www.davidleader.net/>
_______________________________________________________