[Chimera-users] translation matrix

Elaine Meng meng at cgl.ucsf.edu
Mon Dec 2 08:29:52 PST 2013


Hi Antón,
You would first need to superimpose the two structures yourself.  I.e. "measure rotation" simply measures the transformation of one structure relative to another, after you have done something that moves it.  That command does not figure out how they should be moved.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation>

Maybe superimposing the structures was your goal in the first place.  Ways to superimpose structures in Chimera are listed here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

Of the methods mentioned in the above, you might want to use Matchmaker but instead of defaults (trying all chains against all chains, which would take a REALLY long time for ribosomal subunits), choosing the option to specify exactly which chain(s) to use.

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 2, 2013, at 7:37 AM, Antón Vila Sanjurjo <antonvila.s at gmail.com> wrote:

> Hi, 
> I'm trying to get a translation matrix for two different crystal structures of ribisomal subunits. I've been trying to use the "measure rotation" command but I can only get it to display the following message "rotation angle is near zero (0 degrees)". I was wondering whether the command might be failing due to the fact that the ribosome contains numerous chains, or perhaps because the command does not deal with RNA. At any rate, how would one go about obtaining a translation matrix that can be applied to any model?
> best,
> Antón
> 




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