[Chimera-users] coordinate rotation measuring

[Elaine Meng]

Hi Jeffrey,
As an alternative:  Chimera also allows defining planes and axes from whatever sets of atoms you like, and making measurements that involve these objects.   I don't know how well it applies to your situation, but you could define two planes from corresponding sets of atoms in the two structures, then get the angle between those planes.

This can be done with the "Axes/Planes/Centroids" tool (under Tools.... Structure Analysis), or in scripts with the commands "define" and "angle".

<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html>

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 Jun 4, 2011, at 6:58 PM, Jeffrey Hu wrote:

> Hi,
> I'm currently working on a gp140 model and have docked coordinates for 2 different conformations. I am trying to measure the rotation between the docked coordinates using the method in the EM-fit tutorial and i had a few questions.
> How does the "measure rotation #1 #3 showslab true" command measure the rotation? How does it determine the axis of rotation? Is it possible for me to create my own axis? Is there any way to increase the size of the slabs (they are too small visually)?
> 
> -Thanks!