[Chimera-users] domain angel

Elaine Meng meng at cgl.ucsf.edu
Tue Dec 1 10:14:33 PST 2015

```Hi Smith,
Yes, there are a few different ways… which ways are possible depends on your situation and data.  Going from most general to most specific:

(1) the most general way (applicable to most situations) is to define a plane based on some atoms in each domain and then measure the plane-plane angle.  The main issue is deciding which atoms to use.  If the domains are analogous or identical, you would use the analogous or same set of atoms to define the two planes.  You can define planes and measure angles between them using the “Axes/Planes/Centroids” tool (in menu under Tools… Structure Analysis), or define planes with the “define” command and measure angles between them with the “angle” command.  For details see the manual:

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

(2) another way if the domains are equivalent or analogous to each other is to open them as two separate models (e.g. if they are in the same structure you could just open that structure twice), superimpose the two models on those domains, and then use command “measure rotation”

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation>

(3) another way if the domains are in two different models and have exactly the same sequences, numbering, and chain identifiers is to use Keyboard Shortcuts “ab” and “ai” (which could be used as commands “ac ab” and “ac ai” respectively.  This is similar to #2 in that it first superimposes and then measures the transformation.  Details here:

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ac.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/alist.html#abdetails>

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 1, 2015, at 1:08 AM, Smith Liu <smith_liu123 at 163.com> wrote:
>
> Dear All,
> Is any way to calculate the angel between 2 domains by Chimera?
> Smith

```