[Chimera-users] rigid body rotation of subunit

Elaine Meng meng at cgl.ucsf.edu
Fri May 13 10:56:50 PDT 2011

```Dear Dhiraj,
With Chimera, you can define an axis or a plane from any set of atoms, and measure the angles it makes with other axes and planes.  One way is with the Axes/Planes/Centroids tool (under Tools... Structure Analysis in the menu).  Axes are shown with cylinders, planes with thin disks.  You can also create the objects with the "define" command and measure their angles with the "angle" command.
<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>

It sounds like you may be able to define the orientation of chain B using its beta sheet, which could be represented by a plane.  In the Axes/Planes/Centroids tool, click Define plane... then in the main Chimera interface select the atoms you want to use to define the plane, then click OK or Apply. The details of how you would select the atoms depend on the structure, and there are usually several ways (with the Select menu, the Sequence tool, the command "select" with specific residue ranges, the mouse in the graphics window etc.)

You might try using different subsets of atoms in one copy of chain B to define planes and then decide (by looking at the planes) which gives a reasonable description of the domain orientation.  It might be all atoms of the beta sheet, or just the alpha-carbons, or only the central two or three strands of the sheet.  Then define a plane using the same set of atoms in the other copy of B, then measure the angle between the two planes of interest by choosing the corresponding two rows in the Axes/Planes/Centroids dialog.

Another way is to use the accelerator "ai" (command "ac ai"), but that requires the parts being compared to have exactly the same sequence, numbering, and chain ID, and provides less control over exactly which atoms are used in the calculation:
<http://www.cgl.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 May 12, 2011, at 7:25 PM, Dhiraj Srivastava wrote:

> Hi
>    I have the structure of two homologous protein. These proteins are dimeric. when I am superimposing chain A of one protein on to the chain A of other, it looks like chain B of one protein is related to chain B of other protein by rigid body rotation. How can I calculate the angle of rotation in chimera? Is there any way, I can draw a vector along beta sheet?
> Thank you.
> Dhiraj
>

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