[Chimera-users] Request for axes measurements

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 31 08:24:39 PDT 2015

Hi Jram,
Yes, you can do it in Chimera. Example image:

Please see the Axes/Planes/Centroids tool (in menu under Tools… Structure Analysis).  Click the Help button to see its manual page, or view the same page on our website here:

As explained on that page, if you choose Define axes, "each helix" option it will use backbone atoms N,CA,C.  I would recommend using that for helices instead of only CA atoms, which you could do, but it would be a lot more work: you would have to do each helix one by one, select only its CA atoms, and choose the "selected atoms" option instead of "each helix" and give the axis a name, each time.

Also as explained in more detail on that page, after you define the helix axes, it is easy to measure the angle between any two:

The axis definition and measurement could also be done with commands instead of the GUIs, with commands "define" and "angle" respectively.

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

On Mar 31, 2015, at 7:04 AM, Jayaraman T <jram at pusan.ac.kr> wrote:

> Hi, 
> I'm Jayaraman, pursuing PhD in Protein Engineering at Pusan National University. 
> I just want to calculate the Axes for specific set of helical residue CA atoms and then to calculate the angle between them. 
> Is it possible with Chimera and if so, please do help me out that how to do it. 
> It would be grateful and looking forward to hear at your earliest convenience. 
> Thank you. 

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