[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:
<http://www.rbvi.ucsf.edu/chimera/features.html#axesplanes>

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

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:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#objectlist>

The axis definition and measurement could also be done with commands instead of the GUIs, with commands "define" and "angle" respectively.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html>

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 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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