[Chimera-users] Request for Source code

Eric Pettersen pett at cgl.ucsf.edu
Mon Dec 15 14:07:45 PST 2014


I agree with Elaine.  If you really want to the source code for computing an axis though, it's in the axis() function found in share/StructMeasure/__init__.py in your Chimera distribution (on a Mac it's in Chimera.app/Contents/Resources/share/StructMeasure/__init__.py instead).

--Eric

On Dec 15, 2014, at 1:51 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Jayaraman T,
> Chimera download already includes the Python code, but why not just use Chimera?  It seems like that would be much, much easier than trying to find and understand all the parts of the code to do it.  You can script it with Chimera commands “define” to create helix axes cylinders and “angle” to measure the angle between any pair of those.
> 
> See:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/angle.html>
> 
> …and information on looping through structures:
> <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.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 Dec 14, 2014, at 6:25 PM, Jayaraman T <jaai.nasa at gmail.com> wrote:
> 
>> Dear,
>>  I'm Jayaraman T pursuing PhD here in Pusan National University.  Since we are interested to calculate the interhelical angle and axes for a set of proteins, we found Chimera is really helpful for getting us the results. And i would like to do certain analysis on the basis of these interhelical angles, so i kindly request you to provide me the source code and other requirements for calculating the angle between helices. It would be grateful to you and  please help me out at your earliest convenience.
>> Thanks
> 
> 
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