[Chimera-users] Request for Source code

Elaine Meng meng at cgl.ucsf.edu
Tue Dec 16 08:57:09 PST 2014


Dear Jayaraman T,
You can turn off helical correction and mass weighting using command options, for example with this command:

define axis perHelix true helicalCorrection false massWeighting false

See: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>

I’m just trying to convince you this is the easy way!  

However, you already also have the source code in your download, as Eric described in his reply:

<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2014-December/010574.html>

Best,
Elaine

On Dec 15, 2014, at 6:57 PM, Jayaraman T <jaai.nasa at gmail.com> wrote:

> Yes Elaine,  
> 
> We can use Chimera but there are helical correction and mass weighting options exist. And am trying to get it done for all these helices without these options.
> 
> Anyway let me follow up and write you back if there is a need of further assistance.
> 
> I think it would help us more and thanks again for your kindness.
> 
> Good day.
> 
> On Tue, Dec 16, 2014 at 6:51 AM, 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
> 
> 
> 
> -- 
> Regards
> 
> 
>   Jram | 201493155
>   PhD Student
>   Bio molecular Engineering Lab
>   School of Chemical Engineering
>   Pusan National University.
>   30 Jangjeon-dong, Geumjeong-gu,
>   Busan, South Korea -  609-735.
>   +8210 9906 3680
>   jram at pusan.ac.kr
> 




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