[Chimera-users] Selected measure angles

Soumya Govinda Remesh sgremesh at lbl.gov
Thu Dec 1 16:48:13 PST 2016


Thank you Eric.

On Thu, Dec 1, 2016 at 1:40 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Soumya,
> Depends on your familiarity with Python really.  If you don’t know Python
> well then it might be easier to parse the reply log.  If you have some
> familiarity with Python then you would use the Python equivalents of the
> angle/distance commands to get the values and write them to a file
> (runCommand never returns a value itself).
> In Python, you could use runCommand to select the atoms you want to
> measure and then:
>
> *Outside the loop*
> from Midas import distance, angle
>
> *Inside the loop, either*
> d = distance()
> … write the distance to a file...
>
> *or*
> a = angle()
> … write the angle to a file...
>
> —Eric
>
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
>
>
> On Dec 1, 2016, at 12:15 PM, Soumya Govinda Remesh <sgremesh at lbl.gov>
> wrote:
>
> Hello,
>
>  I have just modified the loop script available here (
> http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html)
> to measure certain angles and distances. I just want to know if there is a
> way to export the individual values of angles and distances to a file other
> than parsing from the reply-log. Thank you.
>
> Best,
> Soumya Govinda Remesh, Ph.D.
> Postdoctoral Fellow at Advanced Light Source
> Lawrence Berkeley National Laboratory
>
> 1 Cyclotron Road   MS 6R2100
> Berkeley, CA 94720
> (phone) 510-495-8179
> (cell) 804-402-8730 <(804)%20402-8730>
>
> sgremesh at lbl.gov
>
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>
>


-- 
Soumya Govinda Remesh, Ph.D.
Postdoctoral Fellow at Advanced Light Source
Lawrence Berkeley National Laboratory

1 Cyclotron Road   MS 6R2100
Berkeley, CA 94720
(phone) 510-495-8179
(cell) 804-402-8730

sgremesh at lbl.gov
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