Re: [PyMOL] How to measure the angle between two aromatic rings?

[Jason V. <jas...@sc...>]

Hi Ramiro,

Another option is to fit (in a least-squares sense) a plane to each of
your rings and then calculate the angle between the fitted planes'
normals.  This would help if your rings are not perfectly planar: it
would spread the deviation among all atoms in the ring not just the
ones you selected for the crossproduct.  Cameron Mura created an
excellent example of this in our PLoS article's supplementary
information, posted on the PyMOLWiki
http://www.pymolwiki.org/index.php/PLoS#Case_6:_Higher-order_structures.28.E2.89.A5_intermediate.2Fadvanced.29

The article is all about biomolecular graphics.

Cheers,

-- Jason

On Thu, Sep 23, 2010 at 4:53 AM, Ramiro Téllez Sanz <urc...@gm...> wrote:
>
>
> Hi everyone and thanks for reading this!
>
> I am interested in measuring the angle between aromatic ring planes.
> Is there any easy way/script to do it?
>
> One way that came to my mind is creating a pseudoatom representing the
> centroid for each ring (I already know how to do that), then drawing two
> lines perpendicularly to the planes from both centroids, and finally
> measuring the angle between the lines. Will that be possible? How could
> this be done?
>
> Is there any other way? I'm completely clueless. Any help will be
> greatly appreciated.
>
> Thanks in advance,
>
> Ramiro Tellez Sanz
> Dept. Physical Chemistry
> University of Almeria
> Spain
>
>
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
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