Hi Bing,
you can use the latest version of psico, it provides an
"angle_between_helices" function, which in combination with
"plane_orientation" can calculate angles between planes.
Download:
http://pymolwiki.org/index.php/Psico
Example:
fetch 1ubq, async=0
select ring1, 45/CG+CD1+CD2+CE1+CD2+CZ
select ring2, 59/CG+CD1+CD2+CE1+CD2+CZ
import psico.orientation
angle_between_helices ring1, ring2, plane_orientation
Best,
Marlene
--
Marlene Holder, née Grünwald, PhD
Postdoc
NYULMC Skirball Institute of Biomolecular Medicine
540 First Avenue, 3rd floor, Lab17
New York, NY 10016
2014-09-25 17:28 GMT-04:00 Wang, Bing <[log in to unmask]>:
> Hi everyone,
>
> I want to tell an angel between two aromatic planes which comes from two
> different molecules and cross each other.
>
> First, I tried the easier ways. I presume these two aromatic rings are in
> the perfect planes, that is why I tried plane_wizard.py and
> draw_plane_cgo.py which work very well. However after I got two plates by
> plane_wizard or draw_plane, I don't know how to measure the angle between
> these two plates. I also don't know whether I could get the angle I wanted
> from these two ways. I tried vector_angly.py which cann't loaded into pymol
> properly. If it could, how can i do to get the angel from these two plates I
> drew. Solutions? Since I am in the beginner state, please show me details
> which i could follow step by step.
>
> Second, If these two aromatic rings are not in the perfect planes, how can i
> find the best fit planes? And then find the angle between the best fit
> planes? I tried svdplos.py and makeCGOplates.py which are downloaded on
> line. unfortunately both of these can't be loaded into pymol properly.
> Solutions?
>
> Thanks!
>
> Bing Wang
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