Hi Bing -
You don't need a fancy program to get the angle. If plane_wizard
gave you a vector normal to the ring planes, you can use that.
Otherwise, calculate the cross product between two vectors in the
plane (e.g. C1-C4 and C2-C5 in a six-membered ring). This vector
is normal to the ring plane.
Once you have those ring plane normal vectors, just calculate the
dot product between the two vectors. The result will be the
product of the two vector magnitudes, multiplied by the cosine of
the angle between them. The angle you want is 180 degrees minus
the angle you get here.
OR, you could put both aromatic rings up on a graphics terminal,
and adjust your view so both rings are edge-on (they look like
lines on the screen). Then put a protractor up to the screen and
measure the angle! :D
Hope that helps,
Matt
On 9/25/14 5:28 PM, Wang, Bing wrote:
[log in to unmask]"
type="cite">
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
--
Matthew Franklin, Ph. D.
Senior Scientist
New York Structural Biology Center
89 Convent Avenue, New York, NY 10027
(212) 939-0660 ext. 9374