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:
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
