On Thu, 25 Sep 2014, 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
Wang,
I am sure the other replies will sort your problem in PyMOL itself. But I
thought it might be useful for you to consider checking any calculation of
the angle works properly by using the well-established CCP4 tool GEOMCALC:
http://www.ccp4.ac.uk/html/geomcalc.html
I (and others) use the tool to calculate butterfly bend angles in flavin
rings (this involves finding the angle between two mean-plane rings). If
you want any help on running it then contact me off list and I would be
happy to help.
Good luck,
Oliver
PS. I really like the phrase "tell an angel". Paul Emsley's coot refers to
geometry only optimization as "send in the bond angels".
| Dr Oliver Smart |
| Global Phasing Ltd., Cambridge UK |
| http://www.globalphasing.com/people/osmart/ |
