Thank you guys for the replies! I tried the PISCO method from Marlene Holder. It is pretty cool, and clear method which could used directly in PYMOL. Thank Thomas Holder for the help of PISCO installation!
I also tried the method from Matthew Franklin. From this method, I learned the theory behind the measurement of two planes. It is awesome!
Thank Oliver about the method Geomcalc in CCP4 suit. I will try to get this useful software to calculate the "angel"
later.
Anyway, thank all the replies here and you guys have a good weekend!
Bing
________________________________________
From: Oliver Smart [[log in to unmask]]
Sent: Friday, September 26, 2014 8:36 AM
To: Wang, Bing
Cc: [log in to unmask]
Subject: Re: [ccp4bb] how to measure the angle between two aromatic ring plane in PYMOL?
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/ |
|