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 [osm...@globalphasing.com] Sent: Friday, September 26, 2014 8:36 AM To: Wang, Bing Cc: CCP4BB@JISCMAIL.AC.UK 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/ |
