## Re: [PyMOL] How to measure the angle between two aromatic rings?

 Re: [PyMOL] How to measure the angle between two aromatic rings? From: Ramiro Téllez Sanz - 2010-09-23 10:19:27 ``` Thanks for your kind help, Tsjerk. > Hi Ramiro, > > Assuming your rings are nicely planar, and representing the ring as: > > 1-2-3 > | | > 6-5-4 > > you can get the plane normal vector as the vector cross product from > (3)-(1) and (5)-(1). OK. But I just started to use pymol. Which are the commands to do so? I know how to get the coordinates of a selected atom, but need the pymol commands to treat the data: a) How to create the vectors from 1->3 and from 1->5 b) How to treat the vectors to perform the vector cross product > Doing so for both rings gives you the two normal vectors. The angle > then follows from the dot product of the (normalized) normal vectors: > > angle = acos(n1 . n2) Again, I would need the commands to: c) Normalize the vectors (how to set their modules = 1) I also guess n1 and n2 represent the normalized vectors, don't they? So this command is very clear :) > It becomes a bit more elaborate if the planes are not planar :) > > Hope it helps, > > Tsjerk Again, thanks very much in advance for your kind help. > On Thu, Sep 23, 2010 at 10:53 AM, Ramiro Téllez Sanz > wrote: >> >> Hi everyone and thanks for reading this! >> >> I am interested in measuring the angle between aromatic ring planes. >> Is there any easy way/script to do it? >> >> One way that came to my mind is creating a pseudoatom representing the >> centroid for each ring (I already know how to do that), then drawing two >> lines perpendicularly to the planes from both centroids, and finally >> measuring the angle between the lines. Will that be possible? How could >> this be done? >> >> Is there any other way? I'm completely clueless. Any help will be >> greatly appreciated. >> >> Thanks in advance, >> >> Ramiro Tellez Sanz >> Dept. Physical Chemistry >> University of Almeria >> Spain >> >> >> ------------------------------------------------------------------------------ >> Start uncovering the many advantages of virtual appliances >> and start using them to simplify application deployment and >> accelerate your shift to cloud computing. >> http://p.sf.net/sfu/novell-sfdev2dev >> _______________________________________________ >> PyMOL-users mailing list (PyMOL-users@...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pymol-users@... >> > > ```