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). 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) It becomes a bit more elaborate if the planes are not planar :) Hope it helps, Tsjerk On Thu, Sep 23, 2010 at 10:53 AM, Ramiro Téllez Sanz <urcind...@gmail.com> 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@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology / University of Groningen The Netherlands ------------------------------------------------------------------------------ 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@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
