Hi Ramiro, Another option is to fit (in a least-squares sense) a plane to each of your rings and then calculate the angle between the fitted planes' normals. This would help if your rings are not perfectly planar: it would spread the deviation among all atoms in the ring not just the ones you selected for the crossproduct. Cameron Mura created an excellent example of this in our PLoS article's supplementary information, posted on the PyMOLWiki http://www.pymolwiki.org/index.php/PLoS#Case_6:_Higher-order_structures.28.E2.89.A5_intermediate.2Fadvanced.29
The article is all about biomolecular graphics. Cheers, -- Jason On Thu, Sep 23, 2010 at 4:53 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 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ 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
