On 07/07/2014 06:42 PM, Victor Rosas Garcia wrote: > Hello everybody, > > I have defined a solvated system, and I have defined a plane using three > hydrogen atoms on separate water molecules. Now I have my solute and one of > its bonds is almost perpendicular to the defined plane. How can I find out > the bond-plane angle? Is such a measurement possible in Jmol? > There doesn't seem to be a special function available to do this. But you should be able to write one yourself if you dig a little bit into vector mathematics.
I think this page (http://www.netcomuk.co.uk/~jenolive/vect14.html) illustrates what you are looking for in the section "The angle between a line and a plane". So you would need to define the "normal vector" of your plane (this page might be helpful: http://math.stackexchange.com/questions/137538/calculate-the-vector-normal-to-the-plane-by-given-points) and determine the angles. Jmol math includes vector operations (see http://jena3d.fli-leibniz.de/doc/jmol_scripting/index.htm?ver=14.0#jmolmath). So it shouldn't be to hard to do this. Maybe quaternions (implemented in Jmol) can be helpful here but I don't know enough about them to be sure. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: [email protected] Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 ------------------------------------------------------------------------------ Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
