On Mon, 2 Jun 2008, David Chenoweth wrote:
Dear Chimera team,
I would like to make a plane through the atoms of an aromatic ring and then measure a distance from an atom to the ring centroid. I would also like to measure the angle between the normal to the ring plane and the line joining the centroid and the atom I am measuring from. It would also be nice if I could specify the dimensions, color, and transparency of the plane. In addition it would be great to be able to make multiple planes through atoms, select and color them separately, and measure the angles at the intersection of the planes. Just wondering if there is a way to do this with Chimera.
Thanks in advance, Dave
This sort of thing currently requires writing Python code. For example, if you selected a ring by hand, the following code computes the plane. The plane's origin is the centroid of the atoms: from chimera import selection, Plane atoms = selection.currentAtoms() plane = Plane([a.coord() for a in atoms]) To calculate the plane equation, chimera uses Newell's method, so points should be given in ring order, but the ring doesn't have to be convex. If you computed a least-squared fit plane, the answer would be slightly different. To measure the angle between two planes, just calculate the angle between their normals (arccos of the (normalized) dot product). To visualize the results, I'd recommend creating a SurfaceModel from the _surface module. Since much of chimera is implemented in Python, "example" code that uses chimera Planes and SurfaceModels can be found the Python modules in the CHIMERA/share directory. Specifically, the NucleicAcids and GraspSurface modules. To get started programming chimera with Python, please look at the tutorials in the Chimera Programmer's Guide, <http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/index.html>. And if you have any programming questions, please ask them on the chimera developer's mailing list, chimera-dev@cgl.ucsf.edu. Good luck, Greg Couch UCSF Computer Graphics Lab