On Jul 28, 2010, at 5:30 PM, Jozef Lewandowski wrote:
Hi everybody, Lately, I have been using "measure inertia" command a lot. For my purposes I needed to visualize the inertia axes as arrows instead of the default ellipsoid. I used the vectors from the reply log to write BILD files defining the arrows for the inertia axes. Is there an easy way to script just that? Or differently, is there an easy way to visualize as arrows inertia axes for peptide planes in a protein?
Hi Jozef, Let's say that the atoms you want to base the axes on are selected then: from chimera.selection import currentAtoms, numpyArrayFromAtoms coords = numpyArrayFromAtoms(currentAtoms()) would give you a numpy array of the atoms coordinates. Then: from numpy.linalg import svd centroid = coords.mean(0) centered = coords - centroid ignore, vals, vecs = svd(centered) would give you the eigenvalues, eigenvectors, and centroid of the selection. BTW, the above was gleaned from nosing around StructMeasure/__init__.py. Similarly, by nosing around the new Metal Geometry tool (specifically MetalGeom/gui.py, available only in the daily build), we find some code for constructing BILD arrows on the fly: bildString = ".color orange\n" for val, vec in zip(vals, vecs): bildString += ".arrow %g %g %g %g %g %g .1 .2 .9\n" % ( centroid[0], centroid[1], centroid[2], centroid[0] + val[0] * vec[0], centroid[1] + val[1] * vec[1], centroid[2] + val[2] * vec[2]) from StringIO import StringIO bild = StringIO(bildString) mol = currentAtoms()[0].molecule from chimera import openModels openModels.open(bild, type="Bild", identifyAs="inertial axes", sameAs=mol) Putting all the above in a .py file and opening it in Chimera will show the inertial axes on the display and list them as a model in the Model Panel. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu