Hi Jeff, Here is a Python script to report the angles made by bonds attached selected atoms. Just select the atoms, then open the script. Output will be printed to the reply log. Tested in Chimera 1.2548 but should work in much older versions. Tom Jeff Triffo wrote:

hi Tom,

if I have a Chimera marker file full of interconnected markers, is there a quick/easy way to report all the angles formed in the meshwork? (screenshot attached)

I figure the easiest way is to cycle through the markers and survey the angles it makes with each attached marker, but I don't know how to do that (but it sounds like something that is probably straighforward in python)

thanks for any input there,

-Jeff

# ----------------------------------------------------------------------------- # Report all angles made by bonds originating from selected atoms. # from chimera import selection, angle atoms = selection.currentAtoms() print '%d atoms selected' % len(atoms) c = 0 for a in atoms: bonds = a.bonds for b1 in bonds: for b2 in bonds: if b1 < b2: a1 = b1.otherAtom(a) a2 = b2.otherAtom(a) t = angle(a1.coord(), a.coord(), a2.coord()) print ('Angle %s %s %s = %.3f degrees' % (a1.oslIdent(), a.oslIdent(), a2.oslIdent(), t)) c += 1 print '%d angles reported' % c import Accelerators.standard_accelerators as sa sa.show_reply_log()