[Chimera-users] Help in executing python script in per-frame analysis

Tom Goddard goddard at sonic.net
Thu Feb 5 11:30:50 PST 2015


Hi Ankit,

  Chimera does not have a display style to show the inertia of a molecule as 3 axes.  But here is a quick way to hack that in.  You can change a little bit of Python code in your Chimera 1.10 distribution so that it shows three narrow ellipsoids that represent the axes.  Use a text editor to edit

	chimera/share/measure/inertia.py

or on Mac Chimera.app/Contents/Resources/share/measure/inertia.py and replace the ellipsoid surface function

def ellipsoid_surface(axes, lengths, center, color, surface):

  xf = surface.openState.xform.inverse()
  sa, sc = transform_ellipsoid(axes, center, xf)
  varray, tarray = ellipsoid_geometry(sc, sa, lengths)
  p = surface.addPiece(varray, tarray, color)
  p.save_in_session = True
  return p

with

def ellipsoid_surface(axes, lengths, center, color, surface):

  xf = surface.openState.xform.inverse()
  sa, sc = transform_ellipsoid(axes, center, xf)
  for sx,sy,sz in [(1,.05,.05), (.05,1,.05), (.05,.05,1)]:
    lx,ly,lz = lengths
    varray, tarray = ellipsoid_geometry(sc, sa, (lx*sx,ly*sy,lz*sz))
    p = surface.addPiece(varray, tarray, color)
    p.save_in_session = True
  return p

then save the file, restart Chimera and now “measure inertia #0 color yellow” will show the 3 axes. Make sure to keep the indentation of the code since that is important in the Python computer language.  This change is scaling down 2 of the 3 ellipsoid axes by a factor of 0.05.  You can change the 0.05 value to say 0.01 if you want thinner axis ellipsoids.

	Tom




> On Feb 5, 2015, at 3:41 AM, Ankit Agrawal  wrote:
> 
> Hi
> I am analysing a protein molecule (MD simulations). I wrote a python script to calculate inertia for the protein and ran it over 40000 frames. I got a data in log file but it is creating a ellipsoid around the molecule.
> 
> I want 3 axes of the ellipsoid to be shown in that protein molecule not the ellipsoid as it covers the whole protein molecule. So that I can easily visualize the movement of all 3 axes of ellipsoid over the 40000 frames (means how the axes are changing during trajectory run).
> 
> Thanks
> Ankit
> Department of Chemical Science
> IISER-Mohali, India
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> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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