[Chimera-users] drawing a symmetry axis

[Thomas Goddard]

Hi Philip,

   I don't know an easy way to show the symmetry axis of your dimer as a 
line or rod using the normal Chimera commands.  But you could do this by 
modifying the keyboard shortcut ai Python code.

   You would edit the file

	chimera/share/MatchDomains/__init__.py

or on the Mac it would be

	Chimera.app/Contents/Resources/share/MatchDomains/__init__.py

(and on the Mac you'd need to click the Chimera icon and choose "Show 
package contents" to see in the Chimera.app folder).

   You would change the transform_schematic() routine (line 171) code from

#    tarray = ((0,1,2),(0,2,3))
     tarray = ((0,1,2),(0,2,3),(0,1,5),(0,5,4),(1,2,6),(1,6,5),
               (2,3,7),(2,7,6),(3,0,4),(3,4,7),(4,5,6),(4,6,7))
     g1 = sm.addPiece(varray, tarray, from_rgba)
#    g1.displayStyle = g1.Mesh

     from Matrix import xform_matrix, apply_matrix
     tf = xform_matrix(xform)
     corners2 = [apply_matrix(tf, p) for p in corners]
     varray2 = corners2
     g2 = sm.addPiece(varray2, tarray, to_rgba)
#    g2.displayStyle = g2.Mesh


to

#    tarray = ((0,1,2),(0,2,3))
     tarray = ((0,1,1),)
#    tarray = ((0,1,2),(0,2,3),(0,1,5),(0,5,4),(1,2,6),(1,6,5),
#              (2,3,7),(2,7,6),(3,0,4),(3,4,7),(4,5,6),(4,6,7))
     g1 = sm.addPiece(varray, tarray, from_rgba)
     g1.displayStyle = g1.Mesh
     g1.lineThickness = 3

     from Matrix import xform_matrix, apply_matrix
     tf = xform_matrix(xform)
     corners2 = [apply_matrix(tf, p) for p in corners]
     varray2 = corners2
#    g2 = sm.addPiece(varray2, tarray, to_rgba)
#    g2.displayStyle = g2.Mesh

Then restart Chimera and use the script you referred to.  It will draw a 
line for the axis with width 3 pixels.  In the future we will try to add 
some simpler capability to find and show symmetry axes.

	Tom


Philip Wurm wrote:
> Hi,
> i have a protein dimer and i would like to show the symmetry axis. I 
> found a script in this mailing list:
> 
> http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003140.html
> 
> which works quite nice. But i would like to have a nicer representation 
> of my symmetry axis, not this two slabs. Just a line or thin rod would 
> be nice.
> 
> Does anyone know how to do this?
> 
> Thanks,
> Philip
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