[Chimera-users] drawing a symmetry axis
Thomas Goddard
goddard at cgl.ucsf.edu
Thu Dec 11 16:49:56 PST 2008
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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