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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users