[Chimera-users] Display symmetry axis

[Thomas Goddard]

Katryna Cisek asks about display of symmetry axis:



Hello Tom,
Thank you for your suggestion, the code below is working very well for 
finding
the symmetry information that I need for my dimers. Is it possible to 
visualize
the axis of symmetry and the shift? I'm trying to reproduce a reference 
dimer
conformation/symmetry using two monomers that have been docked to each
other, but have not been able to get the exact symmetry numbers as for my
reference structure,
Thanks,
Katryna

On Fri, Sep 26, 2008 at 3:26 PM, Tom Goddard <goddard at cgl.ucsf.edu> wrote:
 > > Hi Katryna,
 > >
 > >  To find a dimer symmetry axis I would open two copies of the PDB 
model.  If
 > > the monomers are chain A and chain B then align chain A of one copy 
to chain
 > > B of another copy using the matchmaker command. Then print the 
rotation axis
 > > of the transformation between those two models.  Unfortunately 
there is no
 > > command for this last step so I've attached a Python script that 
will print
 > > that information.
 > >
 > >   Tom
 > >
 > > Example use:
 > >
 > > #
 > > # Report the transformation mapping one model to another, including 
axis of
 > > # rotation.  Written to find dimer symmetry axes.  Example:
 > > #
 > > #   open 1f5w
 > > #   open 1f5w
 > > #   mmaker #0:.a #0:.b pairing ss
 > > #   open symaxis.py
 > > #
 > > # Reply log output:
 > > #
 > > #  match 1f5w, chain A (#0) with 1f5w, chain B (#1), score = 601.8
 > > #  RMSD between 118 atom pairs is 0.337 angstroms
 > > #
 > > #  Matrix rotation and translation
 > > #      0.69329933  -0.72016666   0.02638219  22.81733764
 > > #     -0.72021136  -0.69368986  -0.00948567  58.05835625
 > > #      0.02513232  -0.01242434  -0.99960692 102.03253762
 > > #   Axis  -0.92013562   0.39134963  -0.01399645
 > > #   Axis point   0.00000000  33.92575324  50.81758910
 > > #   Rotation angle (degrees) 179.90850597
 > > #   Shift along axis   0.29797742
 > > #
 > >
 > >
 > > Katryna Cisek wrote:
 >> >>
 >> >> Hi,
 >> >> Is there a way of calculating symmetry for a dimer structure
 >> >> in chimera, e.g. axis of symmetry?
 >> >> Thanks,
 >> >> Katryna
 >> >> _______________________________________________
 >> >> Chimera-users mailing list
 >> >> Chimera-users at cgl.ucsf.edu
 >> >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
 >> >>
 > >
 > >
 > > #
 > > # Report the transformation mapping one model to another, including 
axis of
 > > # rotation.  Written to find dimer symmetry axes.  Example:
 > > #
 > > #   open 1f5w
 > > #   open 1f5w
 > > #   mmaker #0:.a #0:.b pairing ss
 > > #   open symaxis.py
 > > #
 > > # Reply log output:
 > > #
 > > #  match 1f5w, chain A (#0) with 1f5w, chain B (#1), score = 601.8
 > > #  RMSD between 118 atom pairs is 0.337 angstroms
 > > #
 > > #  Matrix rotation and translation
 > > #      0.69329933  -0.72016666   0.02638219  22.81733764
 > > #     -0.72021136  -0.69368986  -0.00948567  58.05835625
 > > #      0.02513232  -0.01242434  -0.99960692 102.03253762
 > > #   Axis  -0.92013562   0.39134963  -0.01399645
 > > #   Axis point   0.00000000  33.92575324  50.81758910
 > > #   Rotation angle (degrees) 179.90850597
 > > #   Shift along axis   0.29797742
 > > #
 > > from chimera import openModels
 > > from Matrix import xform_matrix
 > > from FitMap.gui import transformation_description
 > > from Accelerators.standard_accelerators import show_reply_log
 > >
 > > xf0, xf1 = [m.openState.xform for m in openModels.list()]
 > > xf = xf0.inverse()
 > > xf.multiply(xf1)
 > > tf = xform_matrix(xf)
 > > print transformation_description(tf)
 > > show_reply_log()
 > >
 > >