# [Chimera-users] calculating symmetry for a dimer structure

Tom Goddard goddard at cgl.ucsf.edu
Fri Sep 26 12:26:16 PDT 2008

```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
>

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