[Chimera-users] Display symmetry axis

[Thomas Goddard]

Hi Katryna,

   The keyboard shortcut "ai" shows two slabs that indicate the rotation 
and shift between two molecules:

http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/alist.html#abdetails

Here's a Chimera command script and an attached image demonstrating this 
capability.

open 1ijj
open 1ijj
mmaker #0:.a #1:.b pairing ss
select :.a
ac ai
~disp #0
color white :.b
repr sphere #1

Note there was a typo in the mmaker command in my previous email -- 
needed to use models #0 and #1, not #0 twice.

	Tom


Thomas Goddard wrote:
> 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()
>  > >
>  > >
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