# [Chimera-users] symmetric fitting

Thomas Goddard goddard at cgl.ucsf.edu
Mon Oct 6 12:06:32 PDT 2008

```Hi Sudheer,

Figuring out the symmetry matrices for using the symmetric fitting
capability

http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#symcopies

requires some work.  First note that the symmetry matrices you want are
those that transform (rotate and shift) the volume data to an identical
configuration.

Your case is 2 stacked 7-mer rings.  Assuming the z axis is the
symmetry axis of the map (need to set origin so the center of the
cylinder is at xyz = 0,0,0 in the volume dialog Coordinates panel) you
could just compute the needed rotation matrices

cos(a), sin(a), 0
-sin(a), cos(a), 0
0,      0, 1

Could write a script (python script attached) or use a calculator.  Also
you want to flip around x axis by 180 degrees to get 7 more rotations
with the two 7-member rings exchanged.  With that approach I get the
following lines to add to the PDB file:

REMARK 350   BIOMT1     0    1.000000   0.000000   0.000000   0.000000
REMARK 350   BIOMT2     0   -0.000000   1.000000   0.000000   0.000000
REMARK 350   BIOMT3     0    0.000000   0.000000   1.000000   0.000000
REMARK 350   BIOMT1     1    0.623490   0.781831   0.000000   0.000000
REMARK 350   BIOMT2     1   -0.781831   0.623490   0.000000   0.000000
REMARK 350   BIOMT3     1    0.000000   0.000000   1.000000   0.000000
REMARK 350   BIOMT1     2   -0.222521   0.974928   0.000000   0.000000
REMARK 350   BIOMT2     2   -0.974928  -0.222521   0.000000   0.000000
REMARK 350   BIOMT3     2    0.000000   0.000000   1.000000   0.000000
REMARK 350   BIOMT1     3   -0.900969   0.433884   0.000000   0.000000
REMARK 350   BIOMT2     3   -0.433884  -0.900969   0.000000   0.000000
REMARK 350   BIOMT3     3    0.000000   0.000000   1.000000   0.000000
REMARK 350   BIOMT1     4   -0.900969  -0.433884   0.000000   0.000000
REMARK 350   BIOMT2     4    0.433884  -0.900969   0.000000   0.000000
REMARK 350   BIOMT3     4    0.000000   0.000000   1.000000   0.000000
REMARK 350   BIOMT1     5   -0.222521  -0.974928   0.000000   0.000000
REMARK 350   BIOMT2     5    0.974928  -0.222521   0.000000   0.000000
REMARK 350   BIOMT3     5    0.000000   0.000000   1.000000   0.000000
REMARK 350   BIOMT1     6    0.623490  -0.781831   0.000000   0.000000
REMARK 350   BIOMT2     6    0.781831   0.623490   0.000000   0.000000
REMARK 350   BIOMT3     6    0.000000   0.000000   1.000000   0.000000
REMARK 350   BIOMT1     7    1.000000  -0.000000   0.000000   0.000000
REMARK 350   BIOMT2     7   -0.000000  -1.000000   0.000000   0.000000
REMARK 350   BIOMT3     7    0.000000   0.000000  -1.000000   0.000000
REMARK 350   BIOMT1     8    0.623490  -0.781831   0.000000   0.000000
REMARK 350   BIOMT2     8   -0.781831  -0.623490   0.000000   0.000000
REMARK 350   BIOMT3     8    0.000000   0.000000  -1.000000   0.000000
REMARK 350   BIOMT1     9   -0.222521  -0.974928   0.000000   0.000000
REMARK 350   BIOMT2     9   -0.974928   0.222521   0.000000   0.000000
REMARK 350   BIOMT3     9    0.000000   0.000000  -1.000000   0.000000
REMARK 350   BIOMT1    10   -0.900969  -0.433884   0.000000   0.000000
REMARK 350   BIOMT2    10   -0.433884   0.900969   0.000000   0.000000
REMARK 350   BIOMT3    10    0.000000   0.000000  -1.000000   0.000000
REMARK 350   BIOMT1    11   -0.900969   0.433884   0.000000   0.000000
REMARK 350   BIOMT2    11    0.433884   0.900969   0.000000   0.000000
REMARK 350   BIOMT3    11    0.000000   0.000000  -1.000000   0.000000
REMARK 350   BIOMT1    12   -0.222521   0.974928   0.000000   0.000000
REMARK 350   BIOMT2    12    0.974928   0.222521   0.000000   0.000000
REMARK 350   BIOMT3    12    0.000000   0.000000  -1.000000   0.000000
REMARK 350   BIOMT1    13    0.623490   0.781831   0.000000   0.000000
REMARK 350   BIOMT2    13    0.781831  -0.623490   0.000000   0.000000
REMARK 350   BIOMT3    13    0.000000   0.000000  -1.000000   0.000000

If your map origin is not the center of symmetry or an x-axis flip is
not a symmetry then these matrices won't work.  You can try to set the
correct origin -- the right value can be found with some tricky use of
the output of the Fit in Map tool, fitting one copy of the map into
another copy.  Or you could fit one copy of the map to another and use
the matrixget command to output that symmetry matrix to a file, then do
that for all symmetries to create the needed matrix text.

As you see this process has not yet been made easy.

Tom

skmolugu at miners.utep.edu wrote:
> HI,
> In the symmetric fitting model session that explains about the symmetry generation, i did not understand the method to generate the matrix. I am working on a chaperonin protein called GroEL. It has 14 subunits with seven fold symmetry. can you please explain me how to update the pdb and the matrix values that i need to put in the pdb file.
> thankyou,
> sudheer
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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