[Chimera-users] symmetric fitting

[Thomas Goddard]

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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