Hi Sudheer, Figuring out the symmetry matrices for using the symmetric fitting capability http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#symcopi... 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@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@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
# Create symmetry matrices for GroEL 14-mer. format = '''REMARK 350 BIOMT1 %3d %10.6f %10.6f %10.6f %10.6f REMARK 350 BIOMT2 %3d %10.6f %10.6f %10.6f %10.6f REMARK 350 BIOMT3 %3d %10.6f %10.6f %10.6f %10.6f''' from math import pi, sin, cos for i in range(7): a = i*2*pi/7.0 # Rotation by i/7 turn about z. print format % (i, cos(a), sin(a), 0, 0, i, -sin(a), cos(a), 0, 0, i, 0, 0, 1, 0) for i in range(7): a = i*2*pi/7.0 # 180 degree rotation about x, then i/7 turn about z. print format % (i+7, cos(a), -sin(a), 0, 0, i+7, -sin(a), -cos(a), 0, 0, i+7, 0, 0, -1, 0)