Re: [Chimera-users] symmetric fitting
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
Hi Sudheer, Here is an description of the BIOMT matrix format, which you would add with a text editor: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html#biomt> However, it does not explain how you would figure out what values to put into those lines, which is not simple. I would probably try to find another GroEL PDB that already has the BIOMT matrices in it, then match your structure on to it, save the new coordinates for your structure "relative to" the coordinates of that other PDB, then edit in the BIOMT records copied from that other file. However, I don't know if that is precise enough for what you had in mind, and an even bigger problem may be although there are many structures of GroEL, I don't see any with BIOMT information for reproducing the multimer from a single chain. All the ones I looked at simply had the coordinates for all of the chains. Neverthless, here is more information on... superimposing structures: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html#su...
writing coordinates, including "relative to": http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Oct 5, 2008, at 8:54 PM, <skmolugu@miners.utep.edu> <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
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)
participants (3)
-
Elaine Meng -
skmolugu＠miners.utep.edu -
Thomas Goddard