I would first calculate least square superposition of the first monomer between 2 structures (one to be fixed and one to be moved) using a program such as lsqkap or any other programs suggested by others. You may need to define a relevant region for the superimposition.
Then take the output of the moved structure and calculate another least square superposition of the second monomer in the dimer to the second monemer of the fixed structure. Look at the rotation and translation matrix from the output (or log file). That will give you information of how the second monomer is different in the 2 structures. You can calculate the orientation difference (in degrees) from trace of the rotation matrix. Alternatively, after the first monomers are superimposed, you can use program lsqman (or other programs that calculate rmsd of the second monomers without doing least square superposition) if you prefer an rmsd value instead of a rotational angle. George Wisedchasri On Sun, 14 Nov 2010, E rajakumar wrote:
Dear All I have two structures of homo-dimeric protein complex with different DNA. I want to calculate RMS deviation between second monomer from these two complexes by fixing superposed first monomer. This I require to know what is the effect of DNA on relative orientation of two monomers in the dimer. Previously I was using MOLEMAN2 to do this calculation. Please can you suggest me any other program to do this calculation. Thanking you Raj E. Rajakumara Postdoctoral Fellow Strcutural Biology Program Memorial Sloan-Kettering Cancer Center New York-10021 NY 001 212 639 7986 (Lab) 001 917 674 6266 (Mobile)
