Hi Katryna, To find a dimer symmetry axis I would open two copies of the PDB model. If the monomers are chain A and chain B then align chain A of one copy to chain B of another copy using the matchmaker command. Then print the rotation axis of the transformation between those two models. Unfortunately there is no command for this last step so I've attached a Python script that will print that information. Tom Example use: # # Report the transformation mapping one model to another, including axis of # rotation. Written to find dimer symmetry axes. Example: # # open 1f5w # open 1f5w # mmaker #0:.a #0:.b pairing ss # open symaxis.py # # Reply log output: # # match 1f5w, chain A (#0) with 1f5w, chain B (#1), score = 601.8 # RMSD between 118 atom pairs is 0.337 angstroms # # Matrix rotation and translation # 0.69329933 -0.72016666 0.02638219 22.81733764 # -0.72021136 -0.69368986 -0.00948567 58.05835625 # 0.02513232 -0.01242434 -0.99960692 102.03253762 # Axis -0.92013562 0.39134963 -0.01399645 # Axis point 0.00000000 33.92575324 50.81758910 # Rotation angle (degrees) 179.90850597 # Shift along axis 0.29797742 # Katryna Cisek wrote:

Hi, Is there a way of calculating symmetry for a dimer structure in chimera, e.g. axis of symmetry? Thanks, Katryna _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

# # Report the transformation mapping one model to another, including axis of # rotation. Written to find dimer symmetry axes. Example: # # open 1f5w # open 1f5w # mmaker #0:.a #0:.b pairing ss # open symaxis.py # # Reply log output: # # match 1f5w, chain A (#0) with 1f5w, chain B (#1), score = 601.8 # RMSD between 118 atom pairs is 0.337 angstroms # # Matrix rotation and translation # 0.69329933 -0.72016666 0.02638219 22.81733764 # -0.72021136 -0.69368986 -0.00948567 58.05835625 # 0.02513232 -0.01242434 -0.99960692 102.03253762 # Axis -0.92013562 0.39134963 -0.01399645 # Axis point 0.00000000 33.92575324 50.81758910 # Rotation angle (degrees) 179.90850597 # Shift along axis 0.29797742 # from chimera import openModels from Matrix import xform_matrix from FitMap.gui import transformation_description from Accelerators.standard_accelerators import show_reply_log xf0, xf1 = [m.openState.xform for m in openModels.list()] xf = xf0.inverse() xf.multiply(xf1) tf = xform_matrix(xf) print transformation_description(tf) show_reply_log()