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
Katryna Cisek asks about display of symmetry axis: Hello Tom, Thank you for your suggestion, the code below is working very well for finding the symmetry information that I need for my dimers. Is it possible to visualize the axis of symmetry and the shift? I'm trying to reproduce a reference dimer conformation/symmetry using two monomers that have been docked to each other, but have not been able to get the exact symmetry numbers as for my reference structure, Thanks, Katryna On Fri, Sep 26, 2008 at 3:26 PM, Tom Goddard <goddard@cgl.ucsf.edu> wrote: 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()
Hi Katryna, The keyboard shortcut "ai" shows two slabs that indicate the rotation and shift between two molecules: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/alist.... Here's a Chimera command script and an attached image demonstrating this capability. open 1ijj open 1ijj mmaker #0:.a #1:.b pairing ss select :.a ac ai ~disp #0 color white :.b repr sphere #1 Note there was a typo in the mmaker command in my previous email -- needed to use models #0 and #1, not #0 twice. Tom Thomas Goddard wrote:
Katryna Cisek asks about display of symmetry axis:
Hello Tom, Thank you for your suggestion, the code below is working very well for finding the symmetry information that I need for my dimers. Is it possible to visualize the axis of symmetry and the shift? I'm trying to reproduce a reference dimer conformation/symmetry using two monomers that have been docked to each other, but have not been able to get the exact symmetry numbers as for my reference structure, Thanks, Katryna
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
On Fri, Sep 26, 2008 at 3:26 PM, Tom Goddard <goddard@cgl.ucsf.edu> wrote: 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()
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Thomas Goddard