Constraining map-to-map fitting based on symmetry?
Hi, If I have two maps of the same symmetry (say C4), and I align them using fit in map, is there any way to force chimera to keep the rotation axes of the two maps aligned, and to only search rotation around (and translation along) that axis, rather than arbitrary rotations? Cheers, Oliver.
Hi Oliver, No there no way to restrain symmetry axes using Chimera map fitting. You can optimize rotations only preventing any translation, but full rotations will be allowed. You could use the Chimera “measure correlation” command with the rotationAxis and angleRange and plot options to measure the correlation value as one map is rotated relative to the other. This doesn’t report the maximum correlation position but you could find the maximum in the tabulated values in the reply log. http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/measure.html#c... Tom
On Mar 19, 2015, at 9:44 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi,
If I have two maps of the same symmetry (say C4), and I align them using fit in map, is there any way to force chimera to keep the rotation axes of the two maps aligned, and to only search rotation around (and translation along) that axis, rather than arbitrary rotations?
Cheers, Oliver.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thanks Tom, I will try this. I think locking the rotation axis for map fitting to the symmetry axis would be a useful feature for a future version, though I understand that it’s a bit of a niche use case. Best, Oliver.
On Mar 19, 2015, at 3:23 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Oliver,
No there no way to restrain symmetry axes using Chimera map fitting. You can optimize rotations only preventing any translation, but full rotations will be allowed.
You could use the Chimera “measure correlation” command with the rotationAxis and angleRange and plot options to measure the correlation value as one map is rotated relative to the other. This doesn’t report the maximum correlation position but you could find the maximum in the tabulated values in the reply log.
http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/measure.html#c...
Tom
On Mar 19, 2015, at 9:44 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi,
If I have two maps of the same symmetry (say C4), and I align them using fit in map, is there any way to force chimera to keep the rotation axes of the two maps aligned, and to only search rotation around (and translation along) that axis, rather than arbitrary rotations?
Cheers, Oliver.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Oliver, My suggestion for using “measure correlation” only handled rotations about the axis, not translations along the axis. I’ve added a feature request for fitting using just these 2 degrees of freedom. http://plato.cgl.ucsf.edu/trac/chimera/ticket/13829 <http://plato.cgl.ucsf.edu/trac/chimera/ticket/13829> I think it is not that uncommon a case. But we are working hard on Chimera 2 so I don’t think this will be added soon. Thanks for the suggestion. Tom
On Mar 20, 2015, at 7:54 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Thanks Tom, I will try this. I think locking the rotation axis for map fitting to the symmetry axis would be a useful feature for a future version, though I understand that it’s a bit of a niche use case.
Best, Oliver.
On Mar 19, 2015, at 3:23 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Oliver,
No there no way to restrain symmetry axes using Chimera map fitting. You can optimize rotations only preventing any translation, but full rotations will be allowed.
You could use the Chimera “measure correlation” command with the rotationAxis and angleRange and plot options to measure the correlation value as one map is rotated relative to the other. This doesn’t report the maximum correlation position but you could find the maximum in the tabulated values in the reply log.
http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/measure.html#c...
Tom
On Mar 19, 2015, at 9:44 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hi,
If I have two maps of the same symmetry (say C4), and I align them using fit in map, is there any way to force chimera to keep the rotation axes of the two maps aligned, and to only search rotation around (and translation along) that axis, rather than arbitrary rotations?
Cheers, Oliver.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Tom Goddard