Begin forwarded message:

From: Tom Goddard <goddard@sonic.net> Subject: Re: [Chimera-users] constrain measurement of rotation to a particular axis? Date: December 18, 2014 11:07:57 AM PST

I think the sensible thing is to report the hinge angles without trying to use a common rotation axis. I can think of different ways to define the common rotation axis (you have to align all the structure in some way, then say how much the observed rotation about the axis for a particular structure translates into a rotation about a slightly different common axis), all of them arbitrary and hard to explain, and even harder to compute, so I wouldn’t go that way.

Tom

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From: Oliver Clarke <olibclarke@gmail.com> Subject: [Chimera-users] constrain measurement of rotation to a particular axis? Date: December 17, 2014 2:36:45 PM PST To: Mailing List <chimera-users@cgl.ucsf.edu>

Hi all,

When using the “measure rotation” command, is there any way to constrain the rotation to be measured about a particular axis?

I am thinking specifically of a case where I have multiple structures of a protein with different inter domain hinge angles - I can use chimera to measure the hinge angle, but for each pair of structures it chooses a slightly different rotation axis, whereas I would like to keep the same axis so I can directly compare the rotation observed between pairs of structures.

Or perhaps there is there another way to do this that would make more sense? Suggestions are welcome...

Best, Oliver.