[chimerax-users] Measure inertia and measure center on aligned density maps and models

[Kevin Felt]

Dear developers,

I am trying to compare the center of mass of multiple cryo-EM maps and
models. The receptor is the same in all cases, just the ligand bound in the
binding pocket varies. I want to show a directionality to how the ligands
are binding in the pocket between the structures, so I have aligned the
maps and models together and am attempting to run "measure center" and
"measure inertia" to initiate this comparison. However, when I run these
commands, the output markers and ellipsoids are not positioned in an
aligned fashion as their parent objects, but rather in there initial
positions before alignment, which is not useful for comparisons of the
subtle movements between structures.

Additionally, if I could get the measurements to work on the
aligned structures, is there a tool in ChimeraX that would allow me to draw
vectors from a reference point to the center of masses? Furthermore, is
center of mass the correct parameter for comparison of densities that are
variable in shape? (e.g. comparing the relative position of a long and flat
density to a short a globular density?)

Thank you!

Sincerely,

-- 
Kevin C. Felt
PhD Candidate - Chakrapani Lab
Department of Physiology and Biophysics
School of Medicine
Case Western Reserve University
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