Measure inertia and measure center on aligned density maps and models
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
Hi Kevin, My tests confirm that "measure center" and "measure inertia" are not using the transformed position of a map, which is a bug. I will create a bug ticket and add your name to it. However, at least in my tests in the daily build, these commands are correctly using the transformed position of an atomic model. If you have markers in the same model as each other you can add links between them (equivalent to adding a bond between atoms in the same model), e.g. with "marker link" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/marker.html> Often different centroids or markers will be in different models, however, so the easy way to draw a line (cylinder) between them is to measure the distance between them, which will add a pseudobond. You can hide the distance label by unchecking the "eye" checkbox ifor that model in the Models panel, and change the style/color of the pseudobond, e.g. with commands or by selecting the pseudobond (Ctrl-click) and using the Selection Inspector to inspect Pseudobonds and Pseudobond Models: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html#options> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/inspector.html> The best metrics of comparison are totally up to you depending on your research question. You could consider using more than one measurement, e.g. not just centroids, but also length/width, amount of overlap, distance between overlaid isosurfaces, etc. You can place markers on the isosurface of a map interactively (mouseclick) and then use them for distance and other measurements. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/markerplacement.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/distances.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 13, 2023, at 8:48 AM, Kevin Felt via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Kevin, Thanks for pointing out that the measure center and measure inertia command were not showing markers and ellipsoids in the right place if the measured model had been aligned to another model. I've fixed those problems in the ChimeraX 1.6 release candidate and daily builds dated April 14, 2023 or later. Tom
On Apr 13, 2023, at 10:17 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Kevin, My tests confirm that "measure center" and "measure inertia" are not using the transformed position of a map, which is a bug. I will create a bug ticket and add your name to it. However, at least in my tests in the daily build, these commands are correctly using the transformed position of an atomic model.
If you have markers in the same model as each other you can add links between them (equivalent to adding a bond between atoms in the same model), e.g. with "marker link" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/marker.html>
Often different centroids or markers will be in different models, however, so the easy way to draw a line (cylinder) between them is to measure the distance between them, which will add a pseudobond. You can hide the distance label by unchecking the "eye" checkbox ifor that model in the Models panel, and change the style/color of the pseudobond, e.g. with commands or by selecting the pseudobond (Ctrl-click) and using the Selection Inspector to inspect Pseudobonds and Pseudobond Models: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html#options> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/inspector.html>
The best metrics of comparison are totally up to you depending on your research question. You could consider using more than one measurement, e.g. not just centroids, but also length/width, amount of overlap, distance between overlaid isosurfaces, etc. You can place markers on the isosurface of a map interactively (mouseclick) and then use them for distance and other measurements.
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/markerplacement.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/distances.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 13, 2023, at 8:48 AM, Kevin Felt via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Elaine Meng -
Kevin Felt -
Tom Goddard