Hi Junjie, In general there are two ways: (1) use Define Axes/Planes/Centroids tool or "define" command to define axis or plane objects based on specified atoms. Then you can get the crossing angles between any pairs of these objects using the Axes/Planes/Centroids GUI or the "angle" command. See the following for details: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/axesplanes.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/define.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/angle.html> (2) if the two domains are structurally similar to each other, you could open two copies of the structure and fit one onto the other, superimposing the parts you want to superimpose (using whatever method you want, "align" or "matchmaker" or manual movements). Then you can get the relationship between the two models with "measure rotation" -- see the following for details: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 22, 2025, at 8:39 PM, junjie han <hanjunjie2014@gmail.com> wrote:
Hi Elaine,
I hope this email finds you well. May I ask how to measure the angle between two domains from one molecule or two different molecules in ChimeraX. Here are some examples below. Example 1:
<image.png>How to calculate these angles (54°, 38°)？
Example 2:<image.png>How to calculate this angle (75°) ?
Example 3:<image.png>How can I measure the rotation angle between A and B, or between two specific regions of these two molecules in ChimeraX? If I need to calculate the rotation angles of two molecules relative to a specific molecule, how can I define a shared axis for calculating the rotation angles? The rotation axes are different when I use the command “measure rotation A toModel B” to calculate the rotation angles, which is not an ideal way to compare them in parallel.
Thank you in advance for your any suggestions.
Very appreciated, Junjie