I had to use a robot to figure out how to do this. We should have a clear explanation right in the GUI.
output from robot
Overview
Yes—there are concrete, step-by-step guides that show how to pick the center in a visualization program and convert it to the numbers cisTEM expects. The most transferable recipe uses ChimeraX markers to read the 3D point in Å, then convert to pixels if needed elsewhere; for cisTEM’s focused classification center, use the Å values directly as the sphere center in the map coordinate frame.
Step-by-step in ChimeraX
Step by step
- Load your map in ChimeraX, orient to the region of interest, and place a marker exactly at the desired center: in the Markers ribbon, choose Surface under Place markers, then right‑click on the map surface to drop a marker; ChimeraX prints the XYZ in Å in the log.
2. Read the Å coordinates from the log and use those three numbers as the center (X, Y, Z) for cisTEM’s spherical focus mask; cisTEM interprets these in the reconstruction’s physical Cartesian space, consistent with the map’s pixel size and origin used during reconstruction.
additional notes
Point out that the marker can easily be moved (refer to steps) and resized in chimerax
I had to use a robot to figure out how to do this. We should have a clear explanation right in the GUI.
output from robot
Overview
Yes—there are concrete, step-by-step guides that show how to pick the center in a visualization program and convert it to the numbers cisTEM expects. The most transferable recipe uses ChimeraX markers to read the 3D point in Å, then convert to pixels if needed elsewhere; for cisTEM’s focused classification center, use the Å values directly as the sphere center in the map coordinate frame.
Step-by-step in ChimeraX
Step by step
2. Read the Å coordinates from the log and use those three numbers as the center (X, Y, Z) for cisTEM’s spherical focus mask; cisTEM interprets these in the reconstruction’s physical Cartesian space, consistent with the map’s pixel size and origin used during reconstruction.
additional notes
Point out that the marker can easily be moved (refer to steps) and resized in chimerax