How to choose a fulcrum for local refinement?

Local Refinement
3

Easiest way to get arbitrary coordinate in Chimera is:

  1. Open volume eraser
  2. Set volume eraser sphere size to ~3A
  3. Move eraser sphere to desired location
  4. Note volume eraser sphere model number from model pane
  5. measure center #N where N is the volume eraser model number

You can also use measure center directly on a volume or atomic model (including arbitrary atom selection). However, be aware that the coordinates are in Angstroms for the volume eraser* and atomic model based methods, but are in voxels when measuring the center of mass of a regular volume.

*Unless the pixel size is not set in the map headers, check by opening the Volume viewer -> Features -> Coordinates and see if the pixel size is right.

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