Tip

Please do not copy run_all.py only into some folder, and run there (e.g. use run_all.py as in original location of git clone)
- For example, if a user git cloned at
  - ~/script/python/cryoEM/AutoMicroED
    - do
      - python ~/script/python/cryoEM/AutoMicroED/run_all.py
If a user prefers, the user can add - alias MicroED="python /Users/kimd999/script/python/cryoEM/AutoMicroED/run_all.py"
- in ~/.bash_profile
- and source ~/.bash_profile
- then simply run as
  - MicroED
If a user wants to update code, do
- git pull
- at (git repo), for example ~/script/python/cryoEM/AutoMicroED
- this update of code is not necessary right after git clone
Consult with reference/microED_notes.pdf file for abbreviations and additional options.
For catalase, carbamazepine microED data generation (perhaps for other targets as well), rotation rate of the stage is better to be <= 0.5 degree/second for enough sampling. 1 degree/second is too sparse.
imod's header shows stack number
- Usage: 'header (mrcs filename)'
- For example, if 'header merged.mrcs' shows
  - Number of columns, rows, sections ..... 4096 4096 147
- this mrcs has 147 images (e.g. I merged 71 and 76 images)

Tip for File System Path

run AutoMicroED on path that has no space ( ) in it.
- For example, do not run AutoMicroED at "Desktop" or "OneDrive sync" since often these have () in PATH.
Also, do not run AutoMicroED at a folder has too long path name (most operating systems cannot handle properly).