Titan and Leginon checklist for automated collection

Titan and Leginon Check List For Automated Collection

 

  • Set defocus range (e.g. 0.8 – 3.0 microns)
  • Targets are submitted
  • User verification is OFF
  • Turbo pump OFF
  • Objective in and centered
  • Astigmatism
  • Rotation center
  • Dose match
  • New gain references for final exposure time
  • Field compensator reset after final exposure adjustments
  • Save frames data
  • All samples are put away
  • Liquid Nitrogen level

Below is a description of the framesdata pipeline.
Caution – under construction.

  1. Copying frames:
  2. Start the robocopy script to transfer from FastSSD -> D: drive to Archive -> E: drive
  3. Open a command prompt on the DE computer
  4. Enter the following command:  robocopy D:\RawFrames\DE20\ E:\Data\Integrating\ *.mrc /s /ts /v /r:2 /w:2 /move /mot:5 /r:2 /w:5       (the script is also in a file on the DE comp desktop called commands.rtf)
  5. On hermes -> Load the module:  myamidev
  6. Change group to cryo_secm4
  7. Run the transferFrames2.py script -> transferFrames2.py --origpath /mnt/176_Data/Integrating/ --despath /mnt/obscure_lustre/cryo/lustre/framesdata --session 17jan09a --preset ex

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