Basic question for mask making for local refinement

Local Refinement
3

Dear Michael

Thank you very much for your explanation. Let me follow up to make sure that I understand correctly:

Let’s say we have a protein X composed of distinct domain A and B: X=A+B. After homogeneous or Non-Uniform refinement, we want to refine domain A. Apparently, we have two ways to do this:

Option 1:

  1. Make mask that covers domain A

  2. Go to “Local Refinement (BETA)” job and input particles, volume and the mask for domain A and run the job

Or

Option 2:

  1. Make “inverse mask” by subtracting Mask (A) - Mask (A+B=X) = Mask (-B)

  2. Go to “Particle Subtraction (BETA)” job and input input particles, volume and inverse mask, Mask (-B), and run the job

  3. Then go to “Local Refinement (BETA)” job and input “subtracted particles”, volume and Mask (A), and run the job.

Do I understand correctly? If so, the tutorial for yeast U4/U6.U5 tri-snRNP corresponds to Option 2.

Thanks for your help

Best

Yuro

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