Export-import helical segments cs->Relion and back

Helical Processing
10

Hi @mbs,

Apologies for the delay – I can comment on what fields would be equivalent. Please note that this is based on the descriptions available here; I have not (yet) worked through this workflow of exporting segments to RELION and performing subsequent refinements in it. Also see my comment here for a description of all other fields.

  • filament/position_A is the position of the particle along the filament contour, in Angstroms; should be equivalent rlnHelicalTrackLengthAngst
  • filament/filament_uid : This associates each particle with an ID of a unique filament, similar to rlnHelicalTubeID . To the best of my knowledge, this should map one-to-one to rlnHelicalTubeID. The main reason for this parameter is for filament-based half-set splitting during refinement, which I believe is also the case in RELION.
  • filament/filament_pose : Approximate in-plane rotation angle (radians) between helical axis and x-axis. It should be possible to convert this to rlnAnglePsiPrior, but there may be convention differences. Likely, testing is needed to ensure the conversion is correct.

The orientation parameters are the same as in alignments3D/{pose,shift}. CryoSPARC doesn’t use priors over any orientation parameters except for possibly tilt; thus there is no equivalent to rlnAnglePsiFlipRatio, rlnAngleRotFlipRatio, and rlnAnglePsiFlip. Does RELION prescribe a default value for these fields that generates an effectively uniform prior? And if not, I’m curious if RELION allows for running helical refinements without priors over psi, rot, or tilt…

Best,
Michael