Clarification of final pose for local refinement jobs

Hello, I recently noticed that the cryosparc .cs files contain a few different pose information fields for local refinement jobs: alignments3D/pose, alignments3D/object_pose and alignments3D/local_pose. Can I get clarification on which field is the locally refined pose? I am hoping it is alignments3D/pose - consistent with standard refinement jobs - as that is what is currently used as input to cryoDRGN. Thanks! -Ellen

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Dear @zhonge,

Thanks for the post! :smiley: Yes – alignments3D/{pose,shift} are always the actual alignments that particles were backprojected with (congruent with the output volumes) which should be used in further processing. The object_pose is the “center” of the search grid and the local_pose is the “residual” on top of that – but the only reason to look at those fields would be to analyze the deviations in alignments each iteration, for example.


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Amazing – thank you for confirming!