Flip hand all components of a volume

Utilities
1

Hi,

I would like to flip the hand of all the components of a volume (map, map_sharp, half_a, half_b…), all in a single volume tools. Is that possible?

Currently I have to flip each component individually

Thank you

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2

Hi,

I think this is possible externally [eg in chimera(X)] but not within CS.
What I do is to flip the hand of the map (in Volume tools) and then re-run the refinement with this map as an input.

Best,
Left

3

Hi @leobets,

Thanks for the request. Are you attempting to flip the hand of each volume from the output of a homogeneous/non-uniform/local refinement / 3D classification, or are you instead flipping the hand of a 3D Flex model output from 3D Flex Reconstruct (inferred from this post)?

If it’s the former, you may be able to accomplish this via the “Flip the reconstruction hand” in Homogeneous Reconstruction Only, which will take particles re-reconstruct the volume with the particles’ alignments transformed to correct for the hand-flip.

If it’s the latter, unfortunately you’re right that this has to be done manually via Volume Tools for each volume. If this is a step you have to do frequently, and if you’re open to some scripting via CryoSPARC Tools, it would be possible to do so by programmatically creating Volume Tools jobs and then connecting each of the map inputs.

Best,
Michael

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4

Michael,

I would like to use the half maps to calculate the local resolution of my map, so far I have to flip the hand of multiple volumes to carry out this job. Also, I would like to flip the hand of all the volumes from a volume series output in a single job. Unfortunately I forgot to flip the hand in upstream jobs before doing 3D variability and 3D classification.

Concerning the other post, for this question I am not trying to flip the hand of the 3D flex reconstruct.

Thank you for the response, I’ll carry out the Homogeneous Reconstruction Only job for the local resolution estimations.

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5

Not a cryosparc solution, but we use relion_image_handler for this, e.g.:

for file in *.mrc; do relion_image_handler --i ${file} --angpix 0.83 --flipZ true --o ${file%.mrc}_zflip.mrc; done

(I should add that having a version of volume tools that can operate on multiple inputs would indeed be very useful - e.g. cropping/flipping/filtering multiple classes out of 3D classification, for example)

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6

Can anyone report any progress on this, @team ?

7

Hi @AndreGraca! I don’t have any updates on this per se, but if you find yourself having to do this frequently, you could make a workflow of the following steps:

  1. Flip the main map with Volume Tools
  2. Create an Align 3D Maps job, with this flipped map as the Reference map input and the original job’s volume as the Maps to align (individual volumes) input

The Aligned volume 0 output of this Align 3D Maps job will have all of the component volumes flipped.

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