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3dem / relion

Image-processing software for cryo-electron microscopy
https://relion.readthedocs.io/en/latest/
GNU General Public License v2.0
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How to extract refined transformation matrix from STAR files in RELION for XF format? #1213

Open MohamadHarastani opened 6 days ago

MohamadHarastani commented 6 days ago

Hi RELION developers,

I've been processing tomography data in RELION (v4 or v5) and refining tilt-series alignment (refining frame alignment). I noticed that the refined transformation matrix is stored in STAR files as part of the workflow. I am looking for a reliable way to extract this transformation matrix and convert it into IMOD xf format to perform high resolution reconstructions that benefit from this refinement when mapping back the average and interpreting the results.

Could you please provide some guidance on either:

  1. Any existing tools/scripts within RELION or third-party utilities to extract these matrices programmatically.

  2. Any documentation on the meaning of these transformation matrices that can help me script the conversion myself.

Thank you for your time and assistance!

Cheers Mohamad

biochem-fan commented 6 days ago

Does https://relion.readthedocs.io/en/release-3.1/Reference/Conventions.html#orientations help?

I vaguely remember similar topics have been discussed on CCPEM or 3DEM mailing lists.