Feature #6035
open
Write out rlnBeamTiltGroupName column in star file for RELION 3 beam tilt refinement? [Feature Request]
Added by Oliver Clarke almost 6 years ago.
Updated almost 6 years ago.
Description
Hi Anchi,
Relion 3 now supports refining multiple beam tilt groups in a single star file (see: https://bitbucket.org/scheres/relion-3.0_beta/issues/3/beam-tilt-estimation-group-micrographs ).
It does so by use of the `rlnBeamTiltGroupName` column, which defines the groups of micrographs that should have similar beam tilt values.
Would it be possible to add this column to the summary star file which currently has estimated tilt values? This would allow for very convenient estimation of beam tit for groups of micrographs with nominally similar image shift.
Cheers
Oli
- Status changed from New to Assigned
Oli,
This can be added but it will not give the best result. Within the group there will be beam-image shift variation present because stage movement is not accurate. The better option which you may ask as a Relion feature is to take the beam tilt metadata in the star file and ask relion to shift the center of the beam tilt distribution in the refinement because that is harder to be correct. How much beam tilt is obtained by beam-image shift is fairly stable.
Hi Anchi,
That would definitely be better and I will request it - however I would note that splitting the data into image shift groups was used in the Relion 3 paper with good results (see Fig 6 supp 1): https://www.biorxiv.org/content/biorxiv/early/2018/09/19/421123.full.pdf, so while not perfect it may still be helpful I think
Cheers
Oli
Anchi Cheng wrote:
Oli,
This can be added but it will not give the best result. Within the group there will be beam-image shift variation present because stage movement is not accurate. The better option which you may ask as a Relion feature is to take the beam tilt metadata in the star file and ask relion to shift the center of the beam tilt distribution in the refinement because that is harder to be correct. How much beam tilt is obtained by beam-image shift is fairly stable.
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