I wanted to follow up on this thread with a few more questions regarding excluded views in Relion4Beta2.

1. To exclude tilts, does one need to run IMODs “exludeviews” first; then feed the output of “excludeviews” to Relion4 by pointing to the “excludeviews” output tilt series in “rlnTomoTiltSeriesName” in the tomogram_desc.star file?  

2. Or does Relion handle these views itself using the tilt.com “EXCLUDELIST” variable?  

3. Could you describe in more detail the rlnTomoImportCulledFile parameter is the description.star file? After reading the docs, I was hesitant about the role of rlnTomoTiltSeriesName vs. rlnTomoImportCulledFile for cases of excluded views. Is rlnTomoImportCulledFile simply the filename we want Relion to call a file it outputs during preprocessing?  Another interpretation I took from the docs is that rlnTomoTiltSeriesName should point to the tilt series with all views (e.g. tomograms/TS_01/TS_01.mrc) while rlnTomoImportCulledFile would point to the same tilt series but without the excluded views as generated from IMODs “excludeviews” (e.g.  tomograms/TS_01/TS_01_excl.mrc; where TS_01_excl.mrc is generated by the user in IMOD before import into Relion).

My intuition from the docs and the responses below is that the user does not need to run "excludeviews" but simply:

1)  Specifify the aligned TS as rlnTomoTiltSeriesName

2) Specify the name of the file they want relion to make without the excluded views (as rlnTomoImportCulledFile)

3) Provide relion with the tilt.com in the directory structure as specified in the tutorial.

Jacob

 

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From: Collaborative Computational Project in Electron cryo-Microscopy <[log in to unmask]> on behalf of Joaquín Otón <[log in to unmask]>
Sent: Wednesday, October 13, 2021 5:22 PM
To: [log in to unmask] <[log in to unmask]>
Subject: Re: [ccpem] exluded views in Relion4 Beta STA

 

Dear John,

in the case you mention, excluded views during IMOD reconstruction but still present in the .st file, you should set that new rlnTomoImportCulledFile column in tomograms_input.star with the filename of the culled stack which relion_tomo_import_tomograms will be creating from the original one. If you created the culled stack and set it in rlnTomoImportCulledFile I guess it was overwriten, but it should match the one you created. If you still get blurry reconstructions, could you send me your tomograms_input.star and imported tomograms.star files?

You can also check if tomo data has been properly imported by reconstructing the tomogram with relion_tomo_reconstruct_tomogram --t tomograms.star --tn TS_XX --o TS_XX_rec.mrc

In case some views were manually removed before reconstruction in IMOD, usually original unaligned .st file still include them while .tlt doesn't. Here, you need to manually create a new stack file removing the excluded ones matching the angles distribution in the .tlt file. This culled filename should be set in rlnTomoTiltSeriesName, not in rlnTomoImportCulledFile. You could also try this way.

Cheers,

Joaquín

On 12/10/21 19:11, John Heumann wrote:

I have a set of tomograms in which bad views are excluded (but not removed) from some of the tilt series. What the correct way to handle this?
I tried creating additional tilt series with the bad views removed... e.g. TS_01_Culled.mrc and TS_01_Culled.mrc and listing those in the tomogram description star file under _rlnTomoImportCulledFile. Is that corect? I'm getting blurry reconstructions, which make me suspect the mapping back to tilt images may not be correct.

Thanks!
-jh-

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