Re: [scipion-users] Cryo-EM tomography using Scipion

[Pablo C. <pc...@cn...>]

Dear Hongchen Fan!

Scipion tomography functionality is still in beta (not released). We are 
currently moving from relion3 to relion4, so relion3 functionality is 
almost deprecated.

Yes relion4 can be used (in beta) in Scipion3.


I'm afraid I can not answer your very detailed questions. If you are 
willing to deep into tomography using Scipion, we can facilitate access 
to our slack workspace upon request (just email me). There you can join 
developers and other betatesters where hopefully can answer your questions.



On 30/5/22 15:27, 范宏成 wrote:
> Dear all,
> I am new to the cryo-EM tomography. I have some questions  when using 
> some softwares.
> 1. I watched  subtomogram-averaging videos using relion3 on the 
> scipion3 website. I noticed that adding extra restraints like 
> --sigma_tilt 3, --sigma_psi 3 in relion-3d classification maybe in 
> order to improve the alignment accuracy. I wanna know whether these 
> values (--sigma_tilt 3, --sigma_psi 3)  are generally applicable. For 
> subtomogram-averaging analysis, what is the ordinary range of these 
> values when using the relion-3d classification? I recently tried the 
> relion4 too. I found that the relion4 tomo-processing strategy 
> (pseudo-subtomograms) showed much difference from the relion3. I'm not 
> sure whether I need to add these extra retraints in relion4-3d 
> classification or not.
>
> 2. Does relion4 can be used in the Scipion3 now？I noticed the tilt 
> handedness parameter in the relion_tomo_import_tomograms protocol. 
>  The default values is -1. I wanna know the influence of this 
> parameter for subtomo-averaging and which condition to choose the 
> value of 1 . I found that I could also got same chirality androughly 
> same resolution 3D structure when I chose the 1 for  the tilt 
> handedness parameter.
>
> 3. How to  manually judge the alignment accuracy of particles when 
> doing the sub-tomogram analysis in Scipion. There existed some 
> mis-oriented particles after relion-refinement. Can I put these 
> aligned particles to original tomograms to check  which particles are 
> mis-oriented and thus I can manually changed  their relevant euler 
> angles to make them better fit the geometric constraint in tomograms 
> or just deleted them.
>
> 4.I recently tried the Aretomo (v1.1.0) for my project(FIB-milled). I 
> found better tomography reconstruction in aretomo compared to using 
> imod patch-tracking in my project.  I am wondering whether aretomo 
> results can be better than imod even using the sub-tilt refinement in 
> relion4 ? Dose anyone test the performance of aretomo for 
> subtomo-averaing?
>
> 5. I am doing the tomogram segmentation. My tomogram have some 
> microstructures like  mitochondrion, ribosome, microtubule, lipid 
> droplets, endoplasmic reticulum. Are there some softwares recommended 
> or  worth a try ?
>
> Looking forward to your response. Thank you！
>
>
> Hongcheng Fan
>
>
>
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-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*