[3dem] Autopicking

[Takanori Nakane]

Hi,

I answer only the second question.

 > In Relion 3.1.1, I could see the results of autopicking with the command (e.g.):
 >
 > `which relion_manualpick` --i Select/job011/micrographs_split1.star --odir AutoPick/job002/ --pickname autpic --allow_save  --selection
 > Select/job003/micrographs_selected.star --scale 0.2 --sigma_contrast 3 --black 0 --white 0 --lowpass 20 --ctf_scale 1 --particle_diameter 100
 >
 > but I cannot find anything equivalent in Relion 4.0. Is it somewhere else?

Open "autopick.star" from the drop-down list of an AutoPick job.
"ps aux | grep manualpick" will show a command line such as:

relion_manualpick --i AutoPick/jobXXX/autopick.star --scale 0.25 --sigma_contrast 3 --lowpass 20 --particle_diameter 100

Best regards,

Takanori Nakane

On 2021/12/17 4:41, Bullitt, Esther wrote:
> Hello,
> 
> I have a few questions about Autopicking in Relion.
> 
> I would like to have a more reasoned approach for choosing --min_avg_noise and --max_avg_noise.
> is there a calculation somewhere of these values for either single or groups of micrographs?
> more fundamentally, can I see a histogram of intensities of my images?
> Any other details on find parameters for autopicking to pick filaments rather than background (which it is doing exclusively on my new dataset; see 
> attached) would be appreciated -- and yes, the regions below the green circles are background; not a single filament segment picked.
> 
> In Relion 3.1.1, I could see the results of autopicking with the command (e.g.):
> 
> `which relion_manualpick` --i Select/job011/micrographs_split1.star --odir AutoPick/job002/ --pickname autpic --allow_save  --selection 
> Select/job003/micrographs_selected.star --scale 0.2 --sigma_contrast 3 --black 0 --white 0 --lowpass 20 --ctf_scale 1 --particle_diameter 100
> 
> but I cannot find anything equivalent in Relion 4.0. Is it somewhere else?
> 
> thanks very much.
> 
> Sincerely,
> Esther
> 
> 
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