[3dem] Autopicking
Takanori Nakane
tnakane.protein at osaka-u.ac.jp
Thu Dec 16 15:38:59 PST 2021
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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