Thank you, Alpay. This solved my problem.
Lizelle, the GUI of relion 3 doesn't seem to be compatible with relion 4.0.
Best,
Zheng
On Fri, Oct 8, 2021 at 4:28 PM Alpay Burak Seven <[log in to unmask]> wrote:
>
> You can also right-click on the micrographs (Relion GUI/AutopickJob/Display/out: autopick.star), then click on "Set FOM threshold" to change the threshold for visualization of picked particles above that threshold. You can then subset select based on the threshold you decide is best.
>
> These are outlined on this website
> https://relion.readthedocs.io/en/release-4.0/SPA_tutorial/index.html
>
> --
> Alpay B. Seven, Ph.D.
> Skiniotis Lab.
> Stanford University
>
> On Fri, Oct 8, 2021 at 12:31 PM Lizelle Lubbe <[log in to unmask]> wrote:
>>
>> Hi Zheng Ruan,
>>
>> I think you can go to the completed Topaz picking job in Relion v3 then set - -skip_pick True, - - select_threshold to the value you want, and then continue your Topaz picking job. You can visualize the micrographs at different thresholds to select the value which gives the least false positives.
>> Hope this helps!
>>
>>
>>
>> Lizelle Lubbe, PhD
>>
>> Postdoctoral Research Assistant
>> GCRF_START project
>> Division of Chemical and Systems Biology
>> Department of Integrative Biomedical Sciences
>> Faculty of Health Sciences
>> University of Cape Town
>> South Africa
>>
>>
>> ________________________________
>> From: Collaborative Computational Project in Electron cryo-Microscopy <[log in to unmask]> on behalf of Zheng Ruan <[log in to unmask]>
>> Sent: Friday, 8 October 2021, 20:38
>> To: [log in to unmask]
>> Subject: [ccpem] Visualize topaz picking result using a different threshold
>>
>> CAUTION: This email originated outside the UCT network. Do not click any links or open attachments unless you know and trust the source.
>>
>> Dear All,
>>
>> I'm trying to use the relion topaz wrapper for particle picking. The
>> default --topaz_threshold is -6, which is relatively loose and I end
>> up getting many false positives. Is there an easy way to specify a
>> different threshold based on rlnAutopickFigureOfMerit for
>> visualization in relion? I noticed that I can select on
>> rlnAutopickFigureOfMerit for particle extraction, but I feel more
>> comfortable to visually check the picked coordinates by a certain
>> threshold first before extracting particles.
>>
>> Best,
>> Zheng
>>
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