Topaz filament picking in relion4.0

[2019C]

Hello,

I am trying to pick filament with topaz in relion4.0. I have installed the 3dem version topaz from the webpage https://github.com/3dem/topaz. I have created a topaz environment and running relion4.0 inside the environment. The training job finished successfully. I can run topaz picking job if I don't add any additional argument. However, when I add the argument "-f", it reported the following error:

WARNING: there was an error in picking: micrographs/000001041660592124761_FoilHole_2937087_Data_30836795_30836797_20221003_000907_Fractions_patch_aligned_doseweighted.mrc in: /data/csun/apps/relion/relion/src/autopicker.cpp, line 2753 ERROR: AutoPicker::readTopazCoordinate ERROR: Cannot open input file AutoPick/job016/proc/rank000000.txt === Backtrace === /data/csun/apps/relion/relion/build/bin/relion_autopick(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x532821] /data/csun/apps/relion/relion/build/bin/relion_autopick(_ZN10AutoPicker20readTopazCoordinatesE8FileNamei+0xbfa) [0x466c8a] /data/csun/apps/relion/relion/build/bin/relion_autopick(_ZN10AutoPicker26autoPickTopazOneMicrographER8FileNamei+0x9ca) [0x473e2a] /data/csun/apps/relion/relion/build/bin/relion_autopick(_ZN10AutoPicker3runEv+0x22c) [0x4880dc] /data/csun/apps/relion/relion/build/bin/relion_autopick(main+0x73) [0x436ef3] /lib64/libc.so.6(__libc_start_main+0xf5) [0x7f03d7f17555] /data/csun/apps/relion/relion/build/bin/relion_autopick() [0x43b23f]

ERROR: AutoPicker::readTopazCoordinate ERROR: Cannot open input file AutoPick/job016/proc/rank000000.txt

This is a strange error that it said it can't open a file of the current job. The job that I am trying to run is AutoPick/job016 and it only writes the rank000000.mrc in the /proc folder.

Because there are other versions of relion, I have to reset the path everytime after I login to start relion4.

export PATH=/home/csun/.local/bin:/home/csun/bin:/usr/local/cuda/bin:/data/anaconda3/condabin:/data/csun/apps/relion/relion/build/bin:/usr/local/cuda/bin:/usr/local/bin:/usr/bin:/usr/local/sbin

Have anyone encountered a similar error message? Any suggestion would be appreciated.

Thanks, Chen

[zhanghui186]

Did you solve it, please, I also encountered this problem.

[2019C]

No, I didn’t. I used cryosparc filament picking instead and then convert the cryosparc cs file into relion star file.

See my answer in cryosparc forum

https://discuss.cryosparc.com/t/export-import-helical-segments-cs-relion-and-back/7212/17

Hope it helps, Chen

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From: zhanghui186 @.> Sent: Thursday, April 13, 2023 11:30:11 AM To: 3dem/relion @.> Cc: Sun, Chen @.>; Author @.> Subject: Re: [3dem/relion] Topaz filament picking in relion4.0 (Issue #947)

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Did you solve it, please, I also encountered this problem.

— Reply to this email directly, view it on GitHubhttps://github.com/3dem/relion/issues/947#issuecomment-1507258130, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ALI5HCYCU7773D7D7F3SCNDXBASZHANCNFSM6AAAAAATUFB6J4. You are receiving this because you authored the thread.Message ID: @.***>

[zhanghui186]

Thank you very much for your reply. I can now use ”-f“ in Relion, and I would like to share it with you. I cloned the installation package (https://github.com/3dem/topaz) and installed Topaz using "python setup.py install". After that, I was able to use it without any problems. I hope this information is helpful to you too!

[2019C]

Glad to hear that. Thank you for sharing with me.

Best, Chen

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From: zhanghui186 @.> Sent: Monday, April 17, 2023 7:27:47 AM To: 3dem/relion @.> Cc: Sun, Chen @.>; Author @.> Subject: Re: [3dem/relion] Topaz filament picking in relion4.0 (Issue #947)

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Thank you very much for your reply. I can now use ”-f“ in Relion, and I would like to share it with you. I cloned the installation package (https://github.com/3dem/topaz) and installed Topaz using "python setup.py install". After that, I was able to use it without any problems. I hope this information is helpful to you too!

— Reply to this email directly, view it on GitHubhttps://github.com/3dem/relion/issues/947#issuecomment-1511245888, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ALI5HC7SDE66HUZWJS7IUT3XBUZMHANCNFSM6AAAAAATUFB6J4. You are receiving this because you authored the thread.Message ID: @.***>