[3dem] Converting cryolo tomogram particle coordinates to Relion4/5 friendly ones

[Willem Noteborn]

Hey Lorenzo,

This was a 99% straightforward fix! The only thing I had to do after the conversion was to get rid of the data_optics section in it's entirety and rename the "_experiment_id" in "_rlnTomoName" in the data_particles section and Relion liked the particles.star file very much!

Thanks everyone for pointing out the options!

Best,
Willem
________________________________
Van: Lorenzo Gaifas <lorenzo.gaifas at gmail.com>
Verzonden: vrijdag 1 maart 2024 10:23
Aan: Zongli Li <zongli.li at gmail.com>
CC: Willem Noteborn <willemnoteborn at outlook.com>; 3dem at ncmir.ucsd.edu <3dem at ncmir.ucsd.edu>
Onderwerp: Re: [3dem] Converting cryolo tomogram particle coordinates to Relion4/5 friendly ones

Hi Willem,

If you want to simply convert to a star file you could use [cryohub](https://urldefense.com/v3/__https://github.com/teamtomo/cryohub/)'s__;!!Mih3wA!C6v5T9_ZYexscn6cAiYoRJZDxtWvWUs7KklxpNwrUp_h57R2A6KknJ6EqT6hLRvGWv19efLaHLCoQsJwxfF7zMxnPumE$  `convert` command. It's been a while since I touched the cryolo part though, so please let me know if things break :)

Best,
Lorenzo

On Thu, Feb 29, 2024 at 8:11 PM Zongli Li <zongli.li at gmail.com<mailto:zongli.li at gmail.com>> wrote:
Hi Willem,

The EMAN format from cryolo can be directly used in Relion. I have been using this way for SPA all the time, but haven't used it in tomogram particles. I assume they should be the same.

Best,

Zongli



On Thu, Feb 29, 2024 at 1:44 PM Willem Noteborn <willemnoteborn at outlook.com<mailto:willemnoteborn at outlook.com>> wrote:
Dear list,

I was wondering if anyone knows a way to convert cryolo picked tomogram coordinates (for instance the CBOX_3D or coords format) to a format that can be readily imported into Relion. I've been playing around with cryolo_boxmanager_tools.py but can't seem to find a solution. Maybe I'm missing something obvious.

Any information on this would be highly appreciated!

Kind regards,
Willem

Dr. Willem Noteborn
CryoEM Scientist

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