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

[PABLO CONESA MINGO]

Alternative, if you want to forget about command line tools, moving  
files around, tedious note-keeping (or just forgetting what you've  
done)... use Scipion tomography plugins.

https://urldefense.com/v3/__https://scipion-em.github.io/docs/release-3.0.0/docs/user/tutorials/tomo/tomography-intro.html*tomography-intro__;Iw!!Mih3wA!A-2nYwlflMFBTFSNYh0m6N6NjxGGR1-XNM-LLSBTggnuTDGMhUBS_NV29PJrruUiVkiuEo93sHEl15_B-3AMtA$ 



Lorenzo Gaifas <lorenzo.gaifas at gmail.com> escribió:

> 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!C3gXfyWT8EgE25gmWDNXK0HajKA-q41NC9bA8SROt0i0L2mzvqLYGnQzbNKnPNDhoVR0g0Wxpg7xTjotTKAnZuUK1cQ$  `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> 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> 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
>>>
>>> T: +31 (0)7 1527 1424
>>> w.e.m.noteborn at biology.leidenuniv.nl
>>> NeCEN at biology.leidenuniv.nl
>>> https://urldefense.com/v3/__http://www.NeCEN.nl__;!!Mih3wA!C3gXfyWT8EgE25gmWDNXK0HajKA-q41NC9bA8SROt0i0L2mzvqLYGnQzbNKnPNDhoVR0g0Wxpg7xTjotTKAnAg6jpS8$
>>> <https://urldefense.com/v3/__http://www.NeCEN.nl__;!!Mih3wA!EZuage2pQokgJSH-i-JxI2i7DjK_QeRYVEWfI5sx2nh5hsrUkIg2nCI-JMcJHzkooSW_IoEeWqN0fpGQodQb_f5QHp2U$>
>>>
>>>
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>>> <#m_3961501043176285810_m_-8195834432432991172_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
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