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

[Lorenzo Gaifas]

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$ 
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