[3dem] Exporting Selected Motion-Corrected Micrographs from RELION to CryoSPARC

[justacuriousone01 at protonmail.com]

Dear Daniel,

Thank you very much for the script! I was looking for something like that. I have never heard about Relion’s printtable command. Good to know.

I agree with you regarding Patch CTF correction.

Thank you very much for the help!

Kind regards,
Scott.

On Sat, Jun 28, 2025 at 22:06, Daniel Asarnow <[dasarnow at gmail.com](mailto:On Sat, Jun 28, 2025 at 22:06, Daniel Asarnow <<a href=)> wrote:

> Hi Scott,
> You can use the "import micrographs" job to import micrographs into cryoSPARC using an appropriate wildcard or by creating symbolic links in a new directory. For example, in the relion project directory:
> mkdir csimport; cd csimport
> for i in $(relion_star_printtable ../selected_micrographs.star data_micrographs rlnMicrographName); do ln -s ../$i -t .; done
> You will have to run CTF estimation again in cryoSPARC, however fortunately 1) it is cheap and 2) Patch CTF is in my experience superior even to per-particle estimates unless the particles are quite large or there is significant residual beam tilt.
>
> Best,
> -da
>
> On Thu, Jun 26, 2025 at 10:08 AM justacuriousone01--- via 3dem < 3dem at ncmir.ucsd.edu> wrote:
>
>> Dear 3DEM community,
>>
>> I’m looking for a way to export a subset of micrographs—already motion-corrected and CTF-estimated in RELION—for further processing in CryoSPARC, starting from Patch Motion Correction.
>>
>> Is there an easy or recommended method to transfer selected micrographs between the two softwares? If anyone knows of a script or best practice for this workflow, I’d really appreciate your help.
>>
>> Kind regards,
>> Scott
>>
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