Application of gain reference file in import movies job

Import and Export
1

Dear cryoSPARC team and users,

Hello, I’m very new to cryoEM and receiving a great deal of assistance from this forum.

Lately, I collected my dataset using the Falcon 4 detector and received a gain reference file in .gain format from the institute.

I intended to import the movie files with the gain reference file, but the job requires a file in .mrc format.

How can I properly convert the gain reference file from .gain format to .mrc format?

Thanks,

Rookie

2

Hi,

Welcome to the forums!

You can use dm2mrc, in the IMOD package (dm2mrc)

For further discussion: Gain reference in dm4 format: what should I do?

Cheers
Oli

3

Thank you for your quick response.

I installed IMOD and tried to convert the file using the following command.

dm2mrc my_gain_ref_file.gain my_gain_ref_file.mrc

But the program says my .gain file is not recognized as a DM file.

By the way, the instructor asked me to submit .gain file first, and if any errors occur, he’d like to discuss afterwards.

Thank you,

Rookie

4

Sorry I misread - I didn’t realize you’d said .gain and not .dm4! Check here for details re what to do with .gain files: https://groups.google.com/g/warp-em/c/-fOnQ34VMO8

2 Likes
5

I really dislike the “.gain” nonsense for the gain reference. It was one of the (many) issues I’ve mentioned to TFS directly in the past, and while most of them have been addressed this remains.

…

Due to issues with K3 gain drift* during a single acquisition run, I’ve long ago taken to generating my own gain references directly from the dataset (either RELION (relion_estimate_gain) or cisTEM (sum_all_tiff_files/sum_all_mrc_files) for TIFF/MRC or RELION (relion_estimate_gain) for EER). Generating a gain from 200-300 micrographs is usually sufficient for a good gain reference, although I usually use 500 because I’m perhaps overly cautious.

*I am aware this is fixed on newer K3s, but we still have some data off a very early K3 where in a 24 hour acquisition, I needed multiple gain references to avoid gain artefacts as the dataset progressed. It just left a bad impression, and how stable the gain is on our Falcon 4 just rubs salt in the metaphorical wound.

3 Likes
6

I have also tried the method on the link and it didn’t work for me.

By the way, I thought rbs_sci mentioned this thread after your reply so I revisited here too late.

In the thread, Flow tried the same way I did first(just submitting .gain file).

In my case, it gave me properly gain-corrected images but the images were with defect lines.

After the motion correction, the lines disappeared and the further processing steps are working well by now.

Anyway, thank you for your help, and happy new year!