Importing particles from cryoSPARC2

8 posts / 0 new

Wed, 06/19/2019 - 09:07

xtalee

Dear cisTEM experts,

Would any of you be so kind and advise me how to import particles (either local motion corrected or non-local motion corrected) from cryoSPARC2?

csparc2star.py works to covert x.cs to x.star, which contains the file name of micrograph in cryoSPARC2, but quite frankly, it's hard to understand how to modify

an example script written by Matthia Wolf to convert x.star file with picked particle coordinates to import particle information into cisTEM.

I would sincerely appreciate it if any of you kindly advise me how to modify the script file and then import particles.

Thank you in advance.

Wed, 06/19/2019 - 11:34

timgrant

Hi,

Can you post a link to Matthias' script so I can take a look at it?

Thanks,

Tim

Wed, 06/19/2019 - 12:43

(Reply to #2) #3

xtalee

relion_star_to_cistem.sh

Hi Tim,

Thank you in advance for your help!

This is what I found in your cisTEM document

https://cistem.org/documentation#tab-1-3

https://cistem.org/system/tdf/uploads/relion_star_to_cistem.sh?file=1&type=cistem_details&id=17&force=&s3fs=

As far as I understand, this example script has to be modified to import particle information as cisTEM format.

Looking forward to hearing from you.

Cheers,

Wed, 06/19/2019 - 12:48

timgrant

Ok.. so this file imports the

Ok.. so this file imports the particle picking locations into cisTEM.

Is that what you want, or do you just want to import a particle stack with defocus values etc directly?

Tim

Wed, 06/19/2019 - 13:51

xtalee

Hi Tim,

Maybe importing particle stack along with defocus values, ctf fit res, etc would be the best, but currently it's hard to find a right script to do this. Do you happen to know how to do this? especially, importing local-motion-corrected particle stack (and volume) of cryoSPARC into cisTEM?

Thanks in advance.

Wed, 06/19/2019 - 13:53

timgrant

Does CryoSPARC not write out

Does CryoSPARC not write out a particle stack and .star file that can be imported into Relion?

Tim

Wed, 06/19/2019 - 14:08

(Reply to #6) #7

xtalee

Hi Tim,

Let me have a look at cryoSPARC2 once again and get back to you!

Thank you

PS. I really enjoyed using cisTEM to process my 'first' Krios/K3 data throughout all steps from motion correction to map sharpening. Having a new option such as per particle-based motion correction in a new version of cisTEM would be awesome!

straightforward

Mon, 06/24/2019 - 16:17

(Reply to #7) #8

xtalee

Hi Tim,

I figured out how to import *.star *.mrcs files into cisTEM. Daniel Asarnow's csparc2star.py and stack.py worked great to convert cryoSPARC files to right format.

Cheers,