Can't import particles from Relion

[juliacpowell1999]

Hi,

I have a particle stack from an extraction job in Relion that I would like to import into Simple 3 to do an ab initio job. I tried importing the particle.star file using the import star project command, but it gave me an error saying that importstarproject was not supported (perhaps I do not understand what I should put as export type?). I also tried using the convert_relion2simple.pl program to convert the star file to extract CTF parameters, but the script would not seem to run. I also tried the relion2emanbox.pl script to convert the picked particle to .box files, but the script kept erroring by saying the relevant files do not exist (although they do indeed exist and are not corrupted).

Could you please explain how to import my particles.star file?

[hael]

Hi, Thanks for your interest in SIMPLE. The relion2simple.pl script is a bit outdated and may not support modern star files. You could try and cleanout everything that is not per-particles information and see if it runs on that file. If that works you’d be able to run prg=import_particles using the list of all per-micrograph stacks and the CTF parameters extracted from the star file. I have also let Joe (one of our senior developer in Oxford) know what you want to do and he will look into support of star file input for prg=import_particles. I will keep you posted. Best, -- HANS ELMLUND PhD Senior Investigator National Institutes of Health National Cancer Institute—Frederick Campus 1050 Boyles St, Fredrick MD 21702 United States of America T: +1(301)846-5670 M: +1(240)739-9079 E: ***@***.******@***.***> simplecryoem.com From: juliacpowell1999 ***@***.***> Reply-To: hael/SIMPLE ***@***.***> Date: Thursday, August 11, 2022 at 11:23 To: hael/SIMPLE ***@***.***> Cc: Subscribed ***@***.***> Subject: [EXTERNAL] [hael/SIMPLE] Can't import particles from Relion (Issue #15) Hi, I have a particle stack from an extraction job in Relion that I would like to import into Simple 3 to do an ab initio job. I tried importing the particle.star file using the import star project command, but it gave me an error saying that importstarproject was not supported (perhaps I do not understand what I should put as export type?). I also tried using the convert_relion2simple.pl program to convert the star file to extract CTF parameters, but the script would not seem to run. I also tried the relion2emanbox.pl script to convert the picked particle to .box files, but the script kept erroring by saying the relevant files do not exist (although they do indeed exist and are not corrupted). Could you please explain how to import my particles.star file? — Reply to this email directly, view it on GitHub<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fhael%2FSIMPLE%2Fissues%2F15&data=05%7C01%7Chans.elmlund%40nih.gov%7C08d0bd529c384368acb608da7bad6bae%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C637958282007846507%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=JPZg2bNTd6CRk3fO1OCIoELaOmpiBsDQZtqieklfyKE%3D&reserved=0>, or unsubscribe<https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAAJENURFSUZ5PSCQ2EOXMXLVYULGHANCNFSM56ISQ4NQ&data=05%7C01%7Chans.elmlund%40nih.gov%7C08d0bd529c384368acb608da7bad6bae%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C637958282007846507%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=y8IOKli9L5jF4mwlQVvbOyOkfo3o1ty%2F3RTdw1OBL6Q%3D&reserved=0>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

[cosmopolitanadmin]

Improving importing from star files is something we've been working on recently. If you clone the git repository and re-compile simple, you should be able to import your extract job using import_starproject; setting the import_dir argument with the path to the the extract job folder.

For example on the command line: simple_exec prg=import_starproject import_dir=/mnt/user/relion/Extract/job001 projfile=project.simple.

In the GUI you just need to set import_dir to the extract job folder.

Cheers

Joe

[juliacpowell1999]

Hi Joe! Thank you for getting back to me! I tried to run the import star project command as you suggested, but the program keeps erroring by saying that the import star project job is not supported. I am currently running simple 3 installed from sbgrid. Do I need to recompile it on my own in order to run the import star project command? Thanks, Julia

…

On Thursday, August 11, 2022, cosmopolitanadmin ***@***.***> wrote: Improving importing from star files is something we've been working on recently. If you clone the git repository and re-compile simple, you should be able to import your extract job using import_starproject; setting the import_dir argument with the path to the the extract job folder. For example on the command line: simple_exec prg=import_starproject import_dir=/mnt/user/relion/Extract/job001 projfile=project.simple. In the GUI you just need to set import_dir to the extract job folder. Cheers Joe — Reply to this email directly, view it on GitHub <#15 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AV2EUNSSGDD5H5RWQMGR7ZLVYUVRDANCNFSM56ISQ4NQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[cosmopolitanadmin]

Hi Julia

Yes. You'll need to recompile. If you run:

git clone https://github.com/hael/SIMPLE.git
cd SIMPLE

Check the dependencies in README.txt and then follow the installation steps starting with step 2

Cheers

Joe