Variables in relion_schemegui.py

[Cookiemaster33]

Hi everyone.

I am trying to use relion_schemegui.py with variables. The wiki suggests using "$$" flag for variables that are defined in the scheme.star file. But when inputting "$$" in relion_schemegui.py, the program writes out other (which I assume hexadecimal) strings to the job.star file. E.g. when using "$$nclasses", it writes out "334Dnclasses". I can get around that issue going to the job.star file and enter it manually as $$nclasses, but it would be cool if you could do it from the gui, too and not open job.star files all the time when setting up a, or changing a scheme.

No sure if I am doing something wrong or if it needs to be inputted into the gui differently.

Environment:

• OS: [e.g. Ubuntu 18.04.5 LTS]
• RELION version [e.g. RELION-5.0 beta]

[Cookiemaster33]

So I realized that the problem is definitely relion_pipeliner. The '$$' flag is correctly exported into the relion_pipeliner command, but then that one spits it back out as numbers. Would be really nice to have a fix for that. Working with variables in schemes is really cool to automate data processing. But without being able to define them through neither relion_it.py, relion_schemegui.py, or relion_pipeliner makes it really complicated to set up (e.g. stopping the scheme, going to the job.star files, changing them manually, and then restarting)