Running spIsoNet with Relion5

[YUNTAO LIU]

Hi all,

I think there are a few inquiries about whether spIsoNet is compatible with RELION5.

A recent comments from wlugmayr, https://github.com/IsoNet-cryoET/spIsoNet/issues/13#issuecomment-2124296610 saying they have done some tricks to successfully running spIsoNet misalignment correction with RELION5. 

I pasted the message below. I wonder if any of you have a chance to try this out on your RELION5 environment.

Well the solution is quite simple:

• First install Relion5 as described including the (one) conda environment containing blush, modelangelo, ...
• Then install spIsoNet in a second/different conda environment (e.g. conda create -n spisonet-1.0.0 -y python=3.10, ...)
• Now set and load the Relion5 software environment incl. its conda

The trick is to provide the full path to the python executable to spIsoNet. Here some tests:

$ which python
/gpfs/cssb/software/rhel9/anaconda3/envs/relionconda-5.0.1/bin/python
$ /gpfs/cssb/software/rhel9/anaconda3/envs/relionconda-5.0.1/bin/python -m pip list | grep blush
relion-blush 0.0.1
$ /gpfs/cssb/software/rhel9/anaconda3/envs/relionconda-5.0.1/bin/python -m pip list | grep spisonet

$ /gpfs/cssb/software/rhel9/anaconda3/envs/spisonet-1.0.0/bin/python -m pip list | grep blush
$ /gpfs/cssb/software/rhel9/anaconda3/envs/spisonet-1.0.0/bin/python -m pip list | grep spisonet
spIsoNet 1.0

The dedicated python executable knows its packages so there should be no clashes between different conda environments. For the spIsoNet wrapper you do not have to activate the spIsoNet conda.

So instead of setting (which will end up in using the Relion5 python):
export RELION_EXTERNAL_RECONSTRUCT_EXECUTABLE='python /fullpath_to_spisonet_wrapper/relion_wrapper.py'
you set:
export RELION_EXTERNAL_RECONSTRUCT_EXECUTABLE=' /fullpath_to_spisonet_python/python /fullpath_to_spisonet_wrapper/relion_wrapper.py'

In the Relion Gui I have set Reference -> Use Blush regularisation? -> No and the job runs technically to the end generating an mrc output file.

--

Best Regards,

Yuntao Liu,  Postdoc.

California NanoSystem Institute

University of California Los Angeles