Deviating from default parameters

[jadeshi]

Hi,
Thanks a lot for the great tutorial first of all! I learned a lot about how Relion works by going through it. I was just wondering if you have any general guidelines for picking input parameters for the various steps if I were to use this pipeline on my own data. I noticed that for several of the steps in the tutorial, some of the parameters were different from the default values Relion provided, so I'm wondering how those were determined.

Thanks!

[hackprime]

Hi @jadeshi,

I am terribly sorry for my very late response.

Thank you for your feedback! I appreciate that my tutorial was helpful to you.

About the different parameters. You're right, in some steps input parameters were different than the tutorial's one.

I changed them for the following reasons:

• I have played with parameters based on the sources (listed below);
• The HPC cluster I used for computations didn't have GPUs so I used the CPU computations only.

One more thing I wasn't reflected in this tutorial is the sources I used. I will include them in the repo and also leave them here.

Sources:

• The RELION 3.0 tutorial for single particle analysis
• The tutorial made by Yasunaga Lab of Kyushu Institute of Technology (Japanese)
• Materials of the 2nd Cryo-EM Analysis Beginner Workshop held by The High Energy Accelerator Research Organization at Tsukuba City (Japanese)