Hello, everyone! I got a better map after 3D flex reconstruction. Now I want to do another run of 3D refinement in relion using the flex map as reference. Does anyone know which .cs should be used as input for csparc2star.py besides that of passthrough cs file. Below shows the .cs file from 3D flex training.
Updated. I have tried all the .cs file but none of these work.
Hi @Verdandy,
Thanks for your questions, and it’s great to hear that you got a better map from Flex Reconstruction!
If you are looking to use a volume from Flex Reconstruct as a reference for refinement in RELION, you can either download or locate the relevant mrc volume that was output in your Flex Reconstruct job (for example J*_flex_map.mrc ) in the job folder, and import it to RELION.
On the other hand, if you wish to use a volume from a Flex Generate job, note that you will first need to unzip the series zip file of interest, and consider that the volumes in the middle of the series are more likely to be representative of the population average of your sample.
As you also mentioned using the csparc2star function of pyem, let me explain how that may be helpful for you: If you want to export your CryoSPARC particles to refine in RELION, then you can run csparc2star using the *particles.cs and *passthrough_particles.cs files from the refinement that was the input for 3D Flex Data Prep.
I hope that helps!