Exporting particles and binning and reimporting

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Exporting particles and binning and reimporting


         I just joined the forum.  I love using cisTEM as so far it has worked wonderfully for the projects I am working with.  Typically, I have always used Talos data (not motion corrected) in cisTEM. I now have a Titan K3 data ste. I have finished frame alignment and CTF  fitting and particle picking. This was done with the unbinned data.

I now want to export the particles out for the purpose of binning. I know I can prepare a refinement package and then export it out. But my question is what format should I choose to export the particles,  Frealign or Relion Format? And after exporting, what is the command should I use to bin the data?  

Thank you very much.


Hi Abhishek,

Hi Abhishek,

In theory it should work for either, but Frealign is probably a safer bet.  When exported, you can use the resample command line program in the cisTEM directory to resample your stack, then you can re-import the resampled stack with the parameters as a new refinement package.

You can do this slightly faster if you don't use the export function.  Instead, first find the stack filename of the particle stack associated with the refinement package you want to bin.  Then use resample to resample this stack.  Go to the results->3D refinement panel, click on the icon above the angular plot that looks like a document with a plus.  In that window, click on save in the bottom right hand corner and save that .par file.  You can then directly re-import the stack and par file.




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