Per particle CTF (or even particle coordinates for external per particle in gCTF)

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Per particle CTF (or even particle coordinates for external per particle in gCTF)



I have a tilted dataset that needs per particle CTF estimation.  First question: is this possible in cisTEM?   If not, it'd maybe be good to implement in the future.


failing that, I'd like to do this outside of cisTEM using gCTF.   The input for that process is: micrographs and a star file with coordinates point to my particles.   The problem is that cisTEM seems to be able to export only the stacks, but the originating micrograph and coordinates are lost in the process (literally says "unknown.mrc" in  the output star file.  

In cisTEM under actions > particle picks I can see the paticle coordinates.  This suggests that the information is being stored SOMEWHERE, but I don't know where.


Because I don't believe I can simply do gCTF on the individual particles in a stack because there's not enough signal, I've also considered exporting the stack as 500px x 500px particles and then doing gCTF on that stack as full micrographs rather than individual particles within a micrograph.   This seems ridiculous though.


any advice or insight appreciated


many thanks!







In cisTEM you cannot do per particle CTF estimation - although you can do per particle CTF refinement during the refinement.

At the moment, there isn't a niceway to export the particles from the GUI, however you can export them from the database directly using the information provided here :-

I hope that is of some help!




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