Feature request: CTFFIND5 support

Hi CryoSPARC team,

CTFFIND5 (currently part of cisTEM2) includes support for FP16 micrographs. In external tests, I’ve not needed to specify to CTFFIND5 that the micrograph is FP16, it “just works”. :joy:

It also supports tilt estimation (pinging the tilt estimation thread too).

I’ve got a very-high-mag dataset I collected yesterday which Patch CTF really struggles with (poor CTF resolution estimates) but CTFFIND currently seems to be handling OK (much better CTF resolution estimates, better fits to Thon rings) but I had to re-do Patch Motion with FP16 disabled to use it.

I think CTFFIND5 can be treated as a drop-in replacement for CTFFIND4, but otherwise there could be a drop down in the CTFFIND job type offering the choice?

Thanks in advance.


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Actually, I’ll try just dropping in CTFFIND5 in place of the CTFFIND4 executable and seeing whether either CryoSPARC or CTFFIND freaks out as a result.

I think the output is slightly different, so maybe CryoSPARC won’t be able to find the output correctly.

I’ll try when the current run has finished.

Would be very interested to know if this works. We would like to use CTFFIND5 in CryoSPARC also.

It doesn’t work as a drop in replacement, but I think I know how to make it work.

CTFFIND5 expects further input in scripted mode (“Determine samnple [sic] thickness?”) and when it doesn’t get it reports:

 Error: Blank answer in scripted mode, exiting...

So while CTFFIND5 supports mode 12 MRC, the scripting is currently broken for it.

RELION also needed a tweak before it would support CTFFIND5 for the same reason, so it’s up to the CryoSPARC team when CTFFIND5 support will be added.

edit: I can’t get it happy. Missing something.