[scipion-users] Per-particle defocus estimation on tilted micrographs

[Matthews-Palmer, T. <t.m...@im...>]

Dear Scipion users & devs,

I’m very excited to be installing Scipion v3.0.5 at a new job - it has been a while since I used Scipion and very many programs and features have been added, it looks wonderful.

One feature I would really like to use in Scipion is accurate CTF estimation for particles on tilted micrographs.
As far as I know the options are patch-based CTF in gCTF (initially, before particle picking), per-particle in gCTF, geometry aware CTF in goCTF, and something similar in Warp. Maybe there are other options that I’m not aware of - I’d be happy to hear about them!

It looks like local or per-particle CTF are not available with gCTF in Scipion3 - is that right?

Using the plugin manager I installed gctf-1.18
Then, since the github page mentions 1.18 is specifically for phase plate, I installed gctf-1.06 with the plugin manager - but the ProtGctf protocol in Scipion is not changed and still has no options relating to patch or per-particle CTF.

So, can I get accurate particle defocus values from tilted data in a Scipion workflow?

Many thanks,
Teige