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

[Grigory S. <sha...@gm...>]

Hello, Teige,

Gctf plugin uses Gctf 1.18 by default, so you need to create scipion config
file and change Gctf variables there to point to the 1.06 version. Then you
should see a second Gctf protocol in scipion.

Grigory.


On Fri, Nov 6, 2020, 06:55 Matthews-Palmer, Teige <
t.m...@im...> wrote:

> 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
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