Re: [scipion-users] Cryosparc to scipion import / transfer per-particle ctf params to re-extracted particles

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

Hi,

I don't really use cryosparc, so can't comment on the first issue. As for
the second problem you are right, there's currently no way to do this in
scipion.

I've made a pull request <https://github.com/scipion-em/scipion-em/pull/333>
which allows to assign ctf from a second (identical) set of particles, but
this won't be released until the next merge window. You could try it by
manually applying
https://patch-diff.githubusercontent.com/raw/scipion-em/scipion-em/pull/333.diff
 to pwem/protocols/protocol_ctf_assign.py file (make a backup copy first!).

Best regards,
Grigory

--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.

MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. +44 (0) 1223 267228 <+44%201223%20267228>
e-mail: gs...@mr...


On Fri, May 20, 2022 at 3:39 PM Kumpula, Esa-Pekka <
esa...@he...> wrote:

> Hi all,
>
>
>
> I have two issues when importing particles from cryosparc to scipion.
>
> I did initial processing steps in cryosparc (using patch motion
> correction) and have now successfully imported the particles as well as the
> associated micrographs into scipion (by running csparc2star.py and then
> importing using the .star file). The issue then is that all the micrographs
> and particles look very noisy in scipion, but if I reconstruct I get a
> reasonable map. If I run extract coordinates and look at the micrographs
> from there, they look as they should so I think they are essentially ok.
>
>
>
> The issue is that when I run subtract projection, I get negative density
> for the remaining part, which suggests to me that there is some issue with
> the particles, possibly normalization.
>
>
>
> So what I would think to do is to re-extract the particles using relion’s
> extraction protocol to get the normalization correct. The issue is that I
> don’t know how to transfer the previously refined ctf parameters of the
> particles that I imported into these new particles to avoid re-running ctf
> estimation and later per-particle ctf refinement. The particles I imported
> have these parameters after import, but they are not a SetOfCtf type that I
> could use as input for relion particle extraction or assign ctf.
>
>
>
> Any pointers? I have a slightly older Scipion version (3.0.8) so if this
> is not an issue with current releases then I’m happy to update.
>
>
>
> Cheers,
>
> EP
>
>
>
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