Re: [scipion-users] Removing empty particles

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

Hi,

The relion command is only useful for finding particles with all zeros, so
it won't help to find noise particles. You could try xmipp - screen
particles with Z-score sorting.

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 Wed, Apr 14, 2021 at 9:55 PM Dmitry A. Semchonok <sem...@gm...>
wrote:

> Dear Carlos Oscar & Grigory,
>
>
>
> Indeed, by empty particles I mean the projections that contain no
> information about studying sample – so the noised ones, not the ones with
> the ice (the default value in abovemention  xmipp protocol it is 1.1).
>
>
>
> The problem I am tackling is the presence of many empty picked positions
> that somehow doesn’t  classified out after 2D/3D.
>
>
>
> So I understood that I can measure the threshold with relion script that
> you pointed out.
>
>
>
> And I will try to pick better 😊
>
>
>
> Thank you both
>
>
>
> Kind regards,
>
> Dmitry
>
>
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *Grigory Sharov <sha...@gm...>
> *Sent: *Wednesday, April 14, 2021 3:39 PM
> *To: *Mailing list for Scipion users <sci...@li...>
> *Subject: *Re: [scipion-users] Removing empty particles
>
>
>
> Hi Dmitry,
>
>
>
> I haven't used that protocol so can't comment on it. By empty particles do
> you mean completely black particles with 0.0 or some particles with noise
> inside? You could use relion_image_handler with the "--stats" option to
> find the former ones.
>
>
>
> Getting rid of second ones is more difficult.
>
>
> 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 Wed, Apr 14, 2021 at 12:51 PM Dmitry Semchonok <Sem...@gm...>
> wrote:
>
> Dear colleagues,
>
>
> One more question about effective deletion of the empty particles in the
> dataset.
>
> Correct me if I am wrong, but the dedicated tools for that purpose are:
> xmipp - eliminate empty classes // particles.
>
> I would like to ask if there is a possibility to boost the processing
> speed of them? I am afraid that it is using only 1 MPI and in case of few
> millions particles the processing on 1 MPI can take few days.
>
>
> Thank you
>
> Sincerely,
> Dmitry
>
>
>
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