Re: [scipion-users] Removing empty particles

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

In this case I'd suggest optimizing the picking rather than waste computing
resources on classifying out noise.

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 2:48 PM Carlos Oscar Sorzano <co...@cn...>
wrote:

> I am afraid he may be referring to particles in the ice. For getting rid
> of these particles, you may find more useful the deep consensus algorithm
> whose input is a couple of pickings. The eliminate empty classes is
> currently used mostly for classes, and as there are not so many, it does
> not take so long on a single processor.
>
> Cheers, Carlos Oscar
> El 14/04/2021 a las 15:38, Grigory Sharov escribió:
>
> 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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