Re: [scipion-users] 2Dclasses with millions of particles

[Jose M. C. <ca...@cn...>]

I would add that this, by far, our best cleaning tool, snd it would be
interesting to consider it in your workflows

Wbw..jm

On Fri, Jul 12, 2019 at 10:26 PM Carlos Oscar S. Sorzano <co...@cn...>
wrote:

> Dear Ipsita,
>
> you may also want to try deep consensus. If you have several pickings, it
> is quite easy. If not, you can pick noise particles (Ctrl-F, noise),
> extract them and teach the deep consensus (Ctrl-F, deep) what is a particle
> and what is not. Make sure that you have the deepToolKit installed.
>
> Kind regards, Carlos Oscar
> El 12/07/2019 a las 12:52, Ipsita Banerjee escribió:
>
> Hi
>
> This is just a query. I have been trying to screen my particles using
> Xmipp3 particle screening since the last 2 to 3 days… I am using the
> installation of Scipion on Kebnekaise cluster. However, this process is
> taking a very, very long time…
> I am submitting the job in the queue and even gave 24 hours, but the job
> did not finish..
>
> I just wanted to ask whether there is any way to speed up this process or
> am I doing something wrong?
>
> Thanks so much for all the help..
>
> Best regards,
> Ipsita
>
> On 9 Jul 2019, at 05:54, Carlos Oscar S. Sorzano <co...@CN...> wrote:
>
> Dear Ipsita,
>
> another way of cleaning the set of particles is using deep consensus if
> you have several pickings on the same data. This protocol works at the
> level of coordinates so it should not be so much affected by memory issues.
> For using this protocol, make sure you have installed in the plugins the
> deepLearningToolkit under the Xmipp plugin.
>
> Kind regards, Carlos Oscar
> El 08/07/2019 a las 16:07, Ipsita Banerjee escribió:
>
> Hi
>
> Today, after increasing the memory space, I tried to open the
> classification in scipion, but after 10 mins I get this error..
>
>  md.sort(sortByLabel)
> XmippError: Error code: 21 message: no such table: MDTable_2
>   Sqlite query: INSERT INTO MDTable_3( "rlnEnabled", "rlnCoordinateX",
> "rlnCoordinateY", "rlnMicrographName", "rlnMicrographId", "rlnImageId",
> "rlnImageName", "rlnPhaseShift", "rlnDefocusU", "rlnDefocusV",
> "rlnDefocusAngle", "rlnAmplitudeContrast", "rlnSphericalAberration",
> "rlnVoltage", "rlnGroupName", "rlnGroupNumber", "rlnAngleRot",
> "rlnAngleTilt", "rlnAnglePsi", "rlnOriginX", "rlnOriginY",
> "rlnClassNumber", "rlnNormCorrection", "rlnLogLikeliContribution",
> "rlnMaxValueProbDistribution", "rlnNrOfSignificantSamples") SELECT
>  "rlnEnabled", "rlnCoordinateX", "rlnCoordinateY", "rlnMicrographName",
> "rlnMicrographId", "rlnImageId", "rlnImageName", "rlnPhaseShift",
> "rlnDefocusU", "rlnDefocusV", "rlnDefocusAngle", "rlnAmplitudeContrast",
> "rlnSphericalAberration", "rlnVoltage", "rlnGroupName", "rlnGroupNumber",
> "rlnAngleRot", "rlnAngleTilt", "rlnAnglePsi", "rlnOriginX", "rlnOriginY",
> "rlnClassNumber", "rlnNormCorrection", "rlnLogLikeliContribution",
> "rlnMaxValueProbDistribution", "rlnNrOfSignificantSamples" FROM MDTable_2
>
> So, now I am trying to clean my particles with Xmipp screening particles.
>
> Thanks and best regards,
> Ipsita
>
> On 8 Jul 2019, at 08:54, Pablo Conesa <pc...@CN...> wrote:
>
> Hi, try to increase java memory setting
> JAVA_MAX_MEMORY = 3
>
> In your <scipion home>/config/scipion.conf
>
> Additionally, try to prune/clean you set as soon as possible.
>
> Xmipp screening particles could be usefull to reject bad ones at the
> begining.
>
>
> El 5 jul. 2019 21:32, Ipsita Banerjee <ips...@bi...>
> escribió:
>
> Dear Scipion Users,
>
> I have a dataset where I have about 2 million picked particles.. I could
> run relion2D classification for these particles..
> However, when I click on the Analyze results button, and try to open the
> tab "Show classification in Scipion", I don't see anything..
> When i click on the tab "show classes only", I can see the classes only..
> Please, I need some help as to what I can do to continue with the
> processing...
>
> Thanks so much...
>
> Best regards,
> Ipsita
>
>
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> --
> ------------------------------------------------------------------------
> Carlos Oscar Sánchez Sorzano                  e-mail:   co...@cn...
> Biocomputing unit                             http://i2pc.es/coss
> National Center of Biotechnology (CSIC)
> c/Darwin, 3
> Campus Universidad Autónoma (Cantoblanco)     Tlf: 34-91-585 4510
> 28049 MADRID (SPAIN)                          Fax: 34-91-585 4506
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> ------------------------------------------------------------------------
> Carlos Oscar Sánchez Sorzano                  e-mail:   co...@cn...
> Biocomputing unit                             http://i2pc.es/coss
> National Center of Biotechnology (CSIC)
> c/Darwin, 3
> Campus Universidad Autónoma (Cantoblanco)     Tlf: 34-91-585 4510
> 28049 MADRID (SPAIN)                          Fax: 34-91-585 4506
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-- 
Prof. Jose-Maria Carazo
Biocomputing Unit, Head, CNB-CSIC
Spanish National Center for Biotechnology
Darwin 3, Universidad Autonoma de Madrid
28049 Madrid, Spain


Cell: +34639197980