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

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

Hi Ipsita,

I haven't used xmipp screen protocol much, but my advice would be to split
the dataset into 4 parts (~500k ptcls) and run relion 2d classification.
Also make sure you bin your particles to about 64px box. To do the first
cleaning I would also use the following relion oprtions: --maxsig 5 (use
extra options field in scipion), use fast subsets, 10 degrees angular
sampling, maybe some coarse shifts as well. All these options will speed up
the classification. At the end you can join particles from good classes.

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 267542 <+44%201223%20267542>
e-mail: gs...@mr...


On Fri, Jul 12, 2019 at 11:52 AM Ipsita Banerjee <
ips...@bi...> wrote:

> 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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