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Re: [scipion-users] 2Dclasses with millions of particles
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From: Gregory S. <sha...@gm...> - 2019-07-12 13:08:02
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Hi, you can use "scipion - split sets" protocol to split the set of particles. It can be found in Tools -> Sets menu or by Ctrl+F 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 1:56 PM Ipsita Banerjee < ips...@bi...> wrote: > Hi > > Thanks a lot for all the help… However, I have a problem. I think, from > the previous mail that it would be a very good idea if I could split my > dataset..but I have no idea as to how I can do that. > > I would be very grateful if someone can help me to split up my data (of 2 > million particles) into 4 parts? > > Thanks so much.. > > Best regards, > Ipsita > > > > On 12 Jul 2019, at 13:03, Gregory Sharov <sha...@gm...> wrote: > > 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 >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> >> >> >> _______________________________________________ >> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> -- >> ------------------------------------------------------------------------ >> 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 >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
