scipion-users — Mailing list for Scipion users

Re: [scipion-users] Scipion workflow: RCL lost

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

Hi Yangyang,

it's true that this section was unfortunately lost upon transition to
Scipion 2.0. It will be back in the next release. If you need it urgently
you can copy
https://github.com/I2PC/scipion/blob/devel-fixes/pyworkflow/templates/protocols.template
file
into corresponding folder.

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 Tue, Aug 6, 2019 at 9:26 AM Yangyang Yi <yy...@si...> wrote:

> Hello,
>     I am a application engineer in Single Particles. These days I am
> studying using scipion via tutorial.
>     I found in *View* list, there is no *Randow Conical Tilt* directory,
> only SPA and MB. Through I can find *Import tilted micrographs* in All
> category, it seems inconvenient. But in old version scipion 1.2.1, this
> procotol is there. Does other protocols removed in Scipion 2.0? Or
> something wrong about my installation? I used CentOS7 system and just use a
> binary install. Should I use a source code installation instead?
> Sincerely
> Yangyang
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

Re: [scipion-users] Region CTF-refinement error

[Jose M. de la R. T. <del...@gm...>]

Dear Dmitry,

Remember that for CTF - refinement, you need to use an input set of
particles that contains 3D angular assignment,
either coming from Relion - 3d autorefine or any other protocol for 3D
refinement.

Best,
Jose Miguel



On Tue, Aug 6, 2019 at 10:26 AM Dmitry Semchonok <sem...@gm...>
wrote:

> Dear colleagues,
>
> The relion CTF-refinement protocol gives an error
>
> Please see the screenshots.
>
> Sincerely,
> Dmitry
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

[scipion-users] Scipion workflow: RCL lost

[Yangyang Yi <yy...@si...>]

Hello, 
    I am a application engineer in Single Particles. These days I am studying using scipion via tutorial. 
    I found in View list, there is no Randow Conical Tilt directory, only SPA and MB. Through I can find Import tilted micrographs in All category, it seems inconvenient. But in old version scipion 1.2.1, this procotol is there. Does other protocols removed in Scipion 2.0? Or something wrong about my installation? I used CentOS7 system and just use a binary install. Should I use a source code installation instead? 
Sincerely
Yangyang

Re: [scipion-users] The relion bayesian polishing gives an error

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

Hi Dmitry,

the answers are below:

1) Relion polishing training output file is a simple txt file with 3
parameters. These 3 numbers you have to put into scipion protocol for
polishing.
2) Yes, it should work. Motioncor-produced global frame shifts should work
in Relion within Scipion. Let us know if it doesn't.

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 26, 2019 at 7:03 PM Dmitry A. Semchonok <sem...@gm...>
wrote:

> Dear Grigory,
>
> Sorry but  think I made a mistake for the input files - instead of save
> particles from the relion-3d refinement as an input for both -ctf
> refinement & polishing I used just the extracted particles.
> That explains why the software didn't have required tables.
>
> Small question -
> when I do the bayesian polishing there are 2 options - a) training and
> then b) polishing itself.
>
> In relion (separately) it is possible to use the output file from a)
> --opt_params to run b)
>
> But in Scipion i can not find in b) where to insert this file and b)
> starts itself (without using the results from a)
>
> Could you please tell me how to use the opt_parameter file?
>
> Another question - can I use motion cor results (not the relion motion
> cor) for the "input movies" input?
>
> Thank you!
>
> Have a great weekend
>
> Sincerely,
> Dmitry
>
>
> On July 25, 2019 16:47:51 Gregory Sharov <sha...@gm...> wrote:
>
>> Hi Dimitry,
>>
>> Could you please open an issue on github.com :
>> https://github.com/scipion-em/scipion-em-relion/issues
>>
>> On Thu, Jul 25, 2019, 14:28 Dmitry Semchonok <sem...@gm...> wrote:
>>
>>> Dear colleagues,
>>>
>>> The *relion bayesian polishing* gives an error
>>>
>>> ERROR:
>>> 00034:   Runs/007845_ProtRelionBayesianPolishing/input_particles.star
>>> does not contain all of the required columns (rlnOriginX, rlnOriginY,
>>> rlnAngleRot, rlnAngleTilt, rlnAnglePsi and rlnRandomSubset)
>>>
>>>
>>> Could you please fix that?
>>>
>>>
>>>
>>> Sincerely,
>>> Dmitry
>>>
>>> _______________________________________________
>>> 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
>>
>>
>

Re: [scipion-users] The relion bayesian polishing gives an error

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

Hi Dimitry,

Could you please open an issue on github.com :
https://github.com/scipion-em/scipion-em-relion/issues

On Thu, Jul 25, 2019, 14:28 Dmitry Semchonok <sem...@gm...> wrote:

> Dear colleagues,
>
> The *relion bayesian polishing* gives an error
>
> ERROR:
> 00034:   Runs/007845_ProtRelionBayesianPolishing/input_particles.star does
> not contain all of the required columns (rlnOriginX, rlnOriginY,
> rlnAngleRot, rlnAngleTilt, rlnAnglePsi and rlnRandomSubset)
>
>
> Could you please fix that?
>
>
>
> Sincerely,
> Dmitry
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>

[scipion-users] The relion bayesian polishing gives an error

[Dmitry S. <sem...@gm...>]

Dear colleagues,

The relion bayesian polishing gives an error

ERROR: 
00034:   Runs/007845_ProtRelionBayesianPolishing/input_particles.star does not contain all of the required columns (rlnOriginX, rlnOriginY, rlnAngleRot, rlnAngleTilt, rlnAnglePsi and rlnRandomSubset)


Could you please fix that?



Sincerely,
Dmitry

[scipion-users] Region CTF-refinement error

[Dmitry S. <sem...@gm...>]

Dear colleagues,

The relion CTF-refinement protocol gives an error 

Please see the screenshots.


Sincerely,
Dmitry

[scipion-users] Cryosparc and topaz plugins released...

[Pablo C. <pc...@cn...>]

Dear all!

We are pleased to announced that we have released 2 new plugins: 
cryosparc <https://github.com/scipion-em/scipion-em-cryosparc2>, topaz 
<https://github.com/scipion-em/scipion-em-topaz>

You can install them through the plugin manager or through the command 
line (you will need permissions to write on the scipion installation folder)

Please, note that cryosparc plugin will NOT install cryosparc, so you 
will need to install it yourself and then tell Scipion where to find it.


I would like to specially thank Steve (a nice Taiwanese software 
developer that started almost to the end the cryosparc integration), 
Yunior, and Peter (from Madrid team) and Jose Miguel de la Rosa (from 
Stockholm)

for the effort made to release these plugins.

Happy em processing!


NOTE: this only apply to scipion 2.0 version.
-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*

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

[Ipsita B. <ips...@bi...>]

Hi

Thanks a lot for all the suggestions and help..
I will come back if I have more problems..

Thanks and best regards,
Ipsita

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...<mailto: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...<mailto: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...<mailto: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...<mailto: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:   <mailto:co...@cn...> co...@cn...<mailto:co...@cn...>
Biocomputing unit                             <http://i2pc.es/coss> http://i2pc.es/coss
National Center of Biotechnology (CSIC)
c/Darwin, 3
Campus Universidad Autónoma (Cantoblanco)     Tlf: 34-91-585 4510<tel:34-91-5854510>
28049<tel:28049> MADRID (SPAIN)                          Fax: 34-91-585 4506<tel:34-91-5854506>
------------------------------------------------------------------------


_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
<https://lists.sourceforge.net/lists/listinfo/scipion-users>https://lists.sourceforge.net/lists/listinfo/scipion-users





_______________________________________________
scipion-users mailing list
<mailto:sci...@li...>sci...@li...<mailto:sci...@li...>
<https://lists.sourceforge.net/lists/listinfo/scipion-users>https://lists.sourceforge.net/lists/listinfo/scipion-users


--
------------------------------------------------------------------------
Carlos Oscar Sánchez Sorzano                  e-mail:   <mailto:co...@cn...> co...@cn...<mailto:co...@cn...>
Biocomputing unit                             <http://i2pc.es/coss> http://i2pc.es/coss
National Center of Biotechnology (CSIC)
c/Darwin, 3
Campus Universidad Autónoma (Cantoblanco)     Tlf: 34-91-585 4510<tel:34-91-5854510>
28049<tel:28049> MADRID (SPAIN)                          Fax: 34-91-585 4506<tel:34-91-5854506>
------------------------------------------------------------------------


_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users


--
Prof. Jose-Maria Carazo
Biocomputing Unit, Head, CNB-CSIC
Spanish National Center for Biotechnology
Darwin 3, Universidad Autonoma de Madrid
28049<tel:28049> Madrid, Spain


Cell: +34639197980<tel:+34639197980>

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
>
>
> _______________________________________________
> 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 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
>


-- 
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

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

[Carlos O. S. S. <co...@cn...>]

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... 
>> <mailto: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... 
>>>> <mailto: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... 
>>>> <mailto: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... 
>>>> <mailto:sci...@li...>
>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>>
>>>
>>>
>>> _______________________________________________
>>> scipion-users mailing list
>>> sci...@li...
>>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>> -- 
>> ------------------------------------------------------------------------
>> Carlos Oscar Sánchez Sorzano                  e-mail:co...@cn...
>> Biocomputing unithttp://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... 
>> <mailto:sci...@li...>
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
>
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> sci...@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] Reply: Re: 2Dclasses with millions of particles

[Ipsita B. <ips...@bi...>]

Hi

Thanks a lot for all the help... I will come back if I have more problems..

Thanks and best regards,
Ipsita

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


On Fri, Jul 12, 2019 at 1:56 PM Ipsita Banerjee <ips...@bi...<mailto: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...<mailto: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<tel:+44%201223%20267542>
e-mail: gs...@mr...<mailto:gs...@mr...>


On Fri, Jul 12, 2019 at 11:52 AM Ipsita Banerjee <ips...@bi...<mailto: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...<mailto: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...<mailto: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...<mailto: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...<mailto:sci...@li...>
<https://lists.sourceforge.net/lists/listinfo/scipion-users>https://lists.sourceforge.net/lists/listinfo/scipion-users





_______________________________________________
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<https://lists.sourceforge.net/lists/listinfo/scipion-users>https://lists.sourceforge.net/lists/listinfo/scipion-users


--
------------------------------------------------------------------------
Carlos Oscar Sánchez Sorzano                  e-mail:   <mailto:co...@cn...> co...@cn...<mailto:co...@cn...>
Biocomputing unit                             <http://i2pc.es/coss> http://i2pc.es/coss
National Center of Biotechnology (CSIC)
c/Darwin, 3
Campus Universidad Autónoma (Cantoblanco)     Tlf: 34-91-585 4510<tel:34-91-5854510>
28049<tel:28049> MADRID (SPAIN)                          Fax: 34-91-585 4506<tel:34-91-5854506>
------------------------------------------------------------------------


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_______________________________________________
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sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users
_______________________________________________
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Re: [scipion-users] 2Dclasses with millions of particles

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

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
>

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

[Ipsita B. <ips...@bi...>]

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


On Fri, Jul 12, 2019 at 11:52 AM Ipsita Banerjee <ips...@bi...<mailto: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...<mailto: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...<mailto: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...<mailto: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...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users





_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users


--
------------------------------------------------------------------------
Carlos Oscar Sánchez Sorzano                  e-mail:   co...@cn...<mailto: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...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users

_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users
_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
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Re: [scipion-users] Suggestion for Integrating Thunder into Scipion

[Lugmayr, W. <w.l...@uk...>]

hi, 

thunder uses a special licensed nvidia deep learning toolkit. 
this is currently only available though the nvidia development program. 
so each user must sign up and install it by himself unless pre-compiled binaries are provided. 

cheers, 
wolfgang 




From: "范宏成" <187...@16...> 
To: "Mailing list for Scipion users" <sci...@li...>, "scipion" <sc...@cn...> 
Sent: Friday, 12 July, 2019 11:45:56 
Subject: [scipion-users] Suggestion for Integrating Thunder into Scipion 

Hi Developers, 
Have you tried the Thunder single particle program(See this paper [ https://www.nature.com/articles/s41592-018-0223-8) | https://www.nature.com/articles/s41592-018-0223-8) ] ? I find this program can tolerate bad particles and get higher resolution、quality cryo-em map compared to the relion 3.0 using the same particle in my datasets. I hear that the newest version of Thunder will be released next week. Maybe Scipion can integrate this program in plugin? By the way, I also use cryosparc2 . Can Scipion integrat it too? I also sent emails to scipion-userlist. But it gave me response like " Is being held until the list moderator can review it for approval." Is it ok? 

Fan Hongcheng 

[ https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?&name=%E8%8C%83%E5%AE%8F%E6%88%90&uid=m18717124574%40163.com&ftlId=1&iconUrl=http%3A%2F%2Fmail-online.nosdn.127.net%2Fsmfc69753e7457a6e590754a7cd5492c0d.jpg&items=%5B%22m18717124574%40163.com%22%5D | 
            
                
                    
                            
                                
                            
                            
                                范宏成
                            
                    
                        
                            
                                    m18...@16...
                            
                        
                
            
         ] 
签名由 [ https://mail.163.com/dashi/dlpro.html?from=mail81 | 网易邮箱大师 ] 定制 


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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
>
>
> _______________________________________________
> 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
>

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

[Ipsita B. <ips...@bi...>]

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...<mailto: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...<mailto: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...<mailto: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...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users





_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users


--
------------------------------------------------------------------------
Carlos Oscar Sánchez Sorzano                  e-mail:   co...@cn...<mailto: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...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users

Re: [scipion-users] Suggestion for Integrating Thunder into Scipion

[范宏成 <187...@16...>]

I understand it . Thank you Pablo!


| |
范宏成
|
|
m18...@16...
|
签名由网易邮箱大师定制
On 7/12/2019 18:25，Pablo Conesa<pc...@cn...> wrote：

Hi Fan Hongcheng,

We are currently working on Cryosparc and Topaz....many other developer maintain several packages and the more we add the more we need to maintain.

Integrating all the methods that appear every year, plus updating existing ones is out of our reach.

Scipion is full of pickers (Xmipp, Relion, Cryolo, Topaz,  GAutomatch, Eman (boxer, sparx), dogpicker,....)

Of course Thunder, might be great, and if at some point it prove to be in another level, we might invest time in it. All we can do now is to register your interest and make a call to developers (other than us) to collaborate, maybe


Authors of thunder picker could be interested in this. We offer support and help to developers to integrate their packages.

Regarding Cryosparc plugin, we will probably release it today, good news!!




You must subscribe to the list in order for your messages to be authorized, I've let them pass today.

Thank you very much for your suggestion, I'm sorry we, alone, can not afford to integrate/maintain all is out there.




All the best, Pablo.


On 12/7/19 11:45, 范宏成 wrote:

Hi Developers,
Have you tried  the Thunder single particle program(See this paper https://www.nature.com/articles/s41592-018-0223-8)? I find this program can tolerate bad particles and  get higher resolution、quality cryo-em map compared to the relion 3.0 using the same particle in my datasets. I hear that the newest version of Thunder will be released next week. Maybe Scipion can integrate this program in plugin? By the way, I also use cryosparc2 . Can Scipion integrat it too? I also sent emails to scipion-userlist. But it gave me response like "Is being held until the list moderator can review it for approval." Is it ok?


Fan Hongcheng


| |
范宏成
|
|
m18...@16...
|
签名由网易邮箱大师定制



_______________________________________________
scipion-users mailing list
sci...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - Madrid Scipion team

Re: [scipion-users] Suggestion for Integrating Thunder into Scipion

[Pablo C. <pc...@cn...>]

Hi Fan Hongcheng,

We are currently working on Cryosparc and Topaz....many other developer 
maintain several packages and the more we add the more we need to maintain.

Integrating all the methods that appear every year, plus updating 
existing ones is out of our reach.

Scipion is full of pickers (Xmipp, Relion, Cryolo, Topaz, GAutomatch, 
Eman (boxer, sparx), dogpicker,....)

Of course Thunder, might be great, and if at some point it prove to be 
in another level, we might invest time in it. All we can do now is to 
register your interest and make a call to developers (other than us) to 
collaborate, maybe

Authors of thunder picker could be interested in this. We offer support 
and help to developers to integrate their packages.

Regarding Cryosparc plugin, we will probably release it today, good news!!


You must subscribe to the list in order for your messages to be 
authorized, I've let them pass today.

Thank you very much for your suggestion, I'm sorry we, alone, can not 
afford to integrate/maintain all is out there.


All the best, Pablo.

On 12/7/19 11:45, 范宏成 wrote:
> Hi Developers,
> Have you tried  the Thunder single particle program(See this paper 
> https://www.nature.com/articles/s41592-018-0223-8)? I find this 
> program can tolerate bad particles and  get higher resolution、quality 
> cryo-em map compared to the relion 3.0 using the same particle in my 
> datasets. I hear that the newest version of Thunder will be released 
> next week. Maybe Scipion can integrate this program in plugin? By the 
> way, I also use cryosparc2 . Can Scipion integrat it too? I also sent 
> emails to scipion-userlist. But it gave me response like "Is being 
> held until the list moderator can review it for approval." Is it ok?
>
> Fan Hongcheng
>
> 	
> 范宏成
> m18...@16...
>
> <https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?&name=%E8%8C%83%E5%AE%8F%E6%88%90&uid=m18717124574%40163.com&ftlId=1&iconUrl=http%3A%2F%2Fmail-online.nosdn.127.net%2Fsmfc69753e7457a6e590754a7cd5492c0d.jpg&items=%5B%22m18717124574%40163.com%22%5D> 
>
> 签名由 网易邮箱大师 <https://mail.163.com/dashi/dlpro.html?from=mail81> 
> 定制
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*

[scipion-users] Suggestion for Integrating Thunder into Scipion

[范宏成 <187...@16...>]

Hi Developers,
Have you tried  the Thunder single particle program(See this paper https://www.nature.com/articles/s41592-018-0223-8)? I find this program can tolerate bad particles and  get higher resolution、quality cryo-em map compared to the relion 3.0 using the same particle in my datasets. I hear that the newest version of Thunder will be released next week. Maybe Scipion can integrate this program in plugin? By the way, I also use cryosparc2 . Can Scipion integrat it too? I also sent emails to scipion-userlist. But it gave me response like "Is being held until the list moderator can review it for approval." Is it ok?


Fan Hongcheng


| |
范宏成
|
|
m18...@16...
|
签名由网易邮箱大师定制

[scipion-users] Suggestion for Integrating Thunder into Scipion

[范宏成 <187...@16...>]

Hi Developers,
Have you tried  the Thunder single particle program(See this paper https://www.nature.com/articles/s41592-018-0223-8)? I find this program can tolerate bad particles and  get higher resolution、quality cryo-em map compared to the relion 3.0 using the same particle in my datasets. I hear that the newest version of Thunder will be released next week. Maybe Scipion can integrate this program in plugin? By the way, I also use cryosparc2 . Can Scipion integrat it too?


Fan Hongcheng


| |
范宏成
|
|
m18...@16...
|
签名由网易邮箱大师定制

[scipion-users] Suggestion for Integrating Thunder into Scipion

[范宏成 <187...@16...>]

Hi Developers,
Have you tried  the Thunder single particle program(See this paper https://www.nature.com/articles/s41592-018-0223-8)? I find this program can tolerate bad particles and  get higher resolution、quality cryo-em map compared to the relion 3.0 using the same particle in my datasets. I hear that the newest version of Thunder will be released next week. Maybe Scipion can integrate this program in plugin? By the way, I also use cryosparc2 . Can Scipion integrat it too?


Fan Hongcheng


| |
范宏成
|
|
m18...@16...
|
签名由网易邮箱大师定制

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

[Ipsita B. <ips...@bi...>]

Hi

Thank you very much… I will tell if I run into more troubles..

Thanks and best regards,
Ipsita

On 9 Jul 2019, at 05:54, Carlos Oscar S. Sorzano <co...@CN...<mailto: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...<mailto: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...<mailto: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...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users





_______________________________________________
scipion-users mailing list
sci...@li...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users


--
------------------------------------------------------------------------
Carlos Oscar Sánchez Sorzano                  e-mail:   co...@cn...<mailto: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...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users

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

[Carlos O. S. S. <co...@cn...>]

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... 
>> <mailto: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... 
>> <mailto: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... 
>> <mailto:sci...@li...>
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@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
------------------------------------------------------------------------

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

[Ipsita B. <ips...@bi...>]

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...<mailto: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...<mailto: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...<mailto:sci...@li...>
https://lists.sourceforge.net/lists/listinfo/scipion-users