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can't import relion-3.1 particles to cisTEM

yyi

can't import relion-3.1 particles to cisTEM

Relion has recently updated ver3.1 and its star file changes a lot, and then I found it could not import into cisTEM to run. New star file seems like:

data_optics

loop_
_rlnOpticsGroup #1
_rlnOpticsGroupName #2
_rlnAmplitudeContrast #3
_rlnSphericalAberration #4
_rlnVoltage #5
_rlnImagePixelSize #6
_rlnMicrographOriginalPixelSize #7
_rlnImageSize #8
_rlnImageDimensionality #9
           1 opticsGroup0     0.100000     2.700000   300.000000     1.310000     1.310000          256            2

# version 30001

data_particles

loop_

_rlnCoordinateX #1
_rlnCoordinateY #2
_rlnClassNumber #3
_rlnAutopickFigureOfMerit #4
_rlnAnglePsi #5
_rlnImageName #6
_rlnMicrographName #7
_rlnCtfMaxResolution #8
_rlnCtfFigureOfMerit #9
_rlnDefocusU #10
_rlnDefocusV #11
_rlnDefocusAngle #12
_rlnCtfBfactor #13
_rlnCtfScalefactor #14
_rlnPhaseShift #15
_rlnGroupNumber #16
_rlnAngleRot #17
_rlnAngleTilt #18
_rlnNormCorrection #19
_rlnLogLikeliContribution #20
_rlnMaxValueProbDistribution #21
_rlnNrOfSignificantSamples #22

Compared to old formate, the "_data" changes to "data_optics" and "data_particles" or "data_micrographs" and so on. 

However, when I use relion_stack_create then import particle to cisTEM, it cannot work. It reported

Error: Encountered the following error - aborting :-
Error: Couldn't find _rlnDefocusU in star file (/ssd/relion_benchmark/to_cistem.star)

Help?

Now we have a script. Please email support@singleparticle.cn to get the script.

Mon, 10/21/2019 - 15:22

timgrant

Hi,

cisTEM cannot read the new star file format yet.  Just looking at what you wrote above - If you remove the data_optics section, then rename "data_particles" to _data it may work?

Thanks,

Tim

Tue, 10/22/2019 - 14:45

darin.lory@reg…

Can cisTEM be updated to handle both the RELION 3.0 star format AND the 3.1 format.  

Or maybe a python script to convert the 3.1 format to 3.0 format, if possible?

-Darin

Wed, 10/23/2019 - 17:42

timgrant

Hi Darin,

we will work on supporting the new format in the next release.  I'm sure conversion is possible, but I don't have a script for it now.

Cheers,

Tim

Wed, 10/23/2019 - 18:10

darin.lory@reg…

Thank you very much Tim for getting back to me.  

I found in the paper "Estimation of High-Order Aberrations and Anisotopic Magnification from Cryo-EM Dataset in RELION-3.1 by Zivanov, Nakane, and Scheres; "SInce most of the optical properties of a particle are now defined through the optics group to which it belongs, each particle STAR file written out by RELION-3.1 now contains two tables: one listing the optics group and one listing the particles.  The particles table is equivalent to the old one, except that certain optical properties are no longer listed"

Best regards,

-Darin

Wed, 06/03/2020 - 00:41

gayayadav

Hello all,

I am facing a problem with opening the previous project. The error message is as follows:

 SQL Error: attempt to write a readonly database
Trying to execute the following command :-

BEGIN IMMEDIATE;
From core/database.cpp:33
int Database::ExecuteSQL(const char *)

[1]+  Aborted                 cisTEM

 

Does anyone have a suggestion about what went wrong? I never have this issue before. I am using Centos 7.

 

Thanks

Gaya