can't import relion-3.1 particles to cisTEM

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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:


_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



_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/


Now we have a script. Please email to get the script.



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?



darin.lory@rege...'s picture
Can cisTEM be updated to

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?


Hi Darin,

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.



darin.lory@rege...'s picture
Thank you very much Tim for

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,


Figure out to get a script to support v3.1

Hi Darin,

I have just figure out to write a small program for convention these days. If you need it, should I email it to you?

Hi yyi

Hi yyi,

I'd like to try some scripts to convert relion3.1 star file to other programs. Would you mind share your script with me?

Please email my company to get it


Please email us

Our company use email to sent it. Please email us ( with your school+request script in title, and we will send it to you.

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