can't import relion-3.1 particles to cisTEM

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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.

timgrant
Hi,

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

darin.lory@rege...
darin.lory@regeneron.com'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?

-Darin

timgrant
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.

Cheers,

Tim

darin.lory@rege...
darin.lory@regeneron.com'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,

-Darin

yyi
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?

Moriyate
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?

yyi
Please email my company to get it

O

yyi
Please email us

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

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