[3dem] 3D classification issues with Relion 4.0

[Reza Khayat]

?Hi,


The mpirun -np 5 command was accidentally excluded from my earlier e-mail.


Reza?



Reza Khayat, PhD
Associate Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031
________________________________
From: Reza Khayat
Sent: Friday, August 19, 2022 2:30 PM
To: 3dem at ncmir.ucsd.edu
Subject: 3D classification issues with Relion 4.0


Hi,


We are having issues properly running 3D classification on data collected at 3 different pixel values -we are using 4.0-beta-2-commit-2dffb8?. The classification runs with no errors; however, classification is performed on the pixel size rather than then conformation of the complex (i.e. each class is dominated by data with a different pixel size). Web searches identified the following entry in github/3dem/relion/issues (https://urldefense.com/v3/__https://github.com/3dem/relion/issues/530__;!!Mih3wA!Ak-O-hRsP5RCneMPUCgVTOR5qAhWnDVE6OeGl3b-vvjQuJlRDYxHdc3RnGO8pksa-TpHPhD4CribasK9_ZvD8iqc$  ). However, the solutions provided did not alleviate the issue. The command we used, with the suggested modifications, is:


`which relion_refine_mpi` --o Class3D/job134/run --i JoinStar/job028/join_particles.star --ref Refine3D/job034/run_half1_class001_unfil.mrc --firstiter_cc --ini_high 60 --dont_combine_weights_via_disc --pool 30 --pad 2  --skip_gridding  --ctf --iter 25 --tau2_fudge 4 --particle_diameter 315 --fast_subsets  --K 10 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --offset_range 5 --offset_step 2 --sym C1 --norm --scale  --j 2 --gpu ""  --pipeline_control Class3D/job134/?


I appreciate the help.


Best wishes,
Reza



Reza Khayat, PhD
Associate Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031
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