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<p style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;">Hi,<br>
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<p style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;">The mpirun -np 5 command was accidentally excluded from my earlier e-mail.<br>
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<p style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;">Reza<br>
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Reza Khayat, PhD
<div>Associate Professor </div>
<div>City College of New York</div>
<div>Department of Chemistry and Biochemistry</div>
<div>New York, NY 10031</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Reza Khayat<br>
<b>Sent:</b> Friday, August 19, 2022 2:30 PM<br>
<b>To:</b> 3dem@ncmir.ucsd.edu<br>
<b>Subject:</b> 3D classification issues with Relion 4.0</font>
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<p>Hi,<br>
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<p>We are having issues properly running 3D classification on data collected at 3 different pixel values -we are using <span style="color:rgb(33,33,33); font-family:"Segoe UI","Segoe WP","Segoe UI WPC",Tahoma,Arial,sans-serif; font-size:15px; background-color:rgb(255,255,255)">4.0-beta-2-commit-2dffb8</span>.
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
(<a href="https://urldefense.com/v3/__https://github.com/3dem/relion/issues/530__;!!Mih3wA!Ak-O-hRsP5RCneMPUCgVTOR5qAhWnDVE6OeGl3b-vvjQuJlRDYxHdc3RnGO8pksa-TpHPhD4CribasK9_ZvD8iqc$">https://github.com/3dem/relion/issues/530</a>). However, the solutions provided did not alleviate the issue. The command we used, with the suggested modifications, is:</p>
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<p><span style="color:rgb(33,33,33); font-family:"Segoe UI","Segoe WP","Segoe UI WPC",Tahoma,Arial,sans-serif; font-size:15px; background-color:rgb(255,255,255)">`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/</span><br>
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<p>I appreciate the help.</p>
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<p>Best wishes,<br>
Reza</p>
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Reza Khayat, PhD
<div>Associate Professor </div>
<div>City College of New York</div>
<div>Department of Chemistry and Biochemistry</div>
<div>New York, NY 10031</div>
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