<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css" style="display:none"><!-- p { margin-top: 0px; margin-bottom: 0px; }--></style>
</head>
<body dir="ltr" style="font-size:12pt;color:#000000;background-color:#FFFFFF;font-family:Calibri,Arial,Helvetica,sans-serif;">
<pre style="white-space:pre-wrap">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 (<a href="https://urldefense.com/v3/__https://github.com/3dem/relion/issues/530__;!!Mih3wA!GdOSCrM397i8nVaqvkqjA0gF9XHLTLvYS4O-up-fozGgTt6r1j5PRIbijW2L2A-_82It82HymejyOf2MLmuWUYHo$" title="https://urldefense.com/v3/__https://github.com/3dem/relion/issues/530__;!!Mih3wA!GdOSCrM397i8nVaqvkqjA0gF9XHLTLvYS4O-up-fozGgTt6r1j5PRIbijW2L2A-_82It82HymejyOf2MLmuWUYHo$
Ctrl+Click or tap to follow the link">https://urldefense.com/v3/__https://github.com/3dem/relion/issues/530__;!!Mih3wA!GdOSCrM397i8nVaqvkqjA0gF9XHLTLvYS4O-up-fozGgTt6r1j5PRIbijW2L2A-_82It82HymejyOf2MLmuWUYHo$</a> ). 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
</pre>
<div><span style="font-size:12pt">Reza Khayat, PhD</span></div>
<div id="Signature">
<div name="divtagdefaultwrapper" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:; margin:0">
<div>Associate Professor </div>
<div>City College of New York</div>
<div>Department of Chemistry and Biochemistry</div>
<div>New York, NY 10031</div>
</div>
</div>
</body>
</html>