EMPIAR-10059 particle stack
e2convertrelion.py particles.star --voltage 300 --cs 2 --amp 10 --apix 1.2156
e2spa_refine.py --ptcl sets/all.lst --ref emd_8117.hdf --keep .9 --sym c4 --res 20 --parallel thread:32
e2project3d.py r3d_00/threed_01.hdf --outfile gmm_00/projections.hdf --orientgen=eman:delta=5 --parallel=thread:12
e2segment3d.py gmm_00/ref.hdf --pdb gmm_00/model_00.pdb --process=segment.kmeans:nseg=8000:thr=4
e2gmm_refine_new.py --ptclsin gmm_03/projections.hdf --model gmm_03/model_15_odd.pdb --maxres 3. --modelout gmm_03/model_15_odd.txt --niter 40 --trainmodel --evalmodel gmm_03/model_projs.hdf
e2spa_make3d.py --input gmm_00/model_projs.hdf --output gmm_00/model_avg.hdf --threads 24
e2proc3d.py gmm_00/ref.hdf gmm_00/mask_sel.hdf --process=math.linear:scale=0:shift=1 --process=mask.zeroedge3d:z1=100 --process=filter.lowpass.gauss:cutoff_abs=0.1
e2gmm_refine_new.py --model gmm_00/model_00.txt --anchor gmm_00/model_01.txt --conv --midout gmm_00/mid.txt --maxres 10 --minres 50 --learnrate 1e-5 --niter 10 --ptclsin gmm_00/ptcls_sample.lst --heter --selgauss gmm_00/mask_sel.hdf
ptcl_pca_kmean_m3d.py --pts gmm_00/mid.txt --pcaout gmm_00/mid_pca.txt --ptclsin gmm_00/ptcls_sample.lst --ptclsout gmm_00/ptcls_cls.lst --setsf sf_lp.txt --mode regress --ncls 5 --nptcl 8000 --axis 0