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| = Single Particle Tomography in EMAN2 = | = Single Particle Tomography in EMAN2, 2011 WORKSHOP in Houston, TX = |
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| Unfortunately, this technique SPT is very computationally intensive (both in terms of memory and processing speed). 3GB of RAM is the bare minimum recommended to get through the tutorial. For more realistic SPT on full 3D alignments on large sets of large particles particles, 8GB of memory and the use of multiple processing units is advised. |
== OLD E2SPT USERS' GUIDE == |
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| * Single particle tomography USER'S GUIDE (March 2011). | |
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| == E2SPT USERS' GUIDE == * Single particle tomography USER'S GUIDE (updated on June 2012; under major refactoring do to extensive changes in e2spt capabilities; look for an extensively different version soon) [[attachment:e2spt_users_guide_06_2012.pdf| e2spt_users_guide_06_2012.pdf|&do=get]] |
[[attachment:e2spt_users_guide_03_2011.pdf| e2spt_users_guide_03_2011.pdf|&do=get]] |
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TRiC chapeornin data (NOT READY). [[attachment:e2spt_data_apoTRiC.zip| e2spt_data_apoTRiC.zip|&do=get]] == COMMANDS (for easy "copy-pasting" into the command line == === Monstrous command for alignment with e2spt_classaverage.py (used to be e2classaverage3d.py) === e2spt_classaverage.py --input=e15pp_set1_stack.hdf --output=e15pp_set1_aligned.hdf --ref=e15ref_prep_icos_bin2.hdf --npeakstorefine=1 -v 3 --mask=mask.sharp:outer_radius=48 --lowpass=filter.lowpass.gauss:cutoff_freq=.02:apix=4.401 --align=rotate_translate_3d:search=10:delta=8:dphi=8:verbose=1:sym=icos --parallel=thread:2 --ralign=refine_3d_grid:delta=3:range=9:search=2 --averager=mean.tomo --aligncmp=ccc.tomo --raligncmp=ccc.tomo --shrink=3 --shrinkrefine=3 --savesteps --saveali --iter=8 --normproc=normalize --sym=c1 --keep=0.8 --path=whatever_folder_I_want === Monstrous command for alignment with e2spt_hac.py (used to be e2tomoallvsall.py) === e2spt_hac.py -v 1 --path=AVSAs087 --input=CENTEREDvsD8aliVSapo_s087.hdf --shrink=3 --shrinkrefine=2 --iter=87 --mask=mask.sharp:outer_radius=36 --npeakstorefine=16 --preprocess=filter.lowpass.gauss:cutoff_freq=.02:apix=4.401 --align=rotate_translate_3d:search=4:dphi=12:delta=12 --parallel=thread:24 --ralign=refine_3d_grid:delta=3:range=12:search=2 --averager=mean.tomo --aligncmp=ccc.tomo --raligncmp=ccc.tomo --saveali --savesteps -v 2 --postprocess=filter.lowpass.gauss:cutoff_freq=.02:apix=4.401 --autocenter --exclusive_class_min=8 --normproc=normalize === Not-so-monstrous command for e2spt_simulation.py (used to be e2tomosim.py) === e2spt_simulation.py --input=../groRef_scaled_bin2.hdf --snr=5 --nptcls=2 --tiltstep=5 --tiltrange=60 --transrange=10 --saveprjs --noiseproc=math.addnoise === Semi monstrous command for e2spt_resolutionplot.py === e2spt_resolutionplot.py --vol1=half1avg.hdf --vol2=half2avg.hdf --output=whatever3.txt --npeakstorefine=1 --verbose=3 --shrink=3 --shrinkrefine=2 --mask=mask.sharp:outer_radius=36 --preprocess=filter.lowpass.gauss:cutoff_freq=.02:apix=4.401 --align=rotate_translate_3d:search=4:dphi=30:delta=30:sym=icos --parallel=thread:8 --ralign=refine_3d_grid:delta=15:range=30:search=2 --aligncmp=ccc.tomo --raligncmp=ccc.tomo --postprocess=filter.lowpass.gauss:cutoff_freq=.02:apix=4.401 --normproc=normalize --sym=icos === Decent command for e2spt_rotationalplot.py === e2spt_rotationalplot.py --input=initModel.hdf --output=toAs129avsaAVG.txt --daz=1 --shrink=1 --dalt=180 --mask=mask.sharp:outer_radius=28 === Command for e2spt_radialdensityplot.py === e2spt_radialdensityplot.py --vols=volA_aligned.hdf,volB_aligned.hdf --normproc=normalize.edgemean --lowpass=filter.lowpass.gauss:cutoff_freq=0.02:apix=4.401 --singleplot --output=volAali_VS_volBali.png |
Single Particle Tomography in EMAN2, 2011 WORKSHOP in Houston, TX
OLD E2SPT USERS' GUIDE
* Single particle tomography USER'S GUIDE (March 2011).
DATA
Epsilon 15 virus data, used since the EMAN2 Workshop in 2010.