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| Before attempting to average subtomograms with EMAN2, make sure to have the latest EMAN2 release. Download the easy-to-install binaries for the "Daily Release" from EMAN2's download page: http://ncmi.bcm.tmc.edu/ncmi/software/software_details?selected_software=counter_222 (The daily release is close to the middle of the page). |
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| Unfortunately, this technique SPT is very computationally intensive (both in terms of memory and processing speed). | Unfortunately,SPT is very computationally intensive technique (both in terms of memory and processing speed). |
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| 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. | For more realistic SPT on full 3D alignments of large sets (hundreds of particles) comprising large particles particles (like viruses), 8GB of memory and the use of multiple processing units or GPU technology are advised. |
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=== Command for e2spt_autoboxer.py === e2spt_autoboxer.py --tomogram=tomo_inv.rec --ptclradius=8 --path=whatever --concentrationfactor=1 --output=subtomostack.hdf --outputboxsize=36 --verbose=10 --goldstack=gold_ptcls_s05_inv.hdf --pruneprj --goldthreshtomo --keepn=150 --lowpass=filter.lowpass.gauss:cutoff_freq=0.02 |
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| 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 | e2spt_classaverage.py --input=e15pp_set1_stack.hdf --output=e15pp_set1_aligned.hdf --ref=e15ref_prep_icos_bin2.hdf --npeakstorefine=1 -v 0 --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=0: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 |
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| 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 | e2spt_hac.py -v 0 --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 --postprocess=filter.lowpass.gauss:cutoff_freq=.02:apix=4.401 --autocenter --exclusive_class_min=8 --normproc=normalize |
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| 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 | e2spt_resolutionplot.py --vol1=half1avg.hdf --vol2=half2avg.hdf --output=whatever3.txt --npeakstorefine=1 --verbose=0 --shrink=3 --shrinkrefine=2 --mask=mask.sharp:outer_radius=36 --lowpass=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 --normproc=normalize --sym=icos |
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| e2spt_simulation.py --input=groRef_scaled_bin2.hdf --snr=5 --nptcls=2 --tiltstep=5 --tiltrange=60 --transrange=10 --saveprjs --addnoise | e2spt_simulation.py --input=groel.pdb --snr=5 --nptcls=8 --tiltstep=5 --tiltrange=60 --transrange=10 --saveprjs --addnoise --simref --path=TESTsimREF --pad=3 --shrink=2 --finalboxsize=96 --negativecontrast |
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| e2spt_tomosimjobs.py --input=groRef_scaled_bin2.hdf --nptcls=10 --transrange=10 --addnoise --pad --saveprjs --saverandstack --snrlowerlimit=1 --snrupperlimit=10 --snrchange --tiltsteplowerlimit=2 --tiltstepupperlimit=2 --tiltstepchange=2 --tiltrangelowerlimit=60 --tiltrangeupperlimit=60 --tiltrangechange=10 | e2spt_tomosimjobs.py --input=groel.pdb --nptcls=8 --saveprjs --addnoise --simref --path=TESTsimREF --pad=3 --shrink=2 --finalboxsize=96 --snrlowerlimit=0 --snrupperlimit=1 --snrchange=1 --tiltsteplowerlimit=0 --tiltstepupperlimit=1 --tiltstepchange=1 --tiltrangelowerlimit=60 --tiltrangeupperlimit=61 --tiltrangechange=1 --negativecontrast --testalignment === Command for e2symsearch3d.py === |
Before attempting to average subtomograms with EMAN2, make sure to have the latest EMAN2 release. Download the easy-to-install binaries for the "Daily Release" from EMAN2's download page:
http://ncmi.bcm.tmc.edu/ncmi/software/software_details?selected_software=counter_222
(The daily release is close to the middle of the page).
Single Particle Tomography in EMAN2
Unfortunately,SPT is very computationally intensive technique (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 of large sets (hundreds of particles) comprising large particles particles (like viruses), 8GB of memory and the use of multiple processing units or GPU technology are advised.
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 much larger version of the tutorial soon)
DATA
Epsilon 15 virus data, used since the EMAN2 Workshop in 2010.
TRiC chapeornin data (NOT READY).
COMMANDS (for easy "copy-pasting" into the command line
Command for e2spt_autoboxer.py
e2spt_autoboxer.py --tomogram=tomo_inv.rec --ptclradius=8 --path=whatever --concentrationfactor=1 --output=subtomostack.hdf --outputboxsize=36 --verbose=10 --goldstack=gold_ptcls_s05_inv.hdf --pruneprj --goldthreshtomo --keepn=150 --lowpass=filter.lowpass.gauss:cutoff_freq=0.02
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 0 --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=0: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 0 --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 --postprocess=filter.lowpass.gauss:cutoff_freq=.02:apix=4.401 --autocenter --exclusive_class_min=8 --normproc=normalize
Semi monstrous command for e2spt_resolutionplot.py
e2spt_resolutionplot.py --vol1=half1avg.hdf --vol2=half2avg.hdf --output=whatever3.txt --npeakstorefine=1 --verbose=0 --shrink=3 --shrinkrefine=2 --mask=mask.sharp:outer_radius=36 --lowpass=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 --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
Not-so-monstrous command for e2spt_simulation.py (used to be e2tomosim.py)
e2spt_simulation.py --input=groel.pdb --snr=5 --nptcls=8 --tiltstep=5 --tiltrange=60 --transrange=10 --saveprjs --addnoise --simref --path=TESTsimREF --pad=3 --shrink=2 --finalboxsize=96 --negativecontrast
Command for e2spt_tomosimjobs.py
e2spt_tomosimjobs.py --input=groel.pdb --nptcls=8 --saveprjs --addnoise --simref --path=TESTsimREF --pad=3 --shrink=2 --finalboxsize=96 --snrlowerlimit=0 --snrupperlimit=1 --snrchange=1 --tiltsteplowerlimit=0 --tiltstepupperlimit=1 --tiltstepchange=1 --tiltrangelowerlimit=60 --tiltrangeupperlimit=61 --tiltrangechange=1 --negativecontrast --testalignment