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| Before attempting to average subtomograms with EMAN2, make sure to have the latest EMAN2 release. | Last update: October 1, 2013. Before attempting to average subtomograms with EMAN2, '''make sure to have the latest EMAN2 release'''. |
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| 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. |
Unfortunately, SPT is very computationally intensive (both in terms of memory and processing speed). 4GB of RAM is the bare minimum recommended to get through the tutorial. |
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| * 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) | * Single particle tomography USER'S GUIDE (updated on June 2012; under major refactoring do to extensive changes in e2spt capabilities; look for a new and longer version of the tutorial... eventually). |
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| == COMMANDS (for easy "copy-pasting" into the command line == | = COMMANDS (for easy "copy-pasting" into the command line; to see the entire list of parameters for each program, type the program name followed by -h at the command line) = |
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| == CORE PROGRAMS == === SPT BOXER === e2spt_boxer.py <tomogram.rec> --yshort --inmemory --lowpass=100 . === SPT Iterative refinement === |
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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 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 | e2spt_classaverage.py --input= --output= --ref= --npeakstorefine=14 -v 0 --mask=mask.sharp:outer_radius= --lowpass=filter.lowpass.gauss:cutoff_freq=.02:apix=4.401 --parallel=thread:2 --highpass=filter.highpass.gauss:cutoff_freq=0.002:apix=4.401 --averager=mean.tomo --aligncmp=ccc.tomo --raligncmp=ccc.tomo --shrink=3 --shrinkrefine=2 --savesteps --saveali --iter=24 --normproc=normalize --keep=0.8 --path= --align=rotate_translate_3d:search=10:delta=8:dphi=8:verbose=0:sym=icos --ralign=refine_3d_grid:delta=3:range=9:search=2 |
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| . | |
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| === SPT "all vs all" === | |
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| 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 | e2spt_hac.py -v 0 --path=AVSA --input= --shrink=3 --shrinkrefine=2 --iter= --mask=mask.sharp:outer_radius= --npeakstorefine= --lowpass=filter.lowpass.gauss:cutoff_freq=.02:apix=4.401 --highpass=filter.highpass.gauss:cutoff_freq=0.002:apix=4.401 --parallel=thread:24 --averager=mean.tomo --aligncmp=ccc.tomo --raligncmp=ccc.tomo --saveali --savesteps --postprocess=filter.lowpass.gauss:cutoff_freq=.02:apix=4.401 --autocenter --noplot --exclusive_class_min=8 --normproc=normalize --align=rotate_translate_3d:search=4:dphi=12:delta=12 --ralign=refine_3d_grid:delta=3:range=12:search=2 |
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| . | |
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| == OTHER programs (use at your own risk; these commands might be outdated; run the program followed by -h to see current available parameters for each program) == | |
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| 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 --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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=== 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 === e2symsearch3d.py === === e2spt_refinemulti.py === === e2spt_fftamps.py === === e2spt_wedge.py === |
Last update: October 1, 2013.
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 (both in terms of memory and processing speed). 4GB 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 a new and longer version of the tutorial... eventually).
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; to see the entire list of parameters for each program, type the program name followed by -h at the command line)
CORE PROGRAMS
SPT BOXER
e2spt_boxer.py <tomogram.rec> --yshort --inmemory --lowpass=100
.
SPT Iterative refinement
Monstrous command for alignment with e2spt_classaverage.py (used to be e2classaverage3d.py)
e2spt_classaverage.py --input= --output= --ref= --npeakstorefine=14 -v 0 --mask=mask.sharp:outer_radius= --lowpass=filter.lowpass.gauss:cutoff_freq=.02:apix=4.401 --parallel=thread:2 --highpass=filter.highpass.gauss:cutoff_freq=0.002:apix=4.401 --averager=mean.tomo --aligncmp=ccc.tomo --raligncmp=ccc.tomo --shrink=3 --shrinkrefine=2 --savesteps --saveali --iter=24 --normproc=normalize --keep=0.8 --path= --align=rotate_translate_3d:search=10:delta=8:dphi=8:verbose=0:sym=icos --ralign=refine_3d_grid:delta=3:range=9:search=2
.
SPT "all vs all"
Monstrous command for alignment with e2spt_hac.py (used to be e2tomoallvsall.py)
e2spt_hac.py -v 0 --path=AVSA --input= --shrink=3 --shrinkrefine=2 --iter= --mask=mask.sharp:outer_radius= --npeakstorefine= --lowpass=filter.lowpass.gauss:cutoff_freq=.02:apix=4.401 --highpass=filter.highpass.gauss:cutoff_freq=0.002:apix=4.401 --parallel=thread:24 --averager=mean.tomo --aligncmp=ccc.tomo --raligncmp=ccc.tomo --saveali --savesteps --postprocess=filter.lowpass.gauss:cutoff_freq=.02:apix=4.401 --autocenter --noplot --exclusive_class_min=8 --normproc=normalize --align=rotate_translate_3d:search=4:dphi=12:delta=12 --ralign=refine_3d_grid:delta=3:range=12:search=2
.
OTHER programs (use at your own risk; these commands might be outdated; run the program followed by -h to see current available parameters for each program)
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
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
e2symsearch3d.py
e2spt_refinemulti.py
e2spt_fftamps.py