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| 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). |
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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. |
Unfortunately, SPT is very computationally intensive, both in terms of memory and processing speed. However, illustrative exercises and tutorials can be carried out on a laptop with 2-4GB of RAM. For more realistic SPT on full 3D alignments of large sets (hundreds of particles) comprising large particles (like viruses), 8GB of memory and the use of multiple processing units or GPU technology are advised. |
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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 extensively different version soon) | * Single particle tomography USER'S GUIDE (updated summer 2012; under major refactoring due to extensive changes in e2spt capabilities; look for a new and longer version of the tutorial soon). |
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| Epsilon 15 virus data, used since the EMAN2 Workshop in 2010. | Epsilon 15 virus test data, used in the EMAN2 Workshop in 2011. |
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| TRiC chapeornin data (NOT READY). | TRiC chapeornin test data (coming soon). |
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| == COMMANDS (for easy "copy-pasting" into the command line == | Note that the EMAN2 Project Manager, launched through e2projectmanager.py, provides a full pipeline for SPT (particle selection, preprocessing, alignment and averaging) via iterative refinement. However, other additional alignment, processing and analysis tools are available from the command line. |
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| === Monstrous command for alignment with e2spt_classaverage.py (used to be e2classaverage3d.py) === | = 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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| 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 | == CORE PROGRAMS == === SPT BOXER === e2spt_boxer.py <tomogram.rec> --yshort --inmemory --lowpass=100 . === SPT Iterative refinement === === 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" === === 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 --plotccc --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; some parameters in these programs are under experimental development. Tun the program at the command line followed by -h to see current available parameters for each program) == === 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 |
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=== 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 === |
=== Command for e2spt_rotationalplot.py === |
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=== 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 === Command for e2symsearch3d.py === e2symsearch3d.py --input= --output= --mask= === Command for e2spt_refinemulti.py === e2spt_refinemulti.py -v 0 --path=RF --input= --nrefs=2 --refgenmethod=binarytree --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 --normproc=normalize --radius=150 === Command for e2spt_fftamps.py === e2spt_fftamps.py --input=file.hdf === Command for e2spt_wedge.py (GUI available) === |
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. However, illustrative exercises and tutorials can be carried out on a laptop with 2-4GB of RAM. For more realistic SPT on full 3D alignments of large sets (hundreds of particles) comprising large 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 summer 2012; under major refactoring due to extensive changes in e2spt capabilities; look for a new and longer version of the tutorial soon).
DATA
Epsilon 15 virus test data, used in the EMAN2 Workshop in 2011.
TRiC chapeornin test data (coming soon).
Note that the EMAN2 Project Manager, launched through e2projectmanager.py, provides a full pipeline for SPT (particle selection, preprocessing, alignment and averaging) via iterative refinement. However, other additional alignment, processing and analysis tools are available from 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)
CORE PROGRAMS
SPT BOXER
e2spt_boxer.py <tomogram.rec> --yshort --inmemory --lowpass=100
.
SPT Iterative refinement
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"
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 --plotccc --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; some parameters in these programs are under experimental development. Tun the program at the command line followed by -h to see current available parameters for each program)
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
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
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
Command for e2symsearch3d.py
e2symsearch3d.py --input= --output= --mask=
Command for e2spt_refinemulti.py
e2spt_refinemulti.py -v 0 --path=RF --input= --nrefs=2 --refgenmethod=binarytree --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 --normproc=normalize --radius=150
Command for e2spt_fftamps.py
e2spt_fftamps.py --input=file.hdf