Differences between revisions 11 and 19 (spanning 8 versions)
Revision 11 as of 2012-08-24 11:05:01
Size: 4473
Editor: jgalaz
Comment:
Revision 19 as of 2013-10-02 20:46:07
Size: 5334
Editor: jgalaz
Comment:
Deletions are marked like this. Additions are marked like this.
Line 1: Line 1:
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'''.
Line 11: Line 13:
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.
Line 18: Line 20:
* 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).
Line 31: Line 33:
== 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) =
Line 33: Line 35:
== CORE PROGRAMS ==

=== SPT BOXER ===
e2spt_boxer.py <tomogram.rec> --yshort --inmemory --lowpass=100

.

=== SPT Iterative refinement ===
Line 35: Line 45:
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
Line 37: Line 47:
.
Line 38: Line 49:
=== SPT "all vs all" ===
Line 41: Line 52:
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
Line 43: Line 54:
.
Line 44: Line 56:
== 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) ==
Line 45: Line 58:
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
Line 55: Line 68:
Line 58: Line 72:
Line 60: Line 75:


=== 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).

e2spt_users_guide_06_2012.pdf

DATA

Epsilon 15 virus data, used since the EMAN2 Workshop in 2010.

e2spt_data.zip

TRiC chapeornin data (NOT READY).

e2spt_data_apoTRiC.zip

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

e2spt_wedge.py

SPT/Spt (last edited 2016-06-24 21:47:10 by jgalaz)