|
Size: 3274
Comment:
|
← Revision 152 as of 2012-07-05 01:16:47 ⇥
Size: 595
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| = Single Particle Tomography in EMAN2 = == Wednesday - P.M. == |
= Single Particle Tomography in EMAN2, 2011 WORKSHOP in Houston, TX = |
| Line 4: | Line 3: |
| This session will cover the new tools for single particle tomography in EMAN2. Unfortunately, this technique is very memory-intensive and compute-intensive. The 3 gb of ram available on the workshop computers is barely sufficient to do some small examples, and full 3-D alignments of large sets of particles can take many hours of computation. |
The SPT page has move to http://blake.bcm.edu/emanwiki/SPT/Spt |
| Line 8: | Line 5: |
| So, for purposes of the tutorial, we will learn how to use the particle picker, and do a couple of small examples which can be completed in the available time. |
This is just an archaic page with the version of the tutorial used in the EMAN2 Workshop in March 2011. == OLD E2SPT USERS' GUIDE == * Single particle tomography USER'S GUIDE (March 2011). [[attachment:e2spt_users_guide_03_2011_workshop.pdf| e2spt_users_guide_03_2011_workshop.pdf |&do=get]] |
| Line 12: | Line 14: |
| [[attachment:e2spt_data.zip| e2spt_data.zip|&do=get]] | Epsilon 15 virus data, used since the EMAN2 Workshop in 2010. |
| Line 14: | Line 16: |
| == TUTORIAL DOCUMENT == Not available here for now. Get it through this site: http://blake.bcm.edu/emanwiki/Ws2011/Agenda == Monstrous command for alignment with e2classaverage3d.py == e2classaverage3d.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 --preprocess=filter.lowpass.gauss:cutoff_freq=.02 --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 e2tomoallvsall.py == e2tomoallvsall.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 == Monstrous command for e2spt_sim.py == e2tomosim.py --input=../groRef_scaled_bin2.hdf --snr=5 --nptcls=2 --tiltstep=5 --tiltrange=60 --transrange=10 --saveprjs --noiseproc=math.addnoise == 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 == Monstrous command for e2spt_resolutionspt.py == e2spt_resolutionplot.py --vol1=whatever1.hdf --vol2=whatever2.hdf --output=whatever --npeakstorefine=16 -v 3 --mask=mask.sharp:outer_radius=48 --preprocess=filter.lowpass.gauss:cutoff_freq=0.04 --align=rotate_translate_3d:search=10:delta=12:dphi=12:verbose=1 --parallel=thread:8 --ralign=refine_3d_grid:delta=2:range=14:search=3 --aligncmp=ccc.tomo --raligncmp=ccc.tomo --shrink=2 --shrinkrefine=2 --normproc=normalize |
[[http://blake.grid.bcm.edu/wikifiles/SPT/e2spt_data.zip|e2spt_data.zip]] |
Single Particle Tomography in EMAN2, 2011 WORKSHOP in Houston, TX
The SPT page has move to http://blake.bcm.edu/emanwiki/SPT/Spt
This is just an archaic page with the version of the tutorial used in the EMAN2 Workshop in March 2011.
OLD E2SPT USERS' GUIDE
* Single particle tomography USER'S GUIDE (March 2011).
e2spt_users_guide_03_2011_workshop.pdf
DATA
Epsilon 15 virus data, used since the EMAN2 Workshop in 2010.