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| = Single Particle Tomography in EMAN2 = == Wednesday - P.M. == |
= Single Particle Tomography in EMAN2, 2011 WORKSHOP in Houston, TX = |
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| 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. |
== OLD E2SPT USERS' GUIDE == |
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| 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. |
* Single particle tomography USER'S GUIDE (March 2011). [[attachment:e2spt_users_guide_03_2011.pdf| e2spt_users_guide_03_2011.pdf|&do=get]] |
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| [[attachment:e2spt_data.zip| e2spt_data.zip|&do=get]] | Epsilon 15 virus data, used since the EMAN2 Workshop in 2010. |
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| == TUTORIAL DOCUMENT == Not available here for now. Get it through this site: http://blake.bcm.edu/emanwiki/Ws2011/Agenda == Monstrous command for alignment == e2classaverage3d.py --input=e15pp_set1_stack.hdf --output=e15pp_set1_aligned.hdf --ref=e15ref_prep_icos_bin2.hdf --ncoarse=1 -v 3 --mask=mask.sharp:outer_radius=48 --preprocess=filter.lowpass.gauss:cutoff_freq=.025 --align=rotate_translate_3d:search=12:delta=8:dphi=8:verbose=1:sym=icos --parallel=thread:2 --ralign=refine_3d_grid:delta=3:range=9 --averager=mean.tomo --aligncmp=ccc.tomo --raligncmp=ccc.tomo |
[[http://blake.grid.bcm.edu/wikifiles/SPT/e2spt_data.zip|e2spt_data.zip]] |
Single Particle Tomography in EMAN2, 2011 WORKSHOP in Houston, TX
OLD E2SPT USERS' GUIDE
* Single particle tomography USER'S GUIDE (March 2011).
DATA
Epsilon 15 virus data, used since the EMAN2 Workshop in 2010.