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| == 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 |
Single Particle Tomography in EMAN2
Wednesday - P.M.
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.
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.
DATA
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
Under the SPT section.