Differences between revisions 44 and 126 (spanning 82 versions)

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

e2spt_data.zip

TUTORIAL DOCUMENT

Not available here for now. Get it through this site:

http://blake.bcm.edu/emanwiki/Ws2011/Agenda

Monstrous command for alignment

$/!\$ Edit conflict - other version:

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 --averager=mean.tomo --aligncmp=ccc.tomo --raligncmp=ccc.tomo --shrink=3 --shrinkrefine=3 --savesteps --saveali

$/!\$ Edit conflict - your version:

$/!\$ End of edit conflict

-  ⇤ ← Revision 44 as of 2011-03-02 01:25:36 → 
  Size: 2478
  Editor: jgalaz
  Comment:
+   ← Revision 126 as of 2011-05-20 22:33:14 → ⇥
  Size: 1924
  Editor: jgalaz
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 2:
-== Wednesday March 16, 2011 - P.M. Practical EMAN2 SPT tutorial ==
SPT (single particle tomography) capabilities are relatively new in EMAN2. They were inspired by Michael Schmid's studies on sub-volume averaging (mostly on viruses), and a stubborn student's insistence on doing extensive sub-volume averaging on chaperons.
+== Wednesday - P.M. ==
-Line 5:
+Line 4:
-This session will cover the beta version of a small fraction of the possibilities for SPT processing EMAN2 will eventually offer.
+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.
-Line 7:
+Line 8:
-== OUTLINE ==
 * 1) SPT processing through EMAN2's workflow (e2workflow.py)
 * 2) Sub-volume extraction from tomograms using EMAN2's 3D particle picking tool (e2tomoboxer.py)
 * 3) "Preparation" of extracted particles for alignment. [Details later. /!\ For a myriad of reasons, it is NOT recommendable to align and average sub-volumes directly after extraction without "preparing" them first].
 * 4) Reference-based alignment and averaging.
 
 <!> ''PLEASE NOTE that "particle" and "sub-volume" are used interchangeably''
+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.
-Line 15:
+Line 11:
-== SOFTWARE ==
All necessary software is provided as part of EMAN2. If you don't have EMAN2 installed, you can download the most updated version (for your specific platform, Windows, Linux or Mac), from here: 
 
[[http://ncmi.bcm.edu/ncmi/software/counter_222/software_86]]
+== DATA ==
[[attachment:e2spt_data.zip| e2spt_data.zip|&do=get]]
-Line 20:
+Line 14:
-== RAW DATA ==
We have prepared sample data for this tutorial. The tomogram in the link below comes from a tilt series of epsilon15 virus particles ''in vitro'', recorded using Zernike phase-plate technology:
+== TUTORIAL DOCUMENT ==
Not available here for now. Get it through this site:
-Line 23:
+Line 17:
-[[attachment:e15phaseplate.rec]]
+http://blake.bcm.edu/emanwiki/Ws2011/Agenda
-Line 25:
+Line 19:
-The following tomogram also comes from a tilt series of epsilon15 viruses ''in vitro'' but was recorded under conventional cryoEM imaging conditions:
+== Monstrous command for alignment ==
-Line 27:
+Line 21:
-[[attachment:e15normal.rec]]
-Line 29:
+Line 22:
-== BOXING ==
You have two options for opening the tomogram for purposes of boxing it.
+---- /!\ '''Edit conflict - other version:''' ----
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 --averager=mean.tomo --aligncmp=ccc.tomo --raligncmp=ccc.tomo --shrink=3 --shrinkrefine=3 --savesteps --saveali
-Line 32:
+Line 25:
-) Directly, by typing e2tomoboxer.py followed my the path to the tomogram file at the commandline.
+---- /!\ '''Edit conflict - your version:''' ----
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 --averager=mean.tomo --aligncmp=ccc.tomo --raligncmp=ccc.tomo --shrink=3 --shrinkrefine=3 --savesteps --saveali --iter=8 --keep=0.8
-Line 34:
+Line 28:
-) Or you can launch e2workflow.py from the commandline and access a tomogram through the browser in the tomographic menu.

[In theory, you can open a tomogram for contemplation purposes by typing: "e2display.py <my_tomogram_path_name_goes_here>" at the commandline.
/!\ This is NOT recommendable, unless you have a grossly large (VERY, VERY large) amount of virtual memory on your computer; otherwise, catastrophe WILL befall upon you].

Let's explore the FIRST APPROACH.

=== OPENING A TOMOGRAM DIRECTLY WITH e2tomoboxer.py ===
+---- /!\ '''End of edit conflict''' ----