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Trimer processing workflow » History » Revision 3

Revision 2 (Dmitry Lyumkis, 06/24/2013 09:45 PM) → Revision 3/17 (Dmitry Lyumkis, 06/24/2013 09:45 PM)

h1. Trimer processing workflow 

 h1. reconstruct an ab initio model using common lines 

 # select a set of ~20 good class averages, and upload them as a template stack (call it, e.g. "ts_2g12_initial_models") 
 # select as many of the class averages that have reliable features which you think are real and correspond to the Fab-bound complex (could be 50, could be 100, etc …), and upload that as another template stack (call it, e.g. "ts_2g12_refinement") 
 # You can access the common lines method under the menu "ab initio reconstruction" and "automated common lines" in Appion. Go there.  
 # Under "iterative model creation" select the first template stack, "ts_2g12_initial_models" 
 # Under "refinement of aligned and clustered model" select the second template stack, "ts_2g12_refinement" 
 # keep all parameters as default, and use EMAN for iterative model creation. Then fill out the number of images per volume. This should be ~50% of the number of images in the "ts_2g12_initial_models" stack. If you have, e.g. 30 images, this value should be ~15. 
 # Fill out the bottom radii for the particles and give a mass. For example, for 2g12, these should probably be: radius of mask=200 ; inner alignment radius = 0 ; outer alignment radius = 140 ; particle mass = 750 
 

 # Launch the job 
 # repeat 1-8 with an identical job, EXCEPT that uncheck "iteratively align class averages to each other", AND give the run a different name (for example, you can have two runs, titled "acl1" and "acl1_noiteralign" …).