segmentclass: prepare database option

[tanmay...@gmail.com]

Hi Carsten and the SPRING community,

-------------------------------------------------------------------------------    -------------------------------------------------------------------------------   
> spring --version
Spring environment loaded.
GUI from package Emspring-0.80dev
-------------------------------------------------------------------------------     
> springenv e2version.py
Spring environment loaded.
EMAN 2.1 alpha2 (CVS 2013/08/07 17:01:09)
Your EMAN2 is running on:
Traceback (most recent call last):
  File "/lmb/home/tbharat/software/springbox/parts/EMAN2/bin/e2version.py", line 90, in <module>
    main()
  File "/lmb/home/tbharat/software/springbox/parts/EMAN2/bin/e2version.py", line 53, in main
    print 'Your EMAN2 is running on: ', result.split('"')[1], os.uname()[2], os.uname()[-1]   
IndexError: list index out of range
-------------------------------------------------------------------------------        -------------------------------------------------------------------------------   

I am trying to run segmentclass on a "rotated", "ctf phase flipped" stack (let's class this stack1). After this runs, I want to select some good classes and use them in segmentrefine3d. I have additionally run a separate "segment" program, to generate an "unrotated", "ctf convolved" stack (let's call this stack2), which I will also use for segmentrefine3d. I'm having trouble understanding the prepare database option in segmentclass that I should use.

My best guess right now is that I should use obviously stack1 as the input for "segmentclass", but use the spring.db file which was created when I made stack2 in the "Database prepare option". If I do this, then the spring.db for stack2 will be updated, and this spring.db I can use for segmentrefine3d. Put another way - I want to transfer the class assignment from "segmentclass", which was run on the rotated stack to the unrotated stack, thus making it viable for "segmentrefine3d". What is the correct way to do it?

Can anyone help me?

------------------------------------------------------------
Tanmay Bharat
Structural Studies Division
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge CB2 0QH, UK
Tel: +44 1223 267 732
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[Carsten Sachse]

Hi Tanmay,

Your guess is correct.

When the 'Prepare database option' turned on, SEGMENTCLASS will update each segment entry from CTF phase-flipped to CTF convolved. SEGMENTCLASS should be run with the phase-flipped and rotated segment stack. With the updated spring.db you can run 'segmentrefine3d' using convolved images (unrotated) while taking into account the updated spring.db class information for selection purposes.

Best wishes,

Carsten