Merging jobs in relion

[haaris safdari]

Hi,

I have around 440000 particles after extraction job in relion. When I am running 2D classification with these, system mostly crashes with error. So, I was thnking to divide my dataset into three sets of around 150000 each and perform 2D classification. Is there any command to merge the dataset after 2D classification (If I accomplish this)??

[Steve Ludtke]

You'll need to provide more details:

1) full output of e2version.py

2) full 2D refinement command you are running (if you are using the GUI, you can get this from the "command" tab before launching a job, or retrospectively from the .eman2log.txt file in the project folder)

3) box size (pixels) of the particle data

4) the full text of the error message you're getting

There is no general strategy for merging the results of a 2-D refinement because the references evolve as the job runs, so the different 2-D refinements will have different classes at the end. So, it depends on what basis you're using to select the classes for particle extraction...

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)
Co-Director National Center For Macromolecular Imaging                  (ncmi.bcm.edu)
Baylor College of Medicine                             
slu...@bcm.edu

On Jan 18, 2018, at 11:15 AM, haaris safdari <haaris....@gmail.com> wrote:

Hi,

I have around 440000 particles after extraction job in relion. When I am running 2D classification with these, system mostly crashes with error. So, I was thnking to divide my dataset into three sets of around 150000 each and perform 2D classification. Is there any command to merge the dataset after 2D classification (If I accomplish this)??

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[Jason K]

Haaris, it is likely that with more information Steve will help you fix your error, but to your original question of how to classify multiple subsets and merge them together:

I had a similar situation where I wanted to classify a few datasets independently and then later I wanted to pool some together. I ran e2refinemulti.py, which does 3D classification, and gave the same references to each set. e2refinemulti.py outputs a list file (.lst) for each of the 3D references. e2proclst.py --mergesort {output filename .lst} {input list 1 filename} {list 2 filename} ... {list n filename} will combine the lst files together. I know this does not exactly answer you because you were asking about reference-free 2D classification and not 3D, but perhaps it's something else to think about.