Question about creating .box files

[BENJAMIN MERRITT]

Hello,

I am currently attempting to create 2D classes of some data I collected.

I am working through the old 2012 EMAN2 Reconstruction Tutorial (GroEL) because it seems to be the only one with any particle picking tutorial steps.

First problem:  I cannot find the .box files in the .iso CD file included with the tutorial.  Do they perhaps have a different file name suffix?

Second problem: When I want to create my own boxed files, do I hit "Write Output" after selecting all good particles?  Will this create a .box file with box coordinates, which could be used to extract particles?

Thanks

Ben

[Steve Ludtke]

.box files are not directly used in EMAN2, they are an import/export format only.

The 2012 tutorial is not compatible with EMAN2.2 in any way. Many, many things have changed since then. While you may be able to get some idea about picking particles from it, that software has also changed significantly. As you say, it is not in the recent tutorials, because we don't normally have time for it at the workshops (where the tutorials are given).  

The new e2boxer included with 2.2 has several different autopickers available: "local search", "by ref" and "neural net". For "easy" specimens, like viruses, "local search" is the easiest, and can work well. For more accurate results on less ball-shaped particles, "by ref" works well. For tricky problems which normally require a human to manually pick particles, the neural network based picker works very nicely, but requires some additional effort in setup.

It is unfortunately true that we lack a proper particle picking tutorial at the moment. There is a tutorial on using the neural network based picker on the tutorials page on the website, but it doesn't get into the basics very much.

Here is a quick summary:

- To manually pick particles in any mode, simply left-click and drag to center

- To delete existing boxes, a shortcut is to hold down shift, then left-click 

- Left-drag can be used to reposition particles

- middle-click on any image window will open a control-panel to adjust how the image is displayed (and provide other functions)

- mouse-wheel zooms in and out

- right-drag will pan

- Box locations are stored automatically, there is no need to explicitly save them

- Box locations are not stored in .box files (unless you explicitly export them), they are stored in the appropriate info/*.json file

- Some of the autopicking modes require positive and/or negative reference particles. Reference particles appear in the appropriate window, but the location does not persist on the main display

- Particles should be lighter colored on a darker colored background. If this is not the case, you should invert the micrographs prior to picking. The autopickers are sensitive to this.

 

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Steven Ludtke, Ph.D.

Professor, Dept of Biochemistry and Mol. Biol.         (www.bcm.edu/biochem)

Co-Director National Center For Macromolecular Imaging        (ncmi.bcm.edu)

Co-Director CIBR Center                          (www.bcm.edu/research/cibr)

Baylor College of Medicine                             

slu...@bcm.edu

[Benjamin Merritt (RIT Alumni)]

Thank you so much!!!! This forum is so very supportive.

Ben

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Steven Ludtke, Ph.D.

Professor, Dept of Biochemistry and Mol. Biol.         (www.bcm.edu/biochem)

Co-Director National Center For Macromolecular Imaging        (ncmi.bcm.edu)

Co-Director CIBR Center                          (www.bcm.edu/research/cibr)

Baylor College of Medicine                             

slu...@bcm.edu

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