Box size in EMAN2

[Ateeq Alzahrani]

Hi there, How can I select the appropriate box size in EMAN2 for a protein with (260 kD size)? 

Is there any calculations that can be used based on the protein size.

Thanks 

[Steven Ludtke]

This, and many other topics are covered in the Wiki:

http://blake.bcm.edu/emanwiki/EMAN2/BoxSize

http://blake.bcm.edu/emanwiki/EMAN2/AngStep

http://blake.bcm.edu/emanwiki/EMAN2/Concepts

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[Gmail]

Thank you for the quick reply. 

Sent from my iPhone

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[Steven Ludtke]

Let me clarify one other point, since you were asking about mass-based calculations.  In general there is a cubed relationship between protein mass and physical dimensions, of course. However, there is a lot of variation based on shape. That is, if you are referring to a globular protein, then going from 100 to 800 kDa would only give ~2x larger linear dimensions. However, if the protein were a filament of fixed cross-section, then increasing the mass 8-fold will also increase the linear dimensions 8-fold.

So, generally speaking, proteins in the 100kDa-1 MDa range will be ~100 - 200 Å in size, but there can be considerable variation based on shape, so the practical reality is that you need to look at your images, identify the target of interest and measure its longest axis.

On Jan 1, 2015, at 1:44 AM, Ateeq Alzahrani <ate...@gmail.com> wrote: