padding factor for e2spt_extract

[Madeline Rollins]

Hi,

I am working with a dataset at 1.562 A/pix and am using an unbinned box size of 256. If I'm using a padding factor of 2.0 when extracting my particles, is the actual box size being doubled to 512? It looks like some of the density in my map is getting truncated, so I'm trying to figure out if it would be better to increase my box size or increase the padding factor.

Thank you,

Madeline

[Ludtke, Steven J.]

The padding around each particle tilt image is used to better reconstruct Z-displaced density outside the particle box before clipping out the final particle at the end. If your particle is getting clipped at the edges of the 256^3 box you need to increase the box size so the final box size is sufficient to contain the particle with at least a little padding around the edges. Decreasing the padding factor isn't normally advisable, and increasing it much past 2 will rarely do anything very useful.

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Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology        Dept. of Biochemistry 
Deputy Director, Advanced Technology Cores                  and Molecular Pharmacology
Academic Director, CryoEM Core
Co-Director CIBR Center

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