FBEAUT helical reconstruction discontinuity

Submitted by Duncan Sousa on Thu, 2011-02-17 19:27

Forums

Frealign

I'm getting discontinuities (mainly extra density) between helical section repeats using FBEAUT. These discontinuities only show up in Chimera when viewing with a step size of 1.

If I turn FBEAUT off there are no discontinuities, but the helical densities blur out and fade away toward the ends. I presume this would seriously impair the next round of refinement??

I'm running the latest Frealign.

niko Thu, 2011-02-17 19:47

Can you email me a section of the map showing these discontinuities and your helical parameters?

Duncan Sousa Fri, 2011-02-18 18:28

Do you think I should continue my refinement despite the discontinuities? At low resolution I can't see how it could matter, but I'm not sure at higher resolutions. I do a lot of parameter analysis between each Frealign refinement iteration that takes a fair bit of my time otherwise I'd just let it run.

niko Fri, 2011-02-18 19:53

Yes, continue the refinement. I will try to track down the bug but this is a small feature that should not affect your refinement much.

Duncan Sousa Sun, 2011-02-20 19:19

If the discontinuities are due to sub-volume edge effects I have some ideas about how to smoothly stitch volumes together. Let me know if that would be useful.