What's new in FREALIGN v8.11 in terms of helical processing

Submitted by Rui Zhang on Thu, 2013-08-22 18:00

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Frealign

Hi,

What's new in FREALIGN v8.11 in terms of helical processing?

And when doing FREALIGN local refinement (mode 1), what's the difference between setting ASYM to H and 0 (C1)?

Thanks!

Rui

niko Fri, 2013-08-23 11:26

Helical processing has not changed in 8.11. A few other things were updated and small bugs were removed (and maybe new ones added - who knows).

Setting the symmetry to H during refinement (Mode 1) will cause Frealign to reset the parameters to minimize translations of segments along the helical axis. Instead, a certain portion of the translations will be expressed as rotations around the helical axis according to the helical symmetry. Also, using H for symmetry during refinement will impose restraints on the angles to keep filaments straight. The strength of these restraints can be adjusted using the stiffness parameter (a small value, e.g. 1 will impose only weak restraints, a large value, e.g. 100 will impose strong restraints).

Rui Zhang Fri, 2013-08-23 15:18

Hi, Niko, thanks for the explanation!

A follow-up question:
When doing 3D reconstruction (mode 0) with ASYM = H, and for my microtubule data I set NSUBUNITS to 13,
does FREALIGN takes the exact alignment parameter in the .par file and inserts 12 copies into 3D FT space (clockwise 6 times and counter-clockwise 6 times) based on the specified helical symmetry, or it does the translations minimization first (like what you described in refinement mode 1)?

The reason I ask is that microtubule is not a real helical object, so this translation minimization thing is not good because it will alter the seam location.

Thanks!