Helical processing

Hi Niko,

In reference to the below quoted post from the Frealign forum, I see that if helical processing is performed Frealign resets parameters to minimize translations of segments during refinement. This results in changing of the PHI angles of a filament, even if the refinement mask is set to 0 0 0 1 1, which is a problem if you have a pseudo-symetrical object, as all PHI angles are unique. Is there any way for this function to be turned off without losing the symmetrical averaging performed during later reconstruction (which would occur if helical reconstruction was turned off)? Perhaps 'helical stiffness' could be edited to restrict PHI angles too?

Quote from original forum:
'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)’

Hope you can help,
Cheers,
Joe