Imposing 5-fold rotational symmetry on a helical object

Submitted by mengx on Fri, 2012-01-13 12:16

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Frealign

I have generated a pretty good density map using IHRSR with the following parameters.

(1) Rotation between subunits=25.63deg (2) Axial rise=31.14A (3) Rotational symmetry=5 (4) Step size=68A

Now I am trying to get a map using Frealign.
I calculated values of some parameters in the file, mparameters.

ALPHA=360/5+25.63
RISE=31.14A
START=5
SUBUNITS = STARTS x D / RISE = 11

Unfortunately, the reconstruction didn't converage to a correct map and there are no helical arrays on the map. Are the values above wrong? What is the correct way to impose rotational symmetry?

Thanks.

niko Fri, 2012-01-13 14:00

I am not sure what you are referring to with "rotational symmetry". Assuming it refers to the number of starts, you should set the following:

ALPHA = 25.63
RISE = 31.14
STARTS = 5
SUBUNITS = Step size / RISE = 2 (this is only an approximate value and although the averaging also includes the multiple starts, the SUBUNITS value only refers to one start)
STIFFNESS = 10 (try smaller or larger, depending on how flexible your filaments are)

The symmetry definition might be different from IHRSR and if it does not work you should also try -25.63 for ALPHA.