Helical symmetry
Contents
Symmetrizing a particle
Helical operator syntax
Symmetrizing a helical particle can be done with the usual tool dsym:
vh = dsym(v,<operator>);
where operator represents any symmetry operator. The syntax for helical operators is:
h [<phi>,<dz>,<repetitions[optional]>,<rotational symmetry[optional]>]}}
Here:
- phi is the angular increment in degrees
- dz is the axial rise in pixels
- the number of repetitions (defaults to the maximum definible for a given volume)
- additional Cn rotation to account for n-start helices
Using symmetrization in alignment projects
The simplest way is to input one operator with the syntax described #Helical operator syntax above in the Numerical settings area of the dcm GUI.
This allows to impose a given symmetrization. In order to estimate the symmetry, you will need to create a plugin.
Number of repetitions
Symmetrization of a volume is computed by applying the transformation (phi,dz) in both directions to the original volume a number of times (called repetitions) and then averaging the result. For instance, 17 repetitions imply 8 subsequent applications of (phi,dz) to the original volume and 8 application of -(phi,dz). Each time (phi,dz) is applied, the transformed volume will have a "bottom" of dz layers of pixels that are undefined: (they correspond to the theoretically part of the infinite helix below our volume). The averaging procedure will discard contributions of such pixels. As a result, the central area of the symmetrized volume will be representing contributions of more transformed volumes, attaining thus a higher SNR.
If the user does not specify a number of repetitions, Dynamo will take the maximal number of repetitions for the given volume. If the volume is of size N pixels and the operator carries an axial rise of dz pixels, the maximal number of translations along the z axis is floor(N/dz)