Number of 2D classesto 5, and
Force Max over poses/shiftsto true.
Filament diameter (A): The estimated diameter of the filament, in Angstroms
Separation distance between segments (diameters): The distance between adjacent picks along a filament, in terms of multiples of the filament diameter
curvature: This is the estimated curvature (1/Å) of the filament at the pick location. Local curvature is useful to prune out the most bent locations along a filament, without removing all picks from that filament
sinuosity: This is the ratio between the actual filament contour length, and the straight line start-to-end distance. Filament sinuosity is useful to remove entire filaments that may correspond to contaminants or aggregated filaments
Local Power: under 1296550
Curvature: under 0.0004
Sinuosity: under 1.08
Align filament classes vertically (BETA)parameter in any 2D classification job.
Number of 2D classes: 100
Align filament classes vertically (BETA): True
Batchsize per class: 400 (since these filaments are rather small)
filamentin-plane rotation estimates, which are written to either during filament tracing or 2D classification. Note that this generates a "cylindrical" density from the input particles – for filaments with highly oblong cross sections (e.g. amyloid filaments), Ab-Initio Reconstruction may produce a better initial model. We have generally seen that for filaments that are approximately cylindrical, and have constant diameter, directly running a helical refinement from the particles is more successful than running an ab-initio reconstruction job. Conversely, for filaments that are distinctly not cylindrical, ab-initio reconstruction can take advantage of the diversity of views along the helical axis, and often results in a better initial model.