Generating masks from models

One of the uses of a model is to define regions within a density map. The model can therefore be used to segment the map and isolate those regions associated with the model. The general idea is to calculate a mask, and then use that mask to produce a new map with only the densities defined by the model.


Ball-and-stick mask

The model components define spheres and the links cylinders captured in a mask. The component and link radii are used to determine the sizes of the spheres and cylinders:

bmodmask -verb 1 -type model -size 100,100,100 -comp 4 -linkrad 2 -mask -out 36_10_s.cmm

Ball n stick
The map was thresholded to 0.3 to make it slightly larger than the corresonding model.


Shell mask

The shell mask is most useful to model membranes.

Membrane shell

Hull mask

The hull mask differentiates the inside and outside of the model.

Membrane hull

Level mask

Each model generates one level of the level mask.