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.
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 36_10_bns.map -out 36_10_s.cmm 36_10_s.star
The map was thresholded to 0.3 to make it slightly larger than the corresonding model.
The shell mask is most useful to model membranes.
The hull mask differentiates the inside and outside of the model.
Each model generates one level of the level mask.