## 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 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.

## Shell mask

The shell mask is most useful to model membranes.

## Hull mask

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

## Level mask

Each model generates one level of the level mask.