## Module: Mask Map By Molecule (
)

### Description:

> This is an experimental module from the Xtra Library: https://xtras.amira-avizo.com.
> Using this module the density map of a macro molecule (protein) can be modified to isolate user defined segments of the underlying molecule. One prerequisite for this to work is that the atomic structure of the macro molecule is known. The module then works by thresholding a coarse pseudo electron density map of the molecular model. This, in turn, can be done correctly only, if the model fits exactly to the denity map, a condition that is typically met when model and density come from the same source, in other words, when the molecular model has been created from the density map. If the density map originates from a different experiment, the molecule has to be fitted to the density first. This can be done using module Fit Molecule To Map also available in the Xtra library. If the molecule segment to be masked is small compared to the complete molecule, it is recommended to use the complete molecule for fitting and connect the fitted molecule to port Transformation. For convenience, the user has the choice to represent the masked map in the coordinate system of the map or that of the molecule. Also, the mask can be exported as separate object, to be used, e.g., for surface model creation.

### Connections:

> Molecule `[required]`
> This port holds the atomic model of the molecule that is to be masked. Data of type HxMolecule are accepted.

> Map `[required]`
> This port is connected to the map representing the molecule to be masked. Data of type HxUniformScalarField3 are accepted.

> Transformation `[required]`
> To this port any object with the transformation mapping the atomic model to the density map can be connected. Any object of type HxSpatialData will be accepted here, since only its transformation is evaluated.

About
This port prints the version of the module.

Options
Create Mask in Molecule Space: If this option is checked, the masked map is presented in the coordinate system of the (untransformed) atomic model.
Export Mask: If this option is checked, the mask is output as a separate object to be used e.g., for surface generation.