18 Nov 2021

Masking Map by Molecule

Module Mask Map By Molecule lets you mask an EM map of a macro molecule by an atomic model of the entire or partial molecule. This can be useful when validating EM maps from SPA with published models from the Protein Data Bank.


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 density 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 the Fit Molecule To Map module also available in the Xtra library. If the molecule segment to be masked is small compared to the complete molecule, it is recommended that you use the complete molecule for fitting and connect the fitted molecule to a Transformation port. For convenience, you have 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, for example, for surface model creation.

The module is found in the right-click menu of a molecule object (HxMolecule) > Xtra > Compute > Mask Map By Molecule.