8 Mar 2021

Fitting Molecule To Map

This Xtra contains a script module to fit molecular models to density maps, a process frequently called "docking".


Using this module, a molecular model (for example, imported from PDB) can be "docked" into a density map; that is, a scalar field. Internally, the molecular model is converted to an electron density map using Pseudo Electron Density, and then rigidly registered using Register Images. The quality and/or success of the alignment is highly dependent on the proper pre-alignment. For that, the module provides two automatic pre-alignment methods: aligning the centers or aligning the principal axes. In general, however, pre-alignment is done using the Transform Editor. Press Apply to start fitting.