Docking a model into a map


Obtaining the structure of a macromolecule generally requires building an atomic model that fits the cryo-EM map. A docking procedure is used to do this fitting if the model, or a part of the model, is known but has not been placed into the map.

For example, your cryo-EM map might show a molecular complex assembled from components available from other experiments, such as X-ray crystallography. Then, you can dock these components' models into your cryo-EM map to obtain a model for the entire complex.


The program phenix.dock_in_map automatically docks one or several models into a map, using a convolution-based shape search to find a part of the map that is similar to the model. Initially, it performs a low-resolution search that focuses on the overall shape of the molecule, which is performed without rotation to optimize runtime. Alternatively, you can perform an initial fast search by matching the moments of inertia of the model and map, but this option requires an accurate map that looks a lot like the model. Next, if the placement is satisfactory, a full search can be run on multiple processors using real-space rigid-body refinement with the full resolution of the map.

In a standard run of phenix.dock_in_map, you input the model (PDB file) that you want to place, a map (CCP4, MRC, or other map format file), the nominal resolution of the map, and the number of processors to use.The program outputs a search PDB file transformed to superpose on the target map file

How to use phenix.dock_in_map: Click here

Common issues

Related programs