Placing CA atoms in a map with refine_ca_model



The routine refine_ca_model is a tool for adjusting CA/CB positions in a preliminary model to increase its suitability for generating an all-atom model.


How refine_ca_model works:

The refine_ca_model tool takes a set of CA positions, and optionally, a set of CB positions. It adjusts the CA/CB positions to put the atoms in density (if possible) and also to place the CB atoms in plausible positions relative to the CA positions and also to make the CA-CA distances as close to 3.8 A as possible.

Using refine_ca_model:

The tool refine_ca_model is usually run automatically as part of trace_and_build. However you can run it yourself with a CA/CB model, a map, and a resolution.

Input map file: The map file should cover the model you supply.

Resolution: Specify the resolution of your map (usually the resolution defined by your half-dataset Fourier shell correlation

CA/CB model: Supply a model that at least has CA positions. If you supply CB positions the new CB positions will be restrained towards the ones you supply.


Standard run of refine_ca_model:

You can use refine_ca_model to adjust a CA/CB model based on a cryo-EM map:

phenix.refine_ca_model my_map.mrc resolution=2.8 ca_cb_model.pdb

Possible Problems

Specific limitations and problems:


Additional information

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