Processing, docking and rebuilding AlphaFold2 and other predicted models in cryo-EM maps



Dock and rebuild combines the functions of processing, docking and rebuilding predicted models produced by AlphaFold, RoseTTAFold and other prediction software into a cryo EM map.

These steps can also be carried out one at a time. There are three steps in working on an AlphaFold or other predicted model with a cryo-EM structure.

The first step is to process the predicted model by trimming off all the uncertain residues in the predicted model and breaking up the remaining structure into a best guess of rigid domains with phenix.process_predicted_model .

The next step is to dock each of the domains of the processed model into the map, keeping plausible connectivity. This is done with phenix.dock_predicted_model .

The third step is to morph the predicted model onto the docked domains and then to rebuild all the parts of the predicted model using the density in the map.

How dock_and_rebuild works:

The dock_and_rebuild procedure is just a way to connect all three steps in processing, docking and rebuilding a predicted model. You may want to use this procedure if you have a simple case, or if you have many models you want to process. If it does not work well, you may want to take its intermediate outputs (i.e., the docked model) and carry out the following steps individually.

The model input to dock_predicted_model is your starting predicted model file (i.e., an AlphaFold model)

The map input to dock_predicted model is normally your best sharpened or density-modified cryo-EM map. It can also be a map generated by any other procedure (including crystallography).

If you are able to mask your map, keeping only the part representing the region where this model belongs, that can be very helpful. You can also box the map around this region. If you have a map that has many chains, this masking can greatly shorted the time for docking. If you don't know where in your map the model goes at all, you can supply the entire map. If your map has symmetry this will normally be found automatically.

The three steps described above are then carried out: processing the model to obtain domains representing the accurate parts of the model (phenix.process_predicted_model), docking the domains (phenix.dock_predicted_model), and morphing and rebuilding the predicted model to yield a rebuilt version of the predicted model.


Standard run of dock_and_rebuild:

Running dock_and_rebuild is easy. From the command-line you can type:

phenix.dock_and_rebuild model=my_model.pdb \
   full_map=my_map.ccp4 \

This will carry out all the steps of processing, docking and rebuilding to yield my_model_rebuilt.pdb

Possible Problems

If your map has pseudo-symmetry (like a proteasome) you might need to box one subunit or try ssm_search=False to use a more thorough search in docking.

Specific limitations and problems:


Additional information

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