Model rebuilding keeping connectivity and allowing insertions and deletions



Rebuild a model, keeping all connectivity the same but allowing insertions and deletions.

How rebuild_model works:

Rebuild model rebuilds each chain in your model (optionally in segments of about 15-20 residues) and reassembles these into a new model with the same connectivity as the original.

Each segment is rebuilt with several different base methods (default base methods are refinement, fixing insertions and deletions, and rebuilding from CA positions).

For each base method, a sequence of optimization steps is carried out (typically refinement, the base method, replacement of side chains, regularization, and another replacement of side chains).

Rebuilt segments are scored based on map correlation. The highest-scoring segments are used to replace the corresponding segment in the original model.

If there are multiple chains in your model, each is rebuilt separately.

The quick option can be used to speed up the process. It sets the number of refinement cycles to 1 (otherwise there are 3 carried out) and skips all the optimization steps except the base method.


Standard run of rebuild_model:

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

phenix.rebuild_model my_model.pdb my_map.mrc resolution=3 nproc=8

This will rebuild my_model.pdb based on the map my_map.mrc at a resolution of 3 A using 8 processors.

Possible Problems

Specific limitations and problems:


Additional information

List of all available keywords