Rebuild a model using fragments from the PDB



Create a composite model similar to a supplied model using fragments from the PDB.

This tool can be used in early stages of model-building to try and improve parts of a preliminary model by replacing them with similar fragments from a deposited structure.

Note that the composite model may not actually have good geometry because the fragments from the PDB are morphed (distorted) to match the supplied model and also because the junctions between fragments taken from the PDB are not refined.


replace_with_fragments_from_pdb can create composite models for protein chains

You can adjust the maximum number of insertions/deletions in each replacement fragment and whether to morph structures obtained by SSM matching.

You can supply a map file for refinement or calculation of map-model correlations.

You can also choose to exclude or include specific PDB entries in SSM matching and fragment searching, or exclude all PDB entries with sequences similar to a particular PDB entry.

You can choose to create a replacement for just a selected part of your model (by supplying a selection string that specifies what to select).

How replace_with_fragments_from_pdb works:

Search structures in the PDB (using SSM matching and fragment searching) for fragments similar to segments in a supplied model. Then choose the best matching segments for each part of the supplied model and create a composite model using the fragments from the PDB.

replace_with_fragments_from_pdb uses SSM-based (secondary structure matching) to find structures in the PDB that are similar to a supplied model. The SSM matching is the same as in phenix.superpose_and_morph.

replace_with_fragments_from_pdb also uses fragment searching to find shorter fragments matching each loop (segment between two helices or strands) in the supplied model.

The fragments obtained with fragment searching are always morphed (distorted) to make the distance between starting and ending residues match the distance in the supplied structure.

Fragments obtained from SSM matching are optionally morphed to match the target structure as well. The distance over which morphing occurs (the shift-field distance) is adjustable (typically 10 A), where structure is largely preserved over shorter distances and may be changed over longer distances.

The supplied model is then used as a template and matching parts of structures from the PDB are superimposed on the template. The best-matching segments (smallest rmsd and longest length) are chosen and connected. Gaps are filled if possible by a targeted fragment search of the PDB.


Standard run of replace_with_fragments_from_pdb:

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

phenix.replace_with_fragments_from_pdb model.pdb nproc=8

This will find fragments in the PDB similar to model.pdb, put them together and write out a new model using these fragments.

Possible Problems

Specific limitations and problems:

The final model may have poor geometry at connections between fragments, so further refinement is normally required. Additionally the final model may have poor geometry within segments because morphing is carried out to match the target structure.


Additional information

List of all available keywords