Author(s)

• replace_side_chains: Tom Terwilliger

Purpose

replace_side_chains is a tool to take a main-chain model and to add side-chains from a rotamer library based on an electron density map.

NOTE: Normally this method is called from phenix.phase_and_build but you can use it interactively if you want.

You can also use it to identify side chains (sequence) from a model without side chains (or with) and a map using sequence_from_density=True.

Usage

How replace_side_chains works:

replace_side_chains uses resolve to replace the side chains in a model. You can choose to use the default resolve rotamer library or the Lovell et al penultimate rotamer library.

Output files from replace_side_chains

replace_side_chains.pdb: A PDB file with side chains replaced.

Examples

Standard run of replace_side_chains:

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

phenix.replace_side_chains  model.pdb map_coeffs.mtz sequence.dat

You should supply a sequence file that matches the sequence of the model.

Using replace_side_chains to sequence a protein from density:

From the command-line you can type:

phenix.replace_side_chains model.pdb map_coeffs.mtz sequence_from_density=True

You don't need a sequence file but if you supply one the residues allowed are those in your sequence file.

Possible Problems

Specific limitations and problems:

Literature

Additional information