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This document was edited by Frank DiMaio on 5/11/2010.

Overview

Certain protocols (e.g. backrub) accept a user-specified movemap, that tells the algorithm what torsion angles and rigid-body degrees of freedom are allowed to move. For example, one may not want to move highly-conserved sidechains in modeling applications or preserve certain interactions in design applications. This document briefly describes the format used to specify these degrees of freedom.

File Formats

Each line in the movemap file identifies a jump, residue, or residue range, followed by the allowed degrees of freedom. These entities may be specified as follows:

RESIDUE r      # a single residue, 'r'
RESIDUE s t    # all residues s through t
JUMP k         # jump #k

For example:

RESIDUE 36 48 BBCHI  # set res 36-48 bb & chi movable
RESIDUE 89 NO        # set res 89 unmovable
JUMP 1 YES           # set jump 1 movable

Specifying a '*' for the residue or jump number sets the default value:

RESIDUE * CHI        # set all residues chi movable
JUMP * NO            # set all jumps unmovable

Priority:

  • The allowed movement of specific residues always take priority over the defaults.
  • If a residue appears more than once, the last appearance in the file determines the allowed movement.

Setting 'CHI' implies BB not movable, thus don't do:

RESIDUE * CHI
RESIDUE * BB

Instead:

RESIDUE * BBCHI

Notes:

  • Residues are numbered with "Rosetta numbering": the first residue is #1, resids are incremented across chains.
  • Using the default inputters, jump #1 connects chains 1 and 2, jump #2 connects chains 1 and 3, etc. However, protocols may (and often do) change these jumps or even introduce intrachain jumps. Generally one will simply want to specify only a default value for jump movement.
  • If a residue/default is not specified, the movemap default is used (this is protocol-specific)
  • If a value for a jump is not given (e.g. if one gives just "JUMP 4\n"), it defaults to movable (YES)

Sample Files

This example is from a homology modeling exercise where a DNA-binding protein is remodeled with DNA present. Residues 1-117 are the protein residues, and 118-132 and 133-147 are the two DNA chains. Jump 1 connects the protein to the DNA, while Jump 2 connects the two DNA chains.

The example below allows all protein torsions to move, while the DNA remains fixed. The rigid-body orientation of the protein with respect to the DNA is allowed to move, while the relative orientation of the two DNA chains may not change.

RESIDUE * BBCHI
RESIDUE 118 147 NO
JUMP * YES
JUMP 2 NO

See Also