This document was edited by Frank DiMaio on 5/11/2010.
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.
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
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
Setting 'CHI' implies BB not movable, thus don't do:
RESIDUE * CHI RESIDUE * BB
RESIDUE * BBCHI
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