Editing Displacementmap (section)

== Overview ==
DisplacementMap is made for easy investigations of suitable positions for site-directed mutagenesis of amino residues into cysteines and FRET/EPR pair labelling.

A Open and Closed form of a protein should be loaded. New objects should be created for the selected asymmetric unit. Parts of the protein should be aligned, leaving the flexible part in two different positions.

The input is the objects, Open (molecule1) and Closed (molecule2). <br />
Further is the criteria for selecting which atom the distance should be calculated between. Standard is atom='CA' (atom). <br />
Then one selects the Förster distance R0 (mindist). This is the minimum distance between the residues. This depends of the selection of the FRET pair and protein at hand. But usually in the range 40 - 80 Angstrom is suitable. <br />
Then one defines the minimum displacement that is accepted. Usually R0/2 (mindelta). <br />
The script will find the 5 best (listlength=5) positive and negative distance displacement between the two objects. 

It parses the results back to Pymol, that is standard set to show it as sticks (showsticks='yes'). <br />
If one is looking for a particular residue range for the FRET pair, this can be specified with two input.
resi1=24.45-47.86 resi2=100-105.107   resi1 is "from" and resi2 is "to". Individual residues are split by a ".", and ranges are defined with "-".<br />
In the end, it makes a large data-matrix with all the distances. It also produces a gnuplot file, for easy visualisation. Just drag the .plt file for win gnuplot command window and it plots your datamatrix.