ELMDOCK

For two domains (A and B), ELMDOCK determines the best-fit fully anisotropic diffusion tensors for each domain using (a) the provided relaxation data file and (b) PDB file. An angle and distance optimization procedure is invoked to determine the best domain/domain relative orientation and interdomain distance.

Important: ELMDOCK option only becomes available if PDB file contains multiple chains (e.g. A and B).

Temperature Setting

This is a parameter that needs to be optimized according to output. Changing the temperature does not affect the relative domain/domain orientations, but only the positioning of the two domains relative to each other. My personal experience has shown that the default setting of 298 K results in significant overlap of the two domains.

PDB output

Docked structures are outputted as a PDB file; the PDB file is ordered such that the 'lowest energy' structures are presented first.

Axes output

This option writes the axes of anisotropic diffusion tensors for the individual domains in each docked structure. The axes are outputted as CGO objects in Pymol scripts. The axes can be plotted onto structures loaded in Pymol by executing the 'run' command followed by the axes script file.