Hello! I have knowledge of the residues that are interacting between proteins (say Protein A and Protein B, and I know that, for example, residue 5 from protein A is interacting with residue 11 from protein B, etc.) and I was wondering: Is there a Pymol function that would allow me to input these residue interacting pairs and for Pymol to show me how the structure of the protein complex looks like (maybe by orienting the proteins appropriately so the predicted contact regions are close and/or by showing me lines connecting the interacting residues)?
As a second question, if I have Protein A and I know that the residues X, Y, ... are interacting with residues from Protein B with some strengths S_X, S_Y, ..., (so that S_X is associated to residue X, etc.), is there a way for Pymol to allow me to color these residues in a gradient based on the values of the strength (maybe like the larger the strength, the darker it is)?