I'm new to structure visualization and I'm trying to process a large collection of structures and visualize regions of evolutionary relatedness. I have marked pairs of residues on the structures and I'm trying to find a way of orienting the camera to provide 'the best view' of the selected residues before generating the images.
While I don't know what the general way to define the 'best view' of a region of interest in a protein structure I'm guessing it mostly has to do with choosing a camera position which has the least number of uninteresting residues blocking the marked ones.
Does anyone know of a, preferably pymol script, or tool that can determine an optimal viewing position. I have ~1500 structures that I need to visualize so its impracticable to do this by hand. I can probably write something in python but it would be easier if there was already something out there.