Hi,

I have problems trying to calculate the angle between two lines: one is really built as the distance between a residue atom from a protein and the centroid of a benzene ring (from a ligand), and the other is the line corresponding to the axis of the benzene ring. How could I accomplish this objective? I have read similar issues by chimera-users on the web, but I could not find enough information to complete the calculation (I could only estimate the first distance). In case of problems to clearly comprehend this particular task, please refer to the page 3, Fig 1, panel C in the attached research paper (phi angle).

PD: Is it normal that the centroid of a benzene ring is above the ring itself? Because in the process of build the first distance, I don't know whether I have to calculate the distance between the centroid and the residue atom (which I found to be shorter), or instead calculate the distance between the center itself of the plane and the residue atom (which would be a bit longer).

Thanks in advance for your time and assistance in this matter.

Best regards,