[Chimera-users] Determination of angles formed by distances and ring axes

[Felipe Vasquez]

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,


*Andrés Felipe Vásquez J., BSc, MSc.*
Grupo de Fisiología Molecular
Subdirección de Investigación Científica y Tecnológica
Dirección de Investigación en Salud Pública
Instituto Nacional de Salud
Avenida calle 26 No. 51-20 - Zona 6 CAN
+57 (1) 2207700 ext. 1419
Bogotá, D.C., Colombia
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