[PyMOL] PyMOL, hydrogen bonds and PQR files with H-atoms

[Fotis B. <fot...@gm...>]

Dear PyMOL Users,

I am writing a python script that utilizes the "cmd.find_pairs" and
"cmd.distance" functions of the PyMOL API, in order to identify hydrogen
bonds in a PQR file and calculate their properties.
Since crystal structures rarely contain hydrogens, PyMOL guesses the
position of hydrogen atoms for the identification of H-bonds (i.e.
calculation of the D-H-A angle in find_pairs), with a process similar to
the DSSP algorithm. However, my PQR files, generated by PDB2PQR, have their
own hydrogen atoms. In cases such as this, does PyMOL use the H-atoms in
the PQR file for the calculations, or does it sitll guess the position of
H-atoms with its internal algorithm?

Thank you in advance,
Fotis Baltoumas