[PyMOL] save format for molecule files

[Xavier F. <xav...@gm...>]

Hi,

I'm trying to save some molecule files (protein+ligand complex) from pymol
to a format that is readable by maestro. I've tried saving in .mae or .pdb
format, but bond orders in ligands are lost (all bonds are single). I've
played with the "PDB options" in the save command and managed to get double
bonds right, but the aromatic ones are ignored.

Does anyone know how to write files that can be read properly by maestro?

Alternatively, is there a way to convert aromatic bonds into alternating
single/double bonds, as I think this would be easier to output based on my
tests?

thanks,
Xavier

-- 
Xavier Fradera