Have you tried .mol2 files. I would expect Maestro to recognise that and it should include bond order etc
J ________________________________ Joel Tyndall, PhD Associate Professor in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 From: Xavier Fradera <xavier.frad...@gmail.com> Sent: Wednesday, May 17, 2023 11:54 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] save format for molecule files 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
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