Re: [PyMOL] save format for molecule files

[Thomas H. <th...@th...>]

Hi Xavier,

The best option to transfer bond orders from PyMOL to Maestro might be
with .mol2 (or .sdf) format. These formats can store aromatic bond
orders and Maestro will convert that to meaningful double/single bonds
when loading the file.

- .pdb format can't store aromatic bonds (and double bonds only with
an unofficial trick)
- .mae format can't store aromatic bonds
- Maestro doesn't have aromatic bond orders
- PyMOL has limited capabilities for detecting bond orders and can't
convert aromatic bonds to single/double bonds (kekulization)
- .sdf format doesn't have protein and residue level information, but .mol2 does

Cheers,
  Thomas

On Wed, May 17, 2023 at 4:51 PM Xavier Fradera <xav...@gm...> wrote:
>
> 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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