Re: [PyMOL] save format for molecule files

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

Thomas, Joel,

yes, writing to mol2 works. Thanks for the suggestion!

Xavier

Missatge de Thomas Holder <th...@th...> del dia dj., 18 de maig
2023 a les 5:38:

> 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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-- 
Xavier Fradera