Thomas, Joel, yes, writing to mol2 works. Thanks for the suggestion!
Xavier Missatge de Thomas Holder <tho...@thomas-holder.de> 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 <xavier.frad...@gmail.com> > 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 > > _______________________________________________ > > PyMOL-users mailing list > > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > -- Xavier Fradera
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