Re: [PyMOL] save format for molecule files
Thomas, Joel, yes, writing to mol2 works. Thanks for the suggestion! Xavier Missatge de Thomas Holder 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 > 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 ___ 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
Re: [PyMOL] save format for molecule files
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 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 ___ 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
Re: [PyMOL] save format for molecule files
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 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 ___ 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
[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 ___ 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
