Hi, You could try --append in openbabel to add the ID_STRUCTURE to the title of the molecule sdf?
https://openbabel.org/docs/dev/Command-line_tools/babel.html#append-property-values-to-the-title <https://openbabel.org/docs/dev/Command-line_tools/babel.html#append-property-values-to-the-title> Chris > On 14 Jan 2022, at 12:03, pymol-users-requ...@lists.sourceforge.net wrote: > > Send PyMOL-users mailing list submissions to > pymol-users@lists.sourceforge.net > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/pymol-users > or, via email, send a message with subject or body 'help' to > pymol-users-requ...@lists.sourceforge.net > > You can reach the person managing the list at > pymol-users-ow...@lists.sourceforge.net > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of PyMOL-users digest..." > > > Today's Topics: > > 1. conversion of the small molecules from sdf to mol2 > (Enrico Martinez) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 13 Jan 2022 16:23:53 +0100 > From: Enrico Martinez <jmsstarli...@gmail.com> > To: pymol-users <pymol-users@lists.sourceforge.net> > Subject: [PyMOL] conversion of the small molecules from sdf to mol2 > Message-ID: > <CAALQopyYfQGuLwsde74=stbv+_kzl2ukgv09xmvxwd1fswf...@mail.gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Dear Pymol users, dear Friends! > > I have a question regarding file conversion of the small organic > molecules, which is not directly related to pymol but I believe that I > may use it for the solution. > > I am dealing with the conversion of SDF file (2d formulas) to mol2 > format (3d coordinates) > Usually I use it in one line command with babel > obabel --gen3d -isdf ligands.sdf -omol2 > ligands.mol2 > > It creates a multi-model mol2 file, that I may open in pymol and split > the molecules manually using split_states command: > pymol ligands.mol2 > cmd.split_states('ligands', 'prefix=conf') > This creates several separate objects conf0001, conf0002 etc that I > may save as the individual mol2. > Alternatively I may obtain individual mol2 filles for each model of the SDF: > obabel ./ligands.sdf -O ./babel/conf.mol2 --gen3d -m > which creates separate files conf1.mol2 , conf2.mol2 .. confN.mol2 > that I may load in pymol in one command from terminal > pymol ./babel/conf*.mol2 > > The problem that the name of the initial model stored in the initial sdf, as: > <ID_STRUCTURE> > name_of_the_ligand > > always lost during conversion from sdf to mol2 (regardless of the way > of the conversion). So the mol2 files always lack their initials > defined from sdf :-) > > Could you suggest some trick to associate the name of the model (From > initial sdf) to the corresponding object loaded in pymol or > alternatively keep them during the conversion? > Many thanks in advance! > Enrico > > > > ------------------------------ > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > ------------------------------ > > End of PyMOL-users Digest, Vol 188, Issue 11 > ********************************************
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