Re: [PyMOL] conversion of the small molecules from sdf to mol2

[Chris S. <sw...@ma...>]

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, pym...@li... wrote:
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>   1. conversion of the small molecules from sdf to mol2
>      (Enrico Martinez)
> 
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> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 13 Jan 2022 16:23:53 +0100
> From: Enrico Martinez <jms...@gm...>
> To: pymol-users <pym...@li...>
> Subject: [PyMOL] conversion of the small molecules from sdf to mol2
> Message-ID:
> 	<CAALQopyYfQGuLwsde74=sTB...@ma...>
> 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
> 
> 
> 
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