Have you tried the save command after opening both files?
https://pymol.org/dokuwiki/doku.php?id=command:save
Though not sure how the different poses will merge.
Also looking for a solution for a similar problem.

------------------------------

*Saurabh Gayali* / Post Doctoral Fellow
saurabh.gay...@gmail.com / +91 8800412916

*CSIR-IGIB*
<http://example.com/>New Delhi, India


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07/01/22,
05:43:49 pm

On Fri, Jan 7, 2022 at 3:43 PM Enrico Martinez <jmsstarli...@gmail.com>
wrote:

> Dear Autodock Users!
> I am dealing with the structural analysis of the protein-ligand
> interactions observed in the protein-ligand docking using VINA.
> Basically operating with the outputs I have two different pdb files:
> 1) for docking receptor (1 protein model) as well as for 2) docking
> sollutions (100 solutions). So I use pymol to open the both filles and
> visualize them
>
> pymol sollutions.pdb receptor.pdb
>
> May you suggest me some pymol command to merge the both in the pymol
> to. create multi-model PDB consisted of the both receptor and ligand
> poses in order then I could perform some structural analysis of this
> combined complex?
> Many thanks in advance
> Enrico
>
>
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