Hello,
If both models are chosen in the bottom of the File... Save dialog, and you choose File type PDB, then it does save both of them in a single PDB file.  However, they are still in separate MODEL parts of the PDB file and maybe whatever you are using to convert PDB -> xyz only looks at the first MODEL.

So instead of just saving your two models to PDB, you may need to first combine these two models into a single model.  You can do it with the "combine" command,
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html>

...e.g. if your models are #1,2:

combine #1,2 model #3 name combined

...then in the File... Save dialog to save the PDB file, choose only the new model #3 "combined" to save to the file.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                      
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 18, 2024, at 3:45 AM, GOTZONE BARANDIKA via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Dear developers,
> I am a new user of ChimeraX.
> I need to create dimers in order to analyse adsorbate-adsorbant interactions for DFT calculation.
> I am able to create the image on the screen, but I don´t know how to save the atomic coordinates of the dimer in a single file. If I save a .pdb file in order to produce a .xyz file, just  the information of one of the entities is kept. Can you please  help me?
> 
> <image003.jpg>
> Best regards,
> 
> 
> <image004.png>