Hi Sasha, If you already have PDB file with multiple models, you can open it with "coordsets false" to make separate submodels, e.g. open /Users/meng/Desktop/my-multimodel.pdb coordsets false ... or for an example that is already in the PDB database ... open 1plx coordsets false <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#local> Then you can use the "save" comand with a filename that includes "[ID]" to save multiple files with the different numbers in their names, e.g. save /Users/meng/Desktop/my-trajectory[ID].pdb format pdb models #1 This is explained in the "save" help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> 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 Jul 30, 2025, at 2:19 AM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi All, I have a trajectory (xtc) from which I can read selected frames into ChimeraX. I can then write all frames as one pdb with many submodels. But I am not able to find out how to open the frames as separate models, or save the trajectory as separate models. I will appreciate your help. Best Sasha Zahradnikova