Hi John, If I understand correctly and the protein and DNA are in the same model (were opened from the same file), you would need to split the structure into separate models before doing the movements, and then after moving one of them, save the model that moved relative to the model that didn't move. See the "split" command for the splitting part: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/split.html> 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 Dec 11, 2024, at 11:17 AM, John Watters via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi all,

I was wondering if anyone had any suggestions on how to rotate and translate a DNA-bound protein model one base pair at a time (essentially walking the protein down the double helix) so I can compare its interactions with another protein.

My plan was to define a vector between the center of mass of each nucleotide pair to then move the DNA-bound protein one average pitch length using the move command and rotation using the turn command one nucleotide at a time. When I try to save these new models using "save pdf_filepath.pdb models #3 relModel #1" the DNA-bound protein is still in the original position - do I need to modify the save command or move the DNA-bound protein using different commands?

Thanks for any help you can provide!

Best, John