Hi Rayees, It seems that the result has >99,999 atoms so if you write to PDB it will start using atom serial "numbers" with characters in them because the field can't be any wider. I'm told if you instead write mmcif from ChimeraX it will not use those weird serial numbers. 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 Oct 10, 2025, at 11:37 AM, Rayees Mattoo via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi, I have two models #1 Model1.pdb and #2 Model2.pdb having one shared polypeptide, same chain ID but different residue numbers. I wanted to combine them to make a merged_model #3. I used the following combine commandline in chimeraX:

combine #1 #2 close false modelId #3 retainIds true name merged_model

The resulting combined model appeared to be correct, and I proceeded to run phenix.real_space_refine without any issues. However, when I attempted to deposit the refined model (either in .pdb or .cif format) with the wwPDB, I received a file with multiple errors (see attached). Interestingly, I had previously deposited the individual models (#1 and #2) without any problems. This situation raises my concern about whether the combination process was successful. Is there anything I should have done differently to ensure a seamless combination of the models?

Best Rayees<Screenshot 2025-10-10 at 11.27.25 AM.png>