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