Perhaps a beginner question. I am having problems with Rosetta changing the default chain ID (double letter) when reading and writing as mmcif. Specifically I am relaxing a long list of proteins into cryo-em density using rosetta scripts and and the resulting mmcif files written by rosetta have the "auth_asym_id" truncated from ex. "Ac" -> "c" or "Xm" to "m". Does Rosetta not support double letter chain IDs internally? Is there any solution to this problem?
Best and thank for any help,