This is realized by manipulating the atom_site category so that only the atoms matching the specified chain ID (auth_asym_id) are retained. All other categories are not changed so the output mmcif is inconsistent.
use --output-for-ngl to generate output mmcif for NGL viewer. In such a case, only the atom_site category is written to the mmcif file. Otherwise NGL viewer will not display the mmcif.
Only the 1st model is considered.
By default, water molecules are removed. Use --keep-water option to keep them).