Use of read_tps_conf is depecrated
When using legacy tools, structure files are often read in using the old call to read_tps_conf.
This routine depends on an internal conversion of the global topology to the legacy topology and reassigning of chain IDs.
But as structure files are read in as one molecule in case of them being not a TPR, all atoms are given the same chain ID during reassignment.
To avoid this causing issues with selections, the tools should not use the legacy function but one of the modern alternatives.