Dear Phenix community,

I have a very large model with many chains (due to NCS and complexity of model) where chain-id is not unique (e.g. there are several chain A) but segid is. All atom selections (for rigid body refinement, ncs restraints, tls etc...) are defined by segid.
When I look at the output of phenix.secondary_structure_restraints I see that these restraints are defined by chain-id and residue number.
Does this mean I must have unique chain-id names to correctly apply these secondary structure restraints or am I missing something ?

Thank you for your time,

Peter