On Tue, Oct 12, 2010 at 1:59 AM, Peter Grey
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 ?
There are a couple of parameters that will force PHENIX to use the segid: preserve_protein_segid=True preserve_nucleic_acid_segid=True We also encourage the use of two-character chain IDs in these situations, but of course the PDB doesn't accept these either. -Nat