[phenixbb] secondary structure restraints question

Nathaniel Echols nechols at lbl.gov
Tue Oct 12 02:05:28 PDT 2010

On Tue, Oct 12, 2010 at 1:59 AM, Peter Grey <petgxray at gmail.com> wrote:
> 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:


We also encourage the use of two-character chain IDs in these
situations, but of course the PDB doesn't accept these either.


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