[phenixbb] Missing sanity check of duplicate resids within one chain?

Nathaniel Echols nechols at lbl.gov
Tue Aug 26 17:43:57 PDT 2014

On Tue, Aug 26, 2014 at 2:51 PM, Schubert, Carsten [JRDUS] <
CSCHUBER at its.jnj.com> wrote:

>  Phenix (1.9-1692) seemingly happily accepted the input and proceeded
> with refinement and validation. After upgrading my coot installation to the
> latest build the error was flagged.  I think this sort of mistake should
> have at least been flagged in the validation stage or is this out of scope
> for phenix?

As Dale notes, this is technically allowed by the PDB format - however, we
do already look out for it:

nat at laptop> phenix.pdb.hierarchy carsten.pdb
. . .
  ### WARNING: consecutive residue_groups with same resid ###
  number of consecutive residue groups with same resid: 1
    residue group:
      "HETATM 9327 CL    CL S   3 .*.    Cl1-"
    next residue group:
      "HETATM 9328  K     K S   3 .*.     K1+"

We could certainly present this warning elsewhere - the question is where
would it be most likely to be noticed?

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