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

[Dale Tronrud]

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   The PDB file format does not require unique residue names within a
chain (and this "feature" has caused me great problems over the years
since my software does).  As an example, at one point the powers that
be at the PDB decided that inhibitors should be in the same chain as
the protein they bind to (which I have no problem with) but renamed
them all to residue "1".  Most proteins already have a residue "1" so
this caused problems for people like me.  It did not, however, violate
the format.

   Coot is flagging this as a problem when it is not a violation of
the file format.  Coot has other problems with valid PDB files.  It
seems to operate correctly for only a subset of the world of valid PDB
files.

Dale Tronrud

On 8/26/2014 2:51 PM, Schubert, Carsten [JRDUS] wrote:
> Hi,
> 
> 
> 
> this is a bit of an esoteric issue I just stumbled over, but I’d
> like to flag this up anyhow.
> 
> For some reason (most likely boneheaded error on my side) I wound
> up with duplicate resids for two ion-atoms:
> 
> 
> 
> TER
> 
> HETATM 9325 CL    CL S   1      10.578  23.153  35.662  1.00 75.71
> Cl1-
> 
> HETATM 9326 CL    CL S   2      -6.546  32.210  31.507  1.00 80.31
> Cl1-
> 
> HETATM 9327 CL    CL S   3      21.899  28.037  25.883  1.00 86.22
> Cl1-
> 
> HETATM 9328  K     K S   3       7.259  -0.149  19.530  1.00 91.09
> K1+
> 
> TER
> 
> 
> 
> 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?
> 
> 
> 
> Cheers,
> 
> 
> 
> Carsten
> 
> 
> 
> _______________________________________________ phenixbb mailing
> list phenixbb at phenix-online.org 
> http://phenix-online.org/mailman/listinfo/phenixbb
> 
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