[phenixbb] Persistence of CONNECT records?

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Thu Apr 10 10:48:15 PDT 2008

> I noticed that the CONNECT records of ligands generated in elbow
> get deleted in phenix.refine. Even specifing both the protein and
> ligand file (with CONNECT records) in the .def files, does not retain
> these records. For us they are coming in handy since they specify the
> bond order of the ligands. This is important for display in PyMol,
> which assigns bond orders based on these records.
> Would it be possible to keep the CONNECT records in the output file
> of phenix.refine? Obviously the numbering would need to be adjusted
> and I have not yet checked if some of the model building programs
> like coot would be able to handle this situation correctly.

Yes, that's exactly why maintaining the CONECT records is a real
project. As an aside, the PyMOL trick of repeating records to convey
the bond order isn't used anywhere else as far as I know (but I like
the idea).
I'm in the middle of re-doing the fundamentals of how phenix.refine
handles pdb files. Once that's settled we will review how much effort
it would take to maintain CONECT records.


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