[phenixbb] Persistence of CONNECT records?

Schubert, Carsten [PRDUS] CSCHUBER at prdus.jnj.com
Thu Apr 10 09:53:27 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. 



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