[phenixbb] geometry weight and rmsd bonds - angles

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Thu Aug 12 08:18:22 PDT 2010

Hi Lionel,

> Indeed some bond length or angle restraint outliers are from the ligand when
> refining with phenix.
> However I don't think this is the problem, I give to refmac and phenix the
> same ligand dictionary (cif file from ProDRG with link definition added with
> JLigand).

refmac and phenix.refine handle links differently. Could you send me
your pdb file, the .cif file, and your phenix.refine parameter file
(to me directly, not the bb)?


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