Andrzej Send me (off-line) the model PDB file and CIF file from eLBOW. Nigel On Mon, Dec 19, 2011 at 3:56 AM, AFL wrote:

Hi,

 I'm facing an extremely annoying 'problem' when refining structures with ligands.

 When I try to refine a structure with a ligand inserted in coot from what I believe is refmac dictionary I'm getting following error:  Number of atoms with unknown nonbonded energy type symbols: 13    "HETATM 3279  OG2 FLC B   1 .*.     O  "    "HETATM 3280  CGC FLC B   1 .*.     C  "    "HETATM 3281  OG1 FLC B   1 .*.     O  "    "HETATM 3282  CG  FLC B   1 .*.     C  "    "HETATM 3283  CB  FLC B   1 .*.     C  "    "HETATM 3284  OHB FLC B   1 .*.     O  "    "HETATM 3285  CBC FLC B   1 .*.     C  "    "HETATM 3286  OB2 FLC B   1 .*.     O  "    "HETATM 3287  OB1 FLC B   1 .*.     O  "    "HETATM 3288  CA  FLC B   1 .*.     C  "    ... (remaining 3 not shown)

 When FLC (citrate anion) is exported via libcheck and cif file is generated with phenix.elbow everything works fine.

 Why is the phenix.refine not compatible with the refmac dictionary definitions?  Or maybe I am doing something wrong?

Cheers, Andrzej

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