[phenixbb] phenix.refine and ligands

AFL alnyds at gmail.com
Mon Dec 19 03:56:24 PST 2011


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

-- 
  alnyds at gmail.com 		e-mail


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