[phenixbb] phenix refine

sbiswas2 at ncsu.edu sbiswas2 at ncsu.edu
Thu Jun 11 08:56:52 PDT 2009


Hi all,
I tried running phenix refine with a pdb file refined in cns. This has a
glycerol molecule in it. I got the following message:
Number of atoms with unknown nonbonded energy type symbols: 42
    "ATOM   6921  OAA GLC J   1 .*.J       "
    "ATOM   6922  CAD GLC J   1 .*.J       "
    "ATOM   6923  CAF GLC J   1 .*.J       "
    "ATOM   6924  OAC GLC J   1 .*.J       "
    "ATOM   6925  CAE GLC J   1 .*.J       "
    "ATOM   6926  OAB GLC J   1 .*.J       "
    "ATOM   6927  OAA GLC J   2 .*.J       "
    "ATOM   6928  CAD GLC J   2 .*.J       "
    "ATOM   6929  CAF GLC J   2 .*.J       "
    "ATOM   6930  OAC GLC J   2 .*.J       "
    ... (remaining 32 not shown)
  Time building chain proxies: 11.79, per 1000 atoms: 1.69

Sorry: Fatal problems interpreting PDB file:
  Number of atoms with unknown scattering type symbols: 42
  Number of atoms with unknown nonbonded energy type symbols: 42

Does anyone know how to resolve this
thanks,
Shya



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