[phenixbb] Interpreting Cd atoms

James Fraser jamesfraser at berkeley.edu
Sun Apr 15 20:08:05 PDT 2007


Hello,

I'm trying to refine a structure with Cadmium bound.  Is there a
standard way to define "energy type symbols"?

Thanks,

James


Number of atoms with unknown nonbonded energy type symbols: 14
    "CD    CD D   1 "
    "CD    CD D   2 "
    "CD    CD D   3 "
    "CD    CD D   4 "
    "CD    CD D   5 "
    "CD    CD D   6 "
    "CD    CD D   7 "
    "CD    CD D   8 "
    "CD    CD D   9 "
    "CD    CD D  10 "
    ... (remaining 4 not shown)
  Time building chain proxies: 2.36, per 1000 atoms: 1.27

Sorry: Fatal problems interpreting PDB file:
  Number of atoms with unknown nonbonded energy type symbols: 14
  Please edit the PDB file to resolve the problems and/or supply a
  CIF file with matching restraint definitions. Note that
  elbow.builder is available to create restraint definitions.



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