That is very very peculiar!
as far as I know REFMAC doesnt really care whether you call something
ATOM or HETATM .
I suspect the problem is either in the cif file describing the co-factor
- could the atom type fpr MO be set as N? or possibly in the PDB file -
is the Atom name displaced to the left, and is the atom type (last
columns) set to MO?
Eleanor
James Pauff wrote:
> Good morning/day/evening all,
>
> I have a structure that is refined, with the exception
> of the molybdenum (MoOOS) cofactors (there are two of
> them), which are square pyramidal and coordinated to 2
> sulfurs in an enedithiolate of a pterin ring. I have
> brought up my issues with refining this before in
> REFMAC, but something just dawned on me as I work
> through/with it.
>
> Although I define the Mo, O1, O2, S atoms as ATOM
> records in the PDB, with restrained refinement in
> REFMAC, the resulting *_refmac1.pdb file converts the
> MO to a N. If I define the 4 atoms above as HETATM
> records, the same happens with the output PDB,
> changing all 4 atoms back to ATOM records and
> redefining the MO as N.
>
> I am also still getting problems with the connectivity
> of the atoms in the coordination sphere of the
> molybdenum, but that may be a side issue to this
> confusing problem with the record lines in my output
> PDBs here.
>
> Thank you,
> Jim
>
>
>
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