Your ligand may well be MTQ or MTV whcih already
exists in the PDB
(MOLYBDOPTERIN-S,S)-DIOXO-THIO-MOLYBDENUM(V)
S
/ \
this has the peterin Mo(S)(O2)
\ /
S
you can download the dictionary connectivity from
either MSDchem (http://www.ebi.ac.uk/msd-srv/msdchem/)
or
the wwPDB remediation site
http://remediation.wwpdb.org/downloads.html
both contain the model coordinates and correct
connectivity
I am not sure why there are 2 variants
MSS, MTQ, MTV, PCD are related ligands with diff numbers
of S & O to the Mo
kim
On Mon, 11 Jun 2007, William Scott wrote:
I think you can do what you want using elbow.builder in phenix with a
smiles string.
You can use something like this to make the cofactor:
http://www.molinspiration.com/cgi-bin/properties
Then use elbow.builder to make the pdb and cif files, and do your
refinements in phenix.
It may be possible to script all that from within coot, but probably is
not worth the effort.
James Pauff wrote:
Hello again all,
We have a molybdopterin active site cofactor. It is a
single molybdenum atom, with 2 oxygens and 1 sulfur as
ligands, and coordinated to a pterin ring via 2 more
sulfur atoms. The geometry of the molybdenum is very
roughly square pyramidal.
The issue that we are having involves the connectivity
of the cofactor. The refinement wants to connect the
sulfur ligand to the oxygen ligands, in addition to
their respective connections to the molybdenum, and it
wants only a single sulfur off the pterin ring
connected, not to the molybdenum, but to the sulfur
ligand. I have tried playing with the pdb file, but I
am basically just unsure as to how best to get the
connectivity the way it should be. Is there a way to
do this in COOT?
Thank you.
Jim
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