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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>
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Kim HENRICK [log in to unmask] ::telephone: +44 (0) 1223 494629
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