Re: [ccp4bb] Establishing connecitivity...

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Establishing connecitivity...
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2007-06-11

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Date: 2007-06-11

Subject: Re: Establishing connecitivity...
From: Kim Henrick henrick {- at -} EBI {- dot -} AC {- dot -} UK
Date: 2007-06-11

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
>>
>>
>> ____________________________________________________________________________________
>> Park yourself in front of a world of choices in alternative vehicles.
>> Visit the Yahoo! Auto Green Center.
>> http://autos.yahoo.com/green_center/
>>
>

--
Kim HENRICK henrick@ebi.ac.uk ::telephone: +44 (0) 1223 494629

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Establishing connecitivity...
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2007-06-11

Next message:
Subject: Re: problems with phaser for MR
From: Roger Rowlett RRowlett {- at -} MAIL {- dot -} COLGATE {- dot -} EDU
Date: 2007-06-11