Re: [ccp4bb] Establishing connecitivity...

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

Previous message:
Subject: microscope
From: Frank Lee crystallize2004 {- at -} YAHOO {- dot -} COM
Date: 2007-06-11

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

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

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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CCP4bb navigation

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

Previous message:
Subject: microscope
From: Frank Lee crystallize2004 {- at -} YAHOO {- dot -} COM
Date: 2007-06-11

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