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Dear James,
I am not sure I fully picture what your coordination looks like, but my
guess is that if you include distance restraints between the S-atoms
you can distinguish between a tetrahedral geometry and a square pyramid.
You could use external restraints in refmac - just make a dummy run
with prosmat to get the syntax right and copy and modify a few lines
tailored to your problem.
Best,
Tim
On 06/07/2013 10:39 AM, James Naismith wrote:
> Thanks for this other suggestions similar (see below.) My problem
> is not the distances per se, these restrain fine to 2.3A
>
> I am relatively low resolution and my problem is with just
> distance restraints I move to a square planar arrangement. I
> suspect this is a feature of the geometry restraints dominating
> refinement (c'est la vie at low res). I do not force Zn to be
> anything (the cif file just has a distance) I think.
>
> What I need to do is create another restraint someone how that
> imposes a Td geometry.
>
> What I cannot figure how to do is set this up because it involves
> 5 residues (4 cys and 1 Zn).
>
> best Jim
>
> Jim Naismith BSRC, North Haugh [log in to unmask]
>
> Google scholar is free and tracks your outputs, mine are
> http://scholar.google.co.uk/citations?hl=en&user=fLmKKQMAAAAJ
>
> ResearcherID H-3408-2012; SCOPUS_ID 7005691850
>
> http://www.researchgate.net/profile/James_Naismith/
>
> The University of St Andrews is a charity registered in Scotland :
> No SC013532k
>
>
>
>
> On 6 Jun 2013, at 16:11, Roger Rowlett <[log in to unmask]>
> wrote:
>
>> You can find instructions for restraining Zn-ligand distances
>> here:
>>
>> http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Model+Refinement&highlight=metal%20ion#Restraining_metal_ligand_distances_during_refinement_in_REFMAC
>>
>>
>>
>>
Using this method, only Zn-ligand bond distances are restrained.
REFMAC can usually find on its own certain Zn-atom linkages (I think
it can find ZN-SG bonds with Cys by itself, but the version I am using
usually misses or ZN-OD1 or ZN-OD2 bonds with Asp. This I pick up in
the .cif file generated by REFMAC and include in a library file to be
used for refinement. I have not had any issues with REFMAC altering ZN
geometry. What you describe sounds like the geometry of the ZN atom
has been defined or assumed somewhere in your approach.
>>
>> Cheers,
>>
>> _______________________________________ Roger S. Rowlett Gordon
>> & Dorothy Kline Professor Department of Chemistry Colgate
>> University 13 Oak Drive Hamilton, NY 13346
>>
>> tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935
>> email: [log in to unmask]
>>
>> On 6/6/2013 10:36 AM, James Naismith wrote:
>>> I have a structure that I am trying to finish off, I have Zn
>>> ligated by four cys residues. I use the linkR and define
>>> distances (the same link for each ZnS bond) My issue is how to
>>> stop the structure moving to a square pyramid (consistent with
>>> distance restraints) rather than a tetrahedral geometry. Can
>>> anyone help?
>>>
>>> best Jim
>>>
>>> Jim Naismith BSRC, North Haugh [log in to unmask]
>>>
>>> Google scholar is free and tracks your outputs, mine are
>>> http://scholar.google.co.uk/citations?hl=en&user=fLmKKQMAAAAJ
>>>
>>> ResearcherID H-3408-2012; SCOPUS_ID 7005691850
>>>
>>> http://www.researchgate.net/profile/James_Naismith/
>>>
>>> The University of St Andrews is a charity registered in
>>> Scotland : No SC013532k
>>
>
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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