Dear Christian,
Sorry for repeating myself - consider to try MetalCoord which I wrote
about in the thread "3 alternate position of metal ion" from the last
week. It can generate restraints for metal-containing monomers.
https://github.com/Lekaveh/MetalCoordAnalysis/blob/master/tutorial/tutorial.rst
Cheers,
Martin
On 19/03/2025 12:11, Oliver Smart wrote:
Dear Tim and Christian,
The Grade Web Server and Grade2 can handle metal complexes to a
limited extent. However, loading a mol2 file of the complete
asymmetric unit from the polyoxometalate molecule is unlikely to
produce the best set of restraints to help in refinement. Grade2 data
mines the CSD, including some organometallics, but it does not have
any information from the Inorganic Crystal Structure Database (ICSD).
Grade2 was developed to handle organic drug-like molecules and can
cope with some organometallics but is unlikely to work well for
inorganics.
You are working with a derivative of ICSD 173439
https://pubs.acs.org/doi/10.1021/ja077837f
This is a complex structure that "confirms the embedding of an
adamantane-like, Ru_4 O_6 fragment by the divacant,
γ-decatungstosilicate ligand." (I had to look up divacant).
Is it sensible to treat a molecule like this as a monomer like ATP or GTP?
Might it be more productive for you to use SHELX as a refinement
program (as this was used for ICSD 173439) and talk to an inorganic
crystallographer about appropriate restraints?
Good luck with such an interesting study.
Best regards,
Oliver (lead developer for Grade2/GWS).
On Wed, 19 Mar 2025 at 08:25, Christian Buratto
<[email protected]> wrote:
Dear Tim,
Thank you for your suggestion, it worked well for me!
Best regards,
Christian
Il giorno mar 18 mar 2025 alle ore 11:56 Tim Gruene
<[email protected]> ha scritto:
On Tue, 18 Mar 2025 09:21:44 +0100
Christian Buratto <[email protected]> wrote:
> Dear CCP4 community,
> I am currently trying to determine the structure of a
> protein-polyoxometalate complex. I am using a polyoxometalate
> molecule that is a derivative of the one deposited in the
CCDC (ICSD:
> 173439). I am facing difficulties in generating a restraint
file for
> this metal-oxo molecule that can be recognized by Phenix,
both for
> ReadySet and refinement jobs. I have attempted to use ACEdrg and
> ELBOW, but all my trials have been unsuccessful. A common
error in
> refinement states that Phenix is unable to determine the
energy type
> for Ru or W atoms present in my ligand molecule. If anyone
has any
> suggestions or alternative approaches, I would greatly
appreciate
> your input! Thank you all for your time and help.
> Best regards,
> Christian
>
>
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Dear Christian,
sounds like a perfect task for the grade server,
https://grade.globalphasing.org
in combination of babel. Usually, I generate a PDB file (e.g. with
PLATON or SHELXL), then use babel to convert to mol2
obabel -o mol2 -O yourligand.mol2 yourligand.pdb
and upload the mol2-file to the grade server. This honours
your atom
naming. Make sure the PDB input file includes a residue name
(which is
easily done with SHELXL).
Cheers,
Tim
--
--
Tim Gruene
Head of the Core Facility Crystal Structure Analysis
Faculty of Chemistry
University of Vienna
Phone: +43-1-4277-70202
https://ccsa.univie.ac.at
GPG Key ID = A46BEE1A
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