Well, when I solved a structure for a protein-rhenium adduct I had to
manually code a restraint file for the rhenium tricarbonyl fragment,
which is octahedral overall (with proteins ligands and waters), and had
several different types of bond distances for the various ligands. I
started with an incorrect description of a similar ligand cif file from
HIC-UP and hand-edited the cif file to suit. It seems to me it should be
possible (although somewhat painful) to write a similar restraint file
(geometry + bond lengths) for ZN.
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: [email protected]
On 6/7/2013 9:23 AM, Tim Gruene wrote:
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Hi Jim,
the chemical basis would be that the Zn connects to all four S atoms,
and if they are indistinguishable, all Zn-S distances should be alike.
But the S-atoms are not bonded to each other, hence they want to have as
much distance from each other as possible. Since they are four, this
makes them a tetrahedron.
I am not aware of a more automated/ simpler way of turning the angles
at the metal into restraints other than calculating the S-S distances
with a pocket calculator, although that does not mean they do not exist.
Cheers,
Tim
On 06/07/2013 11:56 AM, James Naismith wrote:
Andrew Leslie made a similar suggestion for using CB to S
distances.
Both make me unhappy for the reason that there is not a clear
chemical basis to them (Tim's has more a chemical basis) and how
would I choose the distance. (I can measure it from a known
structure)
I have previously experimented with Tim's (works). I am searching
for anyone who knew a simple way to restrain metal ion geometry in
remfac based on angles at metal.
best Jim
On 7 Jun 2013, at 10:14, Tim Gruene <[email protected]>
wrote:
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 [email protected]
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
<[email protected]> 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: [email protected]
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 [email protected]
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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