Yes there is a way to do something anyway.
Is your metal only linked to protein or are there extra atoms as part of
the metal?
If there is protein lins you need to make a LINK record in your PDB and
provide a dictionary description of your expected geometry.
If you have more details I can be more specific.
On the GUI if you specify "review restraints" as your first REFMAC call
it will make an attempt to produce such a dictionary entry - you will
want to edit it, but it is a start
Eleanor
James Pauff wrote:
Good day all,
I have a metal center in my enzyme active site, in a
roughly square pyramidal coordination. I know from
EXAFS and other work how this coordination sphere
should look, but following REFMAC the cofactor here
does not end up realistically coordinated/oriented.
Although it is in the density and roughly in position,
the coordination sphere and ligands are not correct,
and not correctly connected.
Is there a means by which I can position this
cofactor, establish the connectivity I want, and then
specifically restrain this cofactor/center while
refining?
Thank you,
Jim
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