Has anyone answered this?
Eleanor
hari jayaram wrote:
> Hi
>
> Am trying to build coordinated Zn+2 by CYS -SG atoms and have it
> refine properly in refmac5.5
>
> I added ZN ions in Coot at the Fo-Fc peaks. Then I defined manually
> the coordination relations in a text editor using LINK records.
> the ions were placed in the same chain that was doing the coordination.
>
> LINK ZN ZN A1001 SG CYS A 487 1555 1555 2.34
>
> I found that some of these ions refined well using refmac 5.5 and the
> resulting pdb had LINKR records in place indicating the coordinating
> interactions.
>
> For some of the Zn atoms however , the ions did refine , but coot
> still was covalently disulphide bonding the Cys to each other rather
> than coordinating the ZN and there were no LINKR records in the refmac
> refined pdb file. I know these interactions are legitimate because it
> is a known structure.Should I manually create LINKR records instead of
> LINK records after modeling in the ions?
>
> What is the correct procedure to model coordinating ions and have
> refmac treat them appropriately.
> Thanks in advance.
>
> Hari
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