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
