Re: [ccp4bb] LINKR vs LINK ? procedure for modeling coordinated Zn+2

[Roger Rowlett]

Here's how we do it. (May not be the most elegant, but simple enough for my undergraduates to manage.) http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Model+Refinement#Restraining_metal_ligand_distances_during_refinement_in_REFMAC Cheers, Roger Rowlett On 5/3/2010 2:25 PM, 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 -- Roger S. Rowlett 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: rrowl...@colgate.edu