[phenixbb] Defining an Intermolecular link

Ralf W. Grosse-Kunstleve rwgk at yahoo.com
Wed Jan 19 11:13:04 PST 2011

Hi Ryan,

Probably the easiest way to deal with your situation is to use the
"custom bond" feature described in the phenix.refine documentation:


See also the FAQ on pages 3 and 4 of the newsletter that just came out:


I suggest you inspect the .geo file written by phenix.refine to
verify that the geometry restraints are processed correctly.


----- Original Message ----
> From: Ryan Timothy Vanderlinden <r.vanderlinden at biochem.utah.edu>
> To: "phenixbb at phenix-online.org" <phenixbb at phenix-online.org>
> Sent: Wed, January 19, 2011 9:26:25 AM
> Subject: [phenixbb] Defining an Intermolecular link
> Hi,
> I am working on a complex of three molecules in which, I believe,  there is a 
>covalent bond between the sulfur atom of a cysteine on molecule "A"  and the 
>c-terminal carbon of molecule "C". There are other structures deposited  that 
>have a similar linkage. I have looked at these structures and included a  
>replica description of the supposed link in my input pdb file for refinement. I  
>have redefined this c-terminal residue as a ligand and used phenix elbow do  
>create a .cif file for it. Even when I use the modified pdb file that describes  
>the linkage and the cif file that describes the ligand, the intermolecular link  
>falls apart and the ligand (c-terminal amino acid) separates from the rest of  
>the chain. The resulting mtz file still shows density (2Fo-Fc) supporting the  
>link but the ligand is not in the density. The fact that the ligand moves away  
>from where I would expect it is evidence that modeling the intermolecular  
>linkage is really incorrect or I have not included all the proper files to  
>define this linkage and hold it together during refinement. What are all the  
>necessary files required hold an intermolecular linkage of this nature together  
>during refinement? Are there certain commands that I might be leaving out from  
>my refine script that are necessary to recognize such linkages?
> Thanks in  advance, 
> Ryan VanderLinden
> University of  Utah
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