[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:
https://www.phenix-online.org/documentation/refinement.htm
See also the FAQ on pages 3 and 4 of the newsletter that just came out:
http://www.phenix-online.org/newsletter/CCN_2011_01.pdf
I suggest you inspect the .geo file written by phenix.refine to
verify that the geometry restraints are processed correctly.
Ralf
----- 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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