Re: [phenixbb] Defining an Intermolecular link

Ryan There is also an alpha program elbow.ligand_linking model.pdb that may help. Nigel On Wed, Jan 19, 2011 at 11:13 AM, Ralf W. Grosse-Kunstleve wrote:

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 ----

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From: Ryan Timothy Vanderlinden To: "[email protected]" 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 _______________________________________________ phenixbb mailing  list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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