[phenixbb] Unwanted LINK Records

Whitley, Matthew J mjw100 at pitt.edu
Fri Jan 26 10:00:32 PST 2018

Hello all,

I am currently refining a structure using Phenix 1.13-2998.  Present in this structure is a diphosphate-containing ligand.  In the protein chain surrounding the binding site, there is an arginine side chain that points generally toward the diphosphate group, but I cannot define the specific location of the side chain because the side chain density is very poor.  The density for the ligand is unambiguous.  Upon refinement, Phenix places the Arg side chain so close to the ligand that it draws a covalent bond between the two, and the post-refinement PDB file contains a LINK record for this bond.  In reality, the two are not covalently connected, and ideally Phenix would find a conformation for this side chain that is outside of covalent bonding distance.  I have tried refining after manually moving the side-chain to a non-clashing position multiple times, but in every case the output PDB contains a LINK for a covalent bond between ligand and side chain.

My question: How can I tell Phenix NOT to allow these atoms to come with covalent bonding distance?  Is there some kind of "anti-LINK" information I can feed it that will force phenix.refine to select some other conformation for the side chain?

Thanks for your advice.


Matthew Whitley

Matthew J. Whitley, Ph.D.
Research Instructor
Department of Pharmacology & Chemical Biology
University of Pittsburgh School of Medicine
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