[phenixbb] Unwanted LINK Records

Pavel Afonine pafonine at lbl.gov
Fri Jan 26 10:07:26 PST 2018

Hi Matthew,

could you please send me PDB file before and after refinement (please 
make sure not to send files to the entire phenixbb) and the data file? 
I'd like to reproduce and investigate this. Then I'll see what's best to 
do in this case..


On 1/26/18 10:00, Whitley, Matthew J wrote:
> 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.
> Sincerely,
> Matthew Whitley
> ---
> Matthew J. Whitley, Ph.D.
> Research Instructor
> Department of Pharmacology & Chemical Biology
> University of Pittsburgh School of Medicine
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