[phenixbb] Unwanted LINK Records

Nigel Moriarty nwmoriarty at lbl.gov
Fri Jan 26 10:34:35 PST 2018


There is an "anti-LINK". Use the phil scope below. Make sure you send the
mode file to Pavel and me so we can confirm that it works for you.

  exclude_from_automatic_linking {

    selection_1 = None

    selection_2 = None




Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Fri, Jan 26, 2018 at 10:00 AM, Whitley, Matthew J <mjw100 at pitt.edu>

> 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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