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 InstructorDepartment of Pharmacology & Chemical BiologyUniversity of Pittsburgh School of Medicine
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