[phenixbb] Covalent Linker

Nigel Moriarty nwmoriarty at lbl.gov
Mon Jul 27 08:40:37 PDT 2015


Currently, the only way to check whether a bond is being made is to look in
the .geo file produced by phenix.refine. I'm guessing that you are using a
visual check in Coot after refinement to see if the ligand is bound. Coot
is using LINK records in the PDB file which phenix.refine doesn't currently
write so you can not use a visual clue to say that the bond was not formed
in refinement. Coot is a different program and creates representations of
bonds from different inputs. If you used PyMOL to view the model, the bond
may have been drawn on the screen for you because PyMOL uses the distance
between two atoms to draw a bond on the computer screen.



Nigel W. Moriarty
Building 33R0349, Physical Biosciences Division
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 Mon, Jul 27, 2015 at 8:29 AM, Courtney Daczkowski <daczkocm at gmail.com>

> We are currently trying to build a model that has a nonstandard ligand
> that is covalently bonded to two peptide chains.  We've placed the ligand
> and linked it using Coot, but phenix.refine keeps removing the links.  We
> generated the restraints using Elbow and wrote the .edits file using
> phenix.link_edits, but phenix.refine is still removing the links.  We also
> tried turning on automatic ligand linking in phenix.refine, but that didn't
> work either.  Any advice?
> Thanks.
> Courtney
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