[phenixbb] C-C sugar linkage in real-space refinement

Kevin Jude kjude at stanford.edu
Mon Jun 14 15:47:44 PDT 2021


Thanks to Pavel and Nigel, who pointed out that the LINK records in the pdb
file are ignored by Phenix and that I must apply the links with a .phil
file in the form:

pdb_interpretation {
    apply_cif_link {
      data_link = "MAN-TRP"
      residue_selection_1 = chain C and resname MAN resid 1004
      residue_selection_2 = chain C and resname TRP resid 269
    }
}

Where MAN-TRP is the name of link description that can be prepared in
JLigand. I'm still a little confused since I've done successful
crystallographic refinements of both with and without including the
apply_cif_link instruction, but this works now.

--
Kevin Jude, PhD (he/him/his)
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431


On Mon, Jun 14, 2021 at 12:31 AM Kevin Jude <kjude at stanford.edu> wrote:

> I'm trying to refine a cryoEM structure that contains some MAN/C1-TRP/CD1
> glycosylations. I've done this successfully in crystallographic reciprocal
> space refinement, using cif files to define the MAN geometry and the
> MAN-TRP linkage, plus adding LINK instructions to the pdb file. In this
> cryoEM structure, though, using the same .cif definition files and similar
> LINK instruction, the bond is still not defined in the .geo file and
> instead it's treated as a nonbonded interaction, kicking the mannose away
> from the indole side chain. The NAG-ASN linkages in the cryoEM structure
> are fine. Do I need to do anything differently to define these linkages in
> Real Space Refine compared to phenix.refine?
>
> --
> Kevin Jude, PhD (he/him/his)
> Structural Biology Research Specialist, Garcia Lab
> Howard Hughes Medical Institute
> Stanford University School of Medicine
> Beckman B177, 279 Campus Drive, Stanford CA 94305
> Phone: (650) 723-6431
>
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