[phenixbb] C-C sugar linkage in real-space refinement
Pavel Afonine
pafonine at lbl.gov
Mon Jun 14 00:40:31 PDT 2021
Hi Kevin,
whatever worked ok with phenix.refine is also expected to work with
phenix.real_space_refine in exact same manner. If this is not the case
please send us input files and tell what atoms misbehave.
Thanks!
Pavel
On 6/14/21 00:31, Kevin Jude 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?
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