[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.


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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