[phenixbb] how to bypass/deactivate dictionnary check for restraints in phenix.refine

Pavel Afonine pafonine at lbl.gov
Fri Feb 2 09:23:34 PST 2018

Hi Maxime,

could you please send us PDB file so that we investigate and start from 

Alternatively, you can create your own cif file for the ligand in 
question and provide it to refinement, then it will be used instead of 
the default one.


On 2/2/18 07:36, Maxime Cuypers wrote:
> Hello All,
> I am refining an unusual complex moiety in a protein xl with neutron data.
> Does anyone know if it is possible to bypass/deactivate dictionnary 
> .cif check
> i got the blocking error message "it looks like angle and bond 
> restraints are conflicting." and Phenix.refine stops.
> but really it s not conflicting: my .cif file works great in coot to 
> model the complex. it is hydrogen based, so i really need restraints 
> to get it optimal.
> any clues welcome, many thanks in advance.
> Dr. Maxime Cuypers
> Post-Doctoral Research Associate, Structural Biology
> St Jude Children s Research Hospital,
> 262 Danny Thomas Place
> Memphis, TN 38105-3678, USA

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