[phenixbb] Phenix.refine peptide chain break

Pavel Afonine pafonine at lbl.gov
Tue Jul 26 09:38:02 PDT 2016

Hi Jason,

could you please send me PDB file or fraction of it containing the brake 
in question?


On 7/26/16 07:54, Booe, Jason M (HSC) wrote:
> Dear all,
> I am refining a structure after renumbering my chain such that there 
> is a gap in numbering (i.e. chain A ends at 350 and then starts again 
> at 1000) as this has numbering has been recommended for us to use by 
> the PDB for our fusion proteins. I'm having issues with Phenix.refine 
> not understanding that their is still a peptide bond and breaks the 
> chain and pushes the atoms away. There is no TER card between the 
> chains and I've used LINK records as well to no avail. I'm wondering 
> how to properly deal with this.
> Thanks,
> Jason

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