[phenixbb] Short contact with symmetry mate

Pavel Afonine pafonine at lbl.gov
Wed Jul 22 18:01:38 PDT 2015

Hi Ashok,

you need to define that bond manually. This can be done using custom 
bonds machinery that is documented here:


If you have problems or questions please let me know.


On 7/19/15 06:48, Ashok Nayak wrote:
> Dear Phenix BB,
> I am refining a helical bundle structure where I have been obtaining 
> an invariant short contact (close to 2A) at a Glu residue with Lys of 
> symmetry related molecule of one helix of the bundle. I had been using 
> Rigid body, TLS, occupancy and Indv ADP for the refinement (which gave 
> the best Rfree values). If I include coordinate refinement the short 
> contact seems to be gone rather with higher Rfree values. I ll 
> appreciate some suggestions regarding this.
> Thank you in advance.
> Ashok Nayak
> Lucknow, India
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