[phenixbb] Refine a structure with a disconnected region

Pavel Afonine pafonine at lbl.gov
Thu Feb 2 06:42:16 PST 2017

Hi Yasser,

could you please send me model and data and indicate what loop you are 
talking about, then I will have a look and comment.


On 2/2/17 06:35, Yasser Almeida Hernández wrote:
> I am refining a structure at 1.9A, which contains a 7 residues 
> C-terminal region. The resolution of the map in that region is low but 
> is clear enough to define some side chains and the backbone. I build 
> this region manually in Coot. This region is disconnected from the 
> core of the protein, since the connecting loop cannot be seen in the 
> density map. After running phenix.refine (GUI) and playing with the 
> options several times, the final model of this region is always out of 
> the map, even when the R values are improved. How can I refine the 
> structure, keeping that part of the protein in its place, fitted to 
> the map?

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