[phenixbb] phenix.refine: How to define links and bond distances

Pavel Afonine pafonine at lbl.gov
Tue Apr 3 04:29:18 PDT 2007

Hi Matthew,

elbow.builder creates a cif file that defines the geometry (bonds, 
angles, ...). If you are not happy with the values defined in that file, 
you can manually edit it. Also, you can specify a covalent bond between 
two selected atoms (for example, bond between a protein and a ligand); 
see "Definition of custom bonds" paragraph in the Documentation 


Matthew Bowler wrote:
> Dear All,
> 	I have been trying to find the utility in elbow_builder to define  
> bond distances and link distances with no luck, the .py file has bond  
> order information for my ligand but nothing regarding distances etc,  
> can anyone help?	
>    Thanks in advance, yours, Matt.
> Matthew Bowler
> MRC Dunn Human Nutrition Unit
> Wellcome Trust / MRC Building
> Hills Road
> Cambridge CB2 2XY
> Tel: 0044 (0) 1223 252826
> Fax: 0044 (0) 1223 252825
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