[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
(http://www.phenix-online.org/download/cci_apps/).
Pavel.
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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