[phenixbb] ligand problem in phenix.refine

Pavel Afonine pafonine at lbl.gov
Sun Mar 27 22:58:44 PDT 2011

  Hi Hailiang,

I guess to be able to run phenix.refine you need to follow phenix.refine 
style -;)
Most likely using phenix.elbow or phenix.ready_set and defining custom 
bonds and angles as described here:
should be enough to do what you want. If not, then please send me the 
inputs and tell what exactly you are trying to do, and I will send you 
back a working example.


> I want to run phenix.refine on a glycoprotein, but the sugars are not in
> the standard library. I just wonder whether there is a refmac-style syntax
> (LIBIN) in phenix.refine to include a user-written ligand library, instead
> of adding and modifying the existing phenix library.

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