Hi Pavel,

It is embarrassing that I didn't read this section at all. I was searching around in the GUI and failed to set the constraint group for occupancy, but I am able to run it correctly by command now guided by the documentation.

Thanks

On Thu, Oct 3, 2013 at 3:32 PM, Pavel Afonine <pafonine@lbl.gov> wrote:

Hi Yu,

have you already read section of phenix.refine manual that (I hope) answers your questions in details? If not - please give it a try, and if you still have questions please let me know and I will be more than happy to help.

http://phenix-online.org/documentation/refinement.htm#anch111

Pavel

On 10/3/13 12:27 PM, Zhang yu wrote:

Hi Nigel,

Another question. How do I let phenix.refine know that all atoms in my ligand should have the same occupancy for one conformation? The occupancy refinement in phenix.refine assigned different occupancies to atoms in one conformation.

Thanks

Yu