[phenixbb] Questions about refine glycans using PHENIX

Pavel Afonine pafonine at lbl.gov
Tue Aug 7 09:46:37 PDT 2018


yes, as long as the map shows the glycans clearly enough so that you can 
model them, then there is no problem refining your model using 
phenix.real_space_refine. Normally, there is no need to add anything 
Now I'm puzzled.. do you have a reason to believe that something isn't 
working correctly?

By the way, we will be at Tsinghua University first week of September 
running Phenix workshop. We can discuss things while there!

All the best,

On 8/7/18 08:16, Miao Gui wrote:
> Dear phenix developers,
> I'm a PHENIX user. PHENIX helped me a lot when refining structural 
> models against cryo-EM maps.
> Recently, I built a structural model of a glycoprotein and added the 
> glycans using COOT against a 3.4 A cryo-EM map. Then I want to refine 
> the model using PHENIX.real_space_refine. I always add the second 
> structure restrains when refining the models against cryo-EM maps. Do 
> I need to add other restrains for the glycans? Is it appropriate to 
> refine the glycoprotein using the real_space_refine?
> Thank you.
> Best wishes,
> Dr. Miao Gui
> Tsinghua University, Beijing

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