Thank you very much for your reply.
Actually, the models as well as the glycans look quite good after PHENIX real-space refinement. I just want to make sure that this is the right way since it's my first time to refine a glycan.
Hi,
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
special.
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,
Pavel
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