Miao The glycans should be automatically linked and listed in the log file. You can do a quick check there. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Wed, Aug 8, 2018 at 2:28 AM Miao Gui wrote:

Dear Pavel,

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.

Hope to see you in Tsinghua!

Best wishes,

Miao

At 2018-08-08 00:46:37, "Pavel Afonine" wrote:

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