[phenixbb] Questions about refine glycans using PHENIX

[Nigel Moriarty]

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 : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov


On Wed, Aug 8, 2018 at 2:28 AM Miao Gui <gmhust2007 at 163.com> 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" <pafonine at lbl.gov> 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
>
>
>
>
>
>
>
>
>
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