Hello Iram,

The general workflow for Cryo-EM is described here:

https://phenix-online.org/documentation/overviews/cryo-em_index.html

It looks like you are ready to refine your model, so the tool for it is phenix.real_space_refine:

https://phenix-online.org/documentation/reference/real_space_refine.html

that also has a video tutorial.

Let us know if you have any questions.

Best regards,

Oleg Sobolev.

On Thu, Dec 12, 2024 at 5:54 PM iram aziz <iram.sbs@pu.edu.pk> wrote:

Hello All.
I got a nice 2.45 Angstrom map from cryo em data. I checked handedness, map model fitting on the chimera and opened in the coot. It looks nice. Can you please give me suggestions about the Phenix refinement steps.
Thanks
Iram
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