Hi Iram,

A good place to start is to read the documentation for tools in cryo-EM:

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

We also have a couple of video tutorials on our youtube channel (https://www.youtube.com/@PhenixTutorials), for example for phenix.real_space_refine:

https://www.youtube.com/watch?v=shmBHtyUdCc

Best wishes,

Dorothee

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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Dorothee Liebschner, PhD (she/her)

Research Scientist

Molecular Biophysics and Integrated Bioimaging Division

Lawrence Berkeley National Laboratory

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Web: https://phenix-online.org