Generate a model by

[1] existing model in PDB

[2] creating a homology model by SWISS-MODEL

[3] creating a ab-initial model by AlphaFold

Do the flexible model fitting by [ISOLDE]

Roughly fit the secodary structures into the map

Do model fitting manually in [Coot] or automatically in [Phenix]

Repeat the model fitting until the coordinates fit the map resonably

Validate the quality of the models by using the validation tools in Phenix and the online validation service provided by wwPDB (http://www.wwpdb.org/validation/validation-reports)

Make sure the statistics, particularly the Ramachandran plot, Rotamers, R.m.s. deviations and B-factors are resonable.

Visualize the models and maps by [ChimeraX]

Create figures by [Adobe Illustrator]

Create movies by [iMovie]