Hi Dmitry,

would you mind sharing the Rama-Z number you get as well as the Ramachandran plot (General) that you can quickly get using this command:

phenix.ramalyze plot=True show_labels=False markerfacecolor=yellow markeredgecolor=red model.pdb

That'll give a better starting point to offer suggestions.

Thanks!
Pavel

Dear colleagues, 

Does anyone know how to improve the Ramachandran plot Z score (Rama-Z)? 

Ours seems to be too good (low) 🙂 

Is there any cure in Phenix for that?

Maybe changing certain parameters/restraints can aid?

Thank you.

Kind regards,

Dmitry

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