[phenixbb] real space refinement of the model in cryo-EM map

[Pavel Afonine]

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


On 12/27/23 03:11, Dmitry Semchonok wrote:
> 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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