[phenixbb] real space refinement of the model in cryo-EM map
Pavel Afonine
pafonine at lbl.gov
Wed Dec 27 08:32:40 PST 2023
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
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe:phenixbb-leave at phenix-online.org
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20231227/484f306a/attachment-0001.htm>
More information about the phenixbb
mailing list