[phenixbb] Ringer

Pavel Afonine pafonine at lbl.gov
Sun Nov 9 19:22:38 PST 2014

Hi Ivan,

as Nat mentioned, Ringer in whatever its incarnation is not 
comprehensively supported in Phenix.

Could you please explain in plain language what is the problem that your 
are trying to solve and what you expect as the outcome?

We may have tools already available in Phenix to address it or we may 
have components that are part of Phenix and that we can quickly put 
together to create a tool to do exactly what you want, even specifically 
tailored to your task! Let's talk and see what can be done.

All the best,

On 11/9/14 7:27 AM, Ivan IVANOV wrote:
> Dear All,
>     I am trying to use ringer with a model I have. I followed the
> tutorial for Calmodulin and it worked very well for my protein.
> (http://bl831.als.lbl.gov/ringer/ringer/Tutorial/tutorial.htm). Now I
> have all files sigma vs chi angles for the residues I want and also the
> list of peaks identified above the sigma cutoff I selected.
>     I am struggling to analyse the outputs as it is shown on the
> calmodulin exemple.
>     I found this website
> (http://bl831.als.lbl.gov/ringer/ringer/Documentation/ringerManual.htm#Userparameters) which is explaining very briefly how to plot all different conformation vs chi angles and how to show all selected amino acid conformation in the electron density (4.4 Plotting Accessory).
>     I have to admit that this is not straigthforward for me to plot all
> outputs in a comprehensive way.
>     Does anyone of you have a script to run with ringer outputs and get
> the final figures as it is shown on both websites ??
>     Kind regards,
>   Ivan

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