[phenixbb] Ringer

Ivan IVANOV ivanov at embl.fr
Sun Nov 9 07:27:42 PST 2014

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 Ivanov, PhD
PostDoctoral fellow at EMBL, European Molecular Biology Laboratory,
Structural biology of RNA-protein complexes, Dr. Stephen Cusack,
71, avenue des Martyrs CS 90181
38042 Grenoble Cedex 9
T: +33 (0)4 76 20 7630
T(lab): +33 (0)4 76 20 7014
Email: ivanov at embl.fr
Url: http://www.embl.fr

More information about the phenixbb mailing list