This isn't actually a part of Phenix - there is a re-implementation in
Phenix (mmtbx.ringer) that you are welcome to try but it is undocumented
and not really supported. If you need help with the original program, I
would try contacting Terry Lang ([email protected]), James Holton (
[email protected]), or James Fraser ([email protected]).
-Nat
On Sun, Nov 9, 2014 at 7:27 AM, Ivan IVANOV
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#Userpa...) 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
-- Ivan Ivanov, PhD PostDoctoral fellow at EMBL, European Molecular Biology Laboratory, Structural biology of RNA-protein complexes, Dr. Stephen Cusack, EMBL 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: [email protected] Url: http://www.embl.fr
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