nechols at lbl.gov
Sun Nov 9 17:32:33 PST 2014
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 (compchem1 at gmail.com), James Holton (
jmholton at lbl.gov), or James Fraser (james.fraser at ucsf.edu).
On Sun, Nov 9, 2014 at 7:27 AM, Ivan IVANOV <ivanov at embl.fr> 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
> 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
> phenixbb mailing list
> phenixbb at phenix-online.org
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