<div dir="ltr">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 (<a href="mailto:compchem1@gmail.com">compchem1@gmail.com</a>), James Holton (<a href="mailto:jmholton@lbl.gov">jmholton@lbl.gov</a>), or James Fraser (<a href="mailto:james.fraser@ucsf.edu">james.fraser@ucsf.edu</a>).<div><br></div><div>-Nat</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sun, Nov 9, 2014 at 7:27 AM, Ivan IVANOV <span dir="ltr"><<a href="mailto:ivanov@embl.fr" target="_blank">ivanov@embl.fr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear All,<br>
<br>
I am trying to use ringer with a model I have. I followed the<br>
tutorial for Calmodulin and it worked very well for my protein.<br>
(<a href="http://bl831.als.lbl.gov/ringer/ringer/Tutorial/tutorial.htm" target="_blank">http://bl831.als.lbl.gov/ringer/ringer/Tutorial/tutorial.htm</a>). Now I<br>
have all files sigma vs chi angles for the residues I want and also the<br>
list of peaks identified above the sigma cutoff I selected.<br>
I am struggling to analyse the outputs as it is shown on the<br>
calmodulin exemple.<br>
<br>
I found this website<br>
(<a href="http://bl831.als.lbl.gov/ringer/ringer/Documentation/ringerManual.htm#Userparameters" target="_blank">http://bl831.als.lbl.gov/ringer/ringer/Documentation/ringerManual.htm#Userparameters</a>) 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).<br>
I have to admit that this is not straigthforward for me to plot all<br>
outputs in a comprehensive way.<br>
Does anyone of you have a script to run with ringer outputs and get<br>
the final figures as it is shown on both websites ??<br>
<br>
Kind regards,<br>
Ivan<br>
<br>
<br>
--<br>
Ivan Ivanov, PhD<br>
PostDoctoral fellow at EMBL, European Molecular Biology Laboratory,<br>
Structural biology of RNA-protein complexes, Dr. Stephen Cusack,<br>
EMBL<br>
71, avenue des Martyrs CS 90181<br>
38042 Grenoble Cedex 9<br>
T: <a href="tel:%2B33%20%280%294%2076%2020%207630" value="+33476207630">+33 (0)4 76 20 7630</a><br>
T(lab): <a href="tel:%2B33%20%280%294%2076%2020%207014" value="+33476207014">+33 (0)4 76 20 7014</a><br>
Email: <a href="mailto:ivanov@embl.fr">ivanov@embl.fr</a><br>
Url: <a href="http://www.embl.fr" target="_blank">http://www.embl.fr</a><br>
<br>
<br>
<br>
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</blockquote></div><br></div>