I am using Rampage webserver to obtain a Ramachandran plot. However, the server does not reveal any plot just values (favored, allowed, outlier regions).
Can you recommend other similar web sites?
$\begingroup$
$\endgroup$
6
-
$\begingroup$ Hi @polonio, alot will understand a Ramachandran plot, I don't know anyone here who knows the webserver in question. Please either contact teh developer directly or generalise your question, by posing the problem such that it could be solved using an alternative approach, e.g. via R. $\endgroup$– M__ ♦May 20, 2020 at 23:43
-
$\begingroup$ I must disagree, Rampage, albeit old is the most used site for this. $\endgroup$– Matteo FerlaMay 21, 2020 at 8:52
-
$\begingroup$ Yes, Rampage seems to be not working properly atm and I can confirm that it did show plots a few years back. Mind you the quality was not great —no plotly interactive charts etc. @polonio210 Would you mind dropping the authors an email? $\endgroup$– Matteo FerlaMay 21, 2020 at 8:55
-
$\begingroup$ Thanks guys, I have seen recent publications and actually they work reflect Ramachandran Plots from Rampage. But, I do not know when they got them. $\endgroup$– polonio210May 21, 2020 at 17:50
-
$\begingroup$ @MatteoFerla Yes, I will send an e-mail to them cuz the ramachandran plots of that webserver are really proffesional. $\endgroup$– polonio210May 21, 2020 at 17:52
|
Show 1 more comment
1 Answer
$\begingroup$
$\endgroup$
2
Here is a page with several suggested methods. I agree that Rampage looks the best of the options, but it seems that it provides some suggested workflows for drawing it in R so that it is very customizable and you can probably get it to show any features you want if you're willing to customize a little.
Here is a Python tool for drawing Ramachandran plots.
answered May 21, 2020 at 23:04
-
$\begingroup$ Thanks, it certainly appears that Rampage isnt a good option right now $\endgroup$– M__ ♦May 21, 2020 at 23:13
-