2
$\begingroup$

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?

$\endgroup$
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 '20 at 23:43
  • $\begingroup$ I must disagree, Rampage, albeit old is the most used site for this. $\endgroup$ May 21 '20 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? $\endgroup$ May 21 '20 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. $\endgroup$
    – polonio210
    May 21 '20 at 17:50
  • $\begingroup$ @MatteoFerla Yes, I will send an e-mail to them cuz the ramachandran plots of that webserver are really proffesional. $\endgroup$
    – polonio210
    May 21 '20 at 17:52
4
$\begingroup$

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.

There are additionally several other servers/tools.

$\endgroup$
2
  • $\begingroup$ Thanks, it certainly appears that Rampage isnt a good option right now $\endgroup$
    – M__
    May 21 '20 at 23:13
  • $\begingroup$ Thanks, I will try using Rstudio then. $\endgroup$
    – polonio210
    May 23 '20 at 20:22

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.