arpeggio for RNA or DNA? about arpeggio HOT 4 CLOSED

That shouldn't be a problem. If possible please can you share:

• The command used to run Arpeggio if using the command line; or otherwise the options given to the web server?
• Any error or warning messages you receive when running your failure cases

from arpeggio.

I am sharing links to web server calculations, in each case I used the default settings

• 1Q8N http://biosig.unimelb.edu.au/arpeggioweb/result/oranges-zebra-football/
• 5SWE http://biosig.unimelb.edu.au/arpeggioweb/result/william-neptune-november/
• 3EM2 http://biosig.unimelb.edu.au/arpeggioweb/result/hot-purple-oven/

from arpeggio.

Ah, I think Arpeggio is having an issue there with nucleotide-only structures. It's trying to build an internal representation of polypeptides, and failing where it can't find any.

I can look at updating the command line program but don't have guarantees on when I can be available to do this. I'd welcome any pull request with code changes to fix the issue.

Unfortunately the web server is unlikely to be updated from the original version distributed with the paper; I no longer have access to that version.

You could also try those structures with the PDBe's more active fork https://github.com/PDBeurope/arpeggio

from arpeggio.

Thank you for your prompt reply and clarification!

from arpeggio.