I have attempted several times to start a new FARFAR2 run that uses one or two template PDBs for homology modeling. This seems to work well with default settings, but I need to supply data in the "Residues for 'extra' minimization" text field to relax the homology model near its endpoints. When I include data in this field, it causes the popup "Submitting FARFAR2 job..." to display indefinitely. I waited overnight to see if this was just slowing things down quite a bit, but no success.
In terms of syntax of the text input, I am using the chain ID with a colon, the NT range without spaces and a single hyphen in the middle of the range. For example:
I tried this with and without quotation marks per the "format as" instructions on the job submit page.
Related feature request - it would be great to have the standalone RNA_minimize application available on the Rosie server.
Thank you for your help!