In this repository one can find RosettaScripts to be used both as test and example on how to run the FoldFromLoops protocol.
With them, it can also be find a presentation to guide the tutorial.
This repository does not contain the code to run FoldFromLoops.
To run these examples, one needs the last version of the Rosetta Suite.
The most simple example, the insertion of a single motif segment into a template without binder can be found here.
To find a example that fits a particular type of problem, you can follow this table:
| binder | nobinder | |
|---|---|---|
| one segment | bo | no |
| multiple segment | bm | nm |
Different scenarios can be presented in each example type.
The NubInitioMover, that is the basis of the FFL protocol, relies on ab initio. Thus, in order to run it, fragments for the template protein must be created. Fragment files have been already created for the examples contained here, but if one would make its own runs with new templates, the vall database is needed.
The database can be build following the description in the database folder.
All scenarios can be automatically run one after the other (nstruct=2), by calling the python script:
python scenarios/run_test.py
Running the script with the print parameter
python scenarios/run_test.py print
would just print the commands that are going to be executed, and it is recommended before running the full test.
After this, a scenarios/paths.json.user will be created. In that file the path and version of your Rosetta distribution should be set up.