Automated Setup

The toolbox provides a dedicated set of applications

to help you with setting up the actual structure calculation runs once you have prepared your data files and completed fragment picking.

This suit of programs provides

  • easy setup of structure calculations
  • support for benchmarking of multiple targets
  • extendability to other protocols is used to bundle a set of input files and options for one protein target as a Setup. The application setup_run is used to generate all the input files (flags, score patches, scripts etc.) required to run a structure calculation with Rosetta. The applications provide support for different queuing systems and generates the appropriate job-scripts for job-submission. The application is easily extendable to support other queuing systems.
Currently, the structure calculation protocols abrelax (basic CS-Rosetta), rasrec and autoNOE are supported. The setup application is quite modular and plugins to support other structure calculation protocols can easily be written (Developer's Guide ).

The most important concepts of the setup-suite are the

  • Method A structure calculation protocol (e.g., abrelax, rasrec, autoNOE)
  • Target A protein target, characterized e.g., by its fasta-sequence, and a collection of target-specific restraint files
  • Setup A combination of Method and Target ready to generate a Run
  • Run A directory that contains flag-files and job-scripts ready to run a structure calculation