Calculations with Restraints

This tutorial explains how to add restraints from RDC and NOE data to your abrelax CS-Rosetta[1] or RASREC CS-Rosetta[2] calculation. Please review the basic tutorials Tutorial: Standard CS-Rosetta and Tutorial: RASREC CS-Rosetta to refresh your knowledge how to set up calculations without any restraint data. Due to the length of this article it has been broken down into multiple pages, see book navigation block.

1. Preparation of Input Files:

1.1 List of Input Files

the inputs for this tutorial are the following files:

SgR145.fasta (truncated) FASTA sequence for NESG Target SgR145 backbone chemical shifts
SgR145.frags3.dat.gz fragment library with 3mer fragments
SgR145.frags9.dat.gz fragment library with 9mer fragments
SgR145.med1.rdc RDC data file
SgR145.med2.rdc RDC data file obtained in 2nd alignment medium
SgR145.manual.upl upper limit distance restraints (from NOE data) upper limit distance restraints (output from a CYANA run)

For convenience these input files are also stored in the toolbox-folder csrosetta3/tutorials/inputs. These files are all in consistent residue numbering starting with 1 for the trimmed sequence. See also Tutorial: Fragment Picking with Chemical Shift Data for trimming and renumbering. For the upl-files renumbering is not necessary anymore as the automated setup will take care of this. Nevertheless, a toolbox command still exists to carry out this task

renumber_upl -fasta SgR145.fasta

1.2 Obtaining the Input Files from Tutorial Folder

Either run this tutorial directly in the toolbox folder or link this folder into your current folder like this:

$ which setup_target   # to figure out where the csrosetta toolbox is installed on your system
/net/software/csrosetta3/com_alias/setup_target   # for instance this might be the answer 
                                                  # showing you that /net/software/csrosetta3 is the location of the toolbox
$ mkdir run_tutorials  #create a clean folder
$ cd run_tutorials       
$ ln -s /net/software/csrosetta3/tutorials/inputs

Now you can either work through this tutorial step by step, or run the provided tutorial script:

$ /net/software/csrosetta3/tutorials/ 

2. Adding Restraints to an existing Setup

2.1 Generate a basic (no-restraint data) Setup

First we setup a basic Setup (with fragments, chemical shifts and FASTA sequence) as explained in Tutorial: Standard CS-Rosetta and Tutorial: RASREC CS-Rosetta:

$ cd inputs 
$ setup_target -target SgR145 -method rasrec -fasta SgR145.fasta -frags SgR145.frags* -cs


sampling protocol: