Day 1: Concept

DAY 1 (10.10.16):
  • Setting up the software (50min)
    • A virtual environment is provided where an up-to-date version of Rosetta software is installed.  We use "VirtualBox" from Oracle (link provided below). On their own machine, users can install the virtual machine (VM) that reads the files we created for you. The file provides a linux environment from which we will run the various tasks throughout the workshop.
  • Rosetta essentials (50 min)   click here for presentation PDF
    • What is Rosetta?  
    • Molecular mechanics force field implemented in Rosetta
    • Sampling strategies (Fragments/Rotamers/Monte Carlo)
  • Kinematics tutorial: How to build ligands into Rosetta (50 min)
    • Getting started with modeling, we will start with a simple task of creating and converting a small organic molecule from a modeling software (Avogadro) to a format that Rosetta understands.  This provides an overview of Rosetta residue parameters and atom types. 
      After making a mol2 file in Avogadro (you can also load PDB files into Avogadro), you can use the following python script to make params files for rosetta!
      wget -O leucine.mol2 http://2016.rosetta.ninja/day-1/leucine.mol2
      ~/Rosetta/main/source/scripts/python/public/molfile_to_params.py leucine.mol2 --name LEU

  • Introduction to RosettaScripts (40 min)
    • overview of XML script
    • concepts of Movers and Filters
  • Tutorial: Simple RosettaScripts (40 min)
    • prepare and minimize protein structures
Subpages (2): RosettaScripts VirtualBox
Ċ
Unknown user,
Oct 19, 2016, 12:03 PM
ć
Sergey Ovchinnikov,
Nov 2, 2016, 10:00 AM
ċ
leucine.mol2
(2k)
Sergey Ovchinnikov,
Oct 10, 2016, 1:15 PM