by Elizabeth Swanberg | Dec 21, 2018 | General Tools, Tools
OVERVIEW Loading a structure file into Bench is a two step process. Step One: Select which components of the structure file you wish to be included. Step Two: Bench processes the file contents to define all molecules in a way that allows Rosetta to understand the...
by Elizabeth Swanberg | Dec 20, 2018 | Introductory Workflows, Workflows
There are three design methods that you can run in CAD: Design, Flex Design, and Relax Design. They are all set up in the same way using the following steps… 1.) LOAD A STRUCTURE Click on , which will open a new tab in the center window. Load a structure into...
by Elizabeth Swanberg | Dec 18, 2018 | Actions, Tools
INTRODUCTION Many design tools have been developed by Rosetta labs and the three most refined methods have been incorporated into Cyrus CAD for easy use. These tools (Design, Flex Design, and Relax Design ) have been well-tested in the Rosetta labs where they were...
by Elizabeth Swanberg | Dec 16, 2018 | General Tools, Tools
Create a New Selector Edit an Existing Selector Apply a Selector Delete a Selector Rename a Selector How to Create a New Selector: Load a structure into CAD Click the residue(s) that you wish to select NOTE: Command is equivalent to Control on Windows Command (⌘) +...
by Elizabeth Swanberg | Dec 16, 2018 | Actions, Tools
Relax is one of the most used Rosetta methods for sampling conformational changes in a protein. It is more aggressive than Minimize, so it tries out orientations that are up to a few angstroms away from the starting structure. RUNNING RELAX Select the folder that...
by Elizabeth Swanberg | Dec 16, 2018 | Actions, Tools
Minimize is a quick way to find the optimal conformation of your protein in the near vicinity of the structure’s current orientation. This will find the local energetic minima, but not the global minima. It is often used as a last step during structure optimization....
by Elizabeth Swanberg | Dec 16, 2018 | Rosetta
Overview An Energy Function is one of the most important tools for modeling a molecular structure. It provides a way to determine if a structure is favorable compared to alternate conformations of the structure. For example, a hexose molecule molecule can form the 5...
by Elizabeth Swanberg | Dec 16, 2018 | General Tools, Tools
Click on , which will open a new tab in the center window. Load a structure into CAD by either entering the PDB number into the space , then clicking the plus OR by clicking to load a structure from your computer. Loaded files will be listed in the order they are...
by Elizabeth Swanberg | Dec 16, 2018 | Actions, Tools
OVERVIEW Repack will sample side chain orientations while keeping the backbone fixed in order to find an energetic minima. Running Repack will affect the entire protein. This can be individually by clicking Repack, but is also done during all other Actions that...
by Elizabeth Swanberg | Dec 16, 2018 | Actions, Tools
Prepare runs the Relax protocol, which aggressively minimizes backbone and side chain, while placing very tight constraints on every heavy (non-hydrogen) atom to keep the structure very close to the original crystal structure. So this is more restrained that a normal...
