by Elizabeth Swanberg | Jan 2, 2019 | General Tools, Tools
WHAT IS THE SEQUENCE LOGO? The Sequence Logo is a tool that summarizes the residue(s) at each position across the sequence(s) that has been selected. It is especially useful when beginning to analyze sequences from design results. HOW TO ACCESS THE SEQUENCE LOGO To...
by Elizabeth Swanberg | Jan 2, 2019 | General Tools, Tools
1.) To enter scatter plot view, navigate to a collection with multiple structures and click at the bottom-right as shown below, and select 2.) Once in scatter plot view, you can choose which score terms to plot on the X and Y axes. 3.) You can select the points...
by Elizabeth Swanberg | Jan 2, 2019 | General Tools, Tools
You can now compare structures and sequences between any two (or more) collections directly in CAD. Previously this was not possible and required download of sequences and/or structures for viewing in other software. The Compare feature is available when a tab is open...
by Elizabeth Swanberg | Jan 2, 2019 | General Tools, Tools
Superpose is a feature that positions multiple structures on top of one another, based on a specified region of sequence that is shared among the different structures. The Superpose feature is useful for aligning and comparing multiple structures in the Structure...
by Elizabeth Swanberg | Jan 2, 2019 | General Tools
The Structure Viewer allows selected structures to be displayed where they will be presented in the bottom half of the center window as shown below. To display a structure protein click to the left of the structure name. If your protein does not appear, check that...
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 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 | 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...
