by Elizabeth Swanberg | Jan 8, 2019 | FAQs
Currently CAD does not include a version of Repack that can be limited to a single region; Repack will always include the entire protein. However, this is on our list of features to eventually add to...
by Elizabeth Swanberg | Jan 8, 2019 | FAQs
A common question is how to pick the best Designs among the ones (already likely good energetically) that Rosetta produces. One helpful step is to look at the multiple sequence alignments of outputs and build a phylogenetic tree to understand the diversity over your...
by Elizabeth Swanberg | Jan 8, 2019 | Analyzing Results, Workflows
INTRODUCTION TO PROTEIN DESIGN RESULTS Our Design tools are often used as a way to find multiple mutations that improve Rosetta Energy. We recommend running 100 repeats of a design. Then look at the range of results to find favorable mutations. Instructions on how to...
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...
