Improvements to structure loader

In the top left panel you will see ‘New structure’ has been replaced with ‘Structure Loader’. Clicking this button will take you to a structure loader tab, where you can now upload files while continuing to work on your project in other tabs. Simply enter all RCSB codes for structures you’d like uploaded, separated with commas, and click the button to the right or press ‘Enter’. If you’d like to upload PDB files instead, click the button to the right, and click + shift-click to select all desired PDBs.

Structure Loader CAD Cyrus Biotechnology

Structure Loader

Apply selector by clicking it

We’ve switched the behavior of selectors to be more intuitive; clicking anywhere on the selector besides the buttons on the right will apply it to loaded structures, while clicking the ‘pop-out’ button will open a new selector editor tab.

Apply selector by clicking CAD Cyrus Biotechnology

Apply Selector by Clicking

Simplified tab layout

We’ve added the title of the tab to the top of the tab, and have redesigned the layout of the tab. Now once an Action or ddG finishes, you will see the results collection appear to the right of the disabled ‘Save’ and ‘Save & Run’ buttons.

Simplified tabs CAD Cyrus Biotechnology

Simplified Tabs

Simplified Tabs Executed Highlight CAD Cyrus Biotechnology

Simplified Tabs Executed Highlight

Scatter plot

We’ve added an option to view structures in a scatter plot, sorted by user-selected score terms. Navigate to a collection with multiple structures, click the ‘Structure Viewer’ button, and select ‘Scatter Plot’. …more

Scatter Plot CAD Cyrus Biotechnology

Scatter Plot

Improvements to DDG

We’ve simplified the DDG workflow to be the same as Actions, with a selector chosen within the DDG tab. The DDG table is now scrollable, making it much more responsive with large selections. We’ve also implemented ‘dirty’ and ‘clean’ states in DDG, meaning selections that are made before a result comes back won’t be reset when that result comes back, or when a different tab is switched to. This will be coming to Actions in the next release.

Improvements to DDG CAD Cyrus Biotechnology

Improvements to DDG

Hover information displayed in structure viewer

Hovering with the mouse over a section of the protein will display the relevant information on the bottom-right of the structure viewer. The hover-text will depend on what selection mode you have chosen (structures, chains, residues, or atoms).

Hover for information CAD Cyrus Biotechnology

Hover for Information

Collection comparison

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. …more

Collection Compare CAD Cyrus Biotechnology

Collection Compare

Simplified action flows

Selectors can now be chosen directly from an action tab. Just choose your structure(s) and press the button corresponding to your action in the top right panel, and a tab will pop up in which you can choose your selector.

Simplified Action Flow CAD Cyrus Biotechnology

Simplified Action Flow

Superpose structures

We’ve added a feature that allows you to superpose structures on top of one another over a specific region of interest. This is useful for comparing regions of interest after running an Action that alters the protein backbone. For more information, navigate to Support using the dropdown at the upper right, and search for “Superpose”. …more

Superpose Structures CAD Cyrus Biotechnology

Superpose Structures

Performance improvements and collection filtering

We’ve drastically improved performance when viewing large collections by implementing virtual scrolling. You will see a much faster and more responsive UI when dealing with large collections. Additionally, we have implemented filtering within collections. Click the ‘Selected’ or ‘Loaded in viewer’ links above the collection table to filter by each option.