Hot new plugins for hot new summer

While we work on some big Nanome Core updates, check out these awesome new plugins that are available today!

By Keita Funakawa, Sam Hessenauer, and Sheila Zipfel (Special thanks to Jon Gast, Daniel Gruffat, Paul Wiarda)

We’re hard at work packing new features into v1.24 and v2.0, the next core releases of Nanome. In the meantime, check out these exciting new plugins that will supercharge your Nanome experience today!

There’s a plugin for everyone: visualize molecular properties in color with the updated Chemical Properties Plugin, generate beautiful publication-ready 3d molecular surface renderings with the High-Quality Surface Plugin, visualize and compare proteins in 3d space with the Superimpose Proteins Plugin, or boost collaboration with your colleagues using the Data Table Plugin to easily navigate and share multi-frame structures in VR or MR (in case you haven’t heard, we’re compatible with the Varjo XR3)!

Not Stack Enabled yet? Here’s a little taste of Nanome’s growing plugin ecosystem:

Chemical Properties Plugin update

Screenshot of the new chemical properties plugin

• Use Lipinski’s rule of 5 coloring for molecular descriptor values
• Hover over descriptors to show their full names (e.g. MW = Molecular Weight)
• Pick Custom Colors (even gradients!) for external properties
• Hovering over the 2D chemical preview will allow you to “Click to open preview”

High-Quality Surface Plugin

The High-Quality Surface Plugin is a plugin that computes and renders an elaborately beautiful Michel Sanner Molecule Surface (MSMS) with ambient occlusion to use for publications.

Users can generate high-quality molecular surfaces for the whole structure or chains.

• Users can generate one surface for the whole molecule or you can generate one surface per chain. The latter provides more information and better looking results with ambient occlusion.
• Our application scientists love that the versatility that this can be done by sub selection.

Users can also change the display options of the surfaces as well:

• color by Monochrome, Chains, Residues, Element, Hydrophobicity, Secondary Structure, or Custom Coloring
• Toggle visibility of multiple generated surfaces and manage different surfaces
• A popular feature among our Application Scientists — Calculating surface by Residue

Superimpose Proteins Plugin

• Superimposes multiple proteins in 3D space for visual comparison, and calculates Root Mean Square Deviation (RMSD) values of the aligned components
• Aligns using either the full protein or a chain
• Overlays by backbone alpha carbons only or all protein heavy atoms
• Stores RMSD tables from previous runs for easy comparison

Data Table Plugin: Combining the power of the web browser and plugins!

• Data Table is a plugin used to view multi-frame structure metadata in a table. (Can be used collaboratively using the Share URL feature. First plugin to do so!)
• When you activate the plugin in the Stacks menu, it opens the web browser to the Data Table UI which prompts you to select a structure from the workspaces.
• The plugin is meant to be used on small molecule structures that have many frames with associated data.
• Upon selecting a structure, a table will be displayed containing all the frames, 2D previews of each frame, and data.
• The user can then sort and filter the data columns, and make selections to split out or duplicate a subset of the frames as a new entry in the room.
• Calculate the chemical properties using RDKit of your ligands adding them to the table and metadata
• Now has the ability to add columns that are computed (with mathematical logic) from other columns
• Users can now add graphs to the side-bar of the table
• Supports Scatter plot and Radar Plot

If you’re an enterprise user, please contact us to get these plugins deployed in your enterprise environment. We can’t wait to hear what you think of them!