Cloud-Based Visualization of Value-Added Model Annotations Using Jmol Bob Hanson St. Olaf College, Northfield, MN University of Dundee Dundee, Scotland

General Introduction to Jmol Mission: The high-quality, real-time visualization of molecular structure, dynamics, and energetics. open source Java cross-disciplinary development driven by user input

General Introduction to Jmol small molecules biomolecules PDB, PQR, PyMOL, many other file formats molecular dynamics trajectories multiple files and files with multiple structures automatic addition of hydrogen atoms MMFF94 and UFF minimization model building

Jmol reads 60+ file model file formats, including PyMOL PSE Jaim Prilusky General Introduction to Jmol

General Capabilities of Jmol Output/Export Options Structures can be saved in PDB, MOL, XYZ, and JSON formats. Only the selected atoms are output, allowing for creating files that are subsets of the original file.

General Capabilities of Jmol Output/Export Options Images can be created in high-quality JPG and PNG formats. These images retain the full state of Jmol, allowing dragging of the image back into the application of signed applet to restore the state. In addition, special formats PNGJ and JMOL retain, along with the script, the entire set of files used.

General Introduction to Jmol Scripting Jmol has a rich scripting language that is easily accessed via a console, a pop-up menu, or via an API. There are nearly 2000 semantic tokens and about 150 commands. The HELP command accesses the interactive script documentation; VERY active and friendly user group!

General Introduction to Jmol Scripting Jmol’s scripting language is extensible function loadPDB(xxxx, ext) { + (ext ? “/” + ext : “”)} select protein or nucleic cartoons only; color structure select * } loadpdb “1crn”

General Introduction to Jmol Configurations: Application

General Introduction to Jmol Configurations: Java Applet easily added highly customizable highly interactive highly modular signed or unsigned in 20 languages

General Introduction to Jmol Configurations: JavaScript App identical to Java works in all popular browsers, including Safari for the iPad, android phones, etc. somewhat slower than Java

Jmol Examples from the Web

Jmol Examples from the Web

Surfaces Using Jmol, we have been experimenting with different ways of creating and using surfaces.

Surfaces Electron Density Mesh

Surfaces Van der Waals and “solvent-accessible” representations

Surfaces Numerical data can be mapped onto atoms and surfaces for visualization

Surfaces Numerical data can be mapped onto surfaces for visualization, or used to change atom properties, such as displayed atom radius

Contact Mapping contact {ligand} SURFACE

Contact Mapping contact {ligand} TRIM

Contact Mapping contact {ligand} TRIM

Contact Mapping contact {ligand} HBOND

Contact Mapping

Annotations Models are more than atom positions. Approximations Constraints Ambiguity Correlations

Annotations The future is in combining data from various sources.

Annotations The future is in combining data from various sources.

Annotations The future is in combining data from various sources. load =1d66

Annotations The future is in combining data from various sources. load =1d66 cartoons only

Annotations The future is in combining data from various sources. load =1d66 cartoons only color structure

Annotations Visualizing validation data load =4tvj/val cartoons only color structure

Annotations Visualizing validation data load =4tvj/val cartoons only color structure

Annotations Visualizing validation data load =4tvj/val

Annotations Visualizing validation data load =4tvj/val color property_rsrz

Annotations Visualizing validation data load =4tvj/val {*}.radius = {*}.property_clashes.all

Annotations Visualizing validation data load =4tvj/val color property_clashes contact {Lys325} {Thr323}

Annotations Visualizing validation data load =2bxa/val; wireframe only select property_rsrz > 3; wireframe 0.2 Isosurface “=2bxa”

Annotations JSON format from EBI A simple RESTful call Fully generalizable JSON code (shown here using pretty=true) load =4tvj/val

Annotations - Domains =xxxx/dom or *xxxx/dom

Annotations - Domains =xxxx/dom or *xxxx/dom

Annotations - Domains =xxxx/dom or *xxxx/dom

Annotations - Domains

Annotations – RNA/DNA secondary structure Additional annotations =xxxx/dssr

Annotations – RNA/DNA secondary structure Additional annotations =xxxx/dssr

Annotations – RNA/DNA secondary structure Additional annotations =xxxx/dssr

Annotations – RNA/DNA secondary structure Additional annotations =xxxx/dssr

Annotations – RNA/DNA secondary structure Additional annotations =xxxx/dssr

Summary We now have ready access to a wide variety of metadata relating to biomolecules. You can think of a model with annotations as a mini “database” that can be queried. Jmol is at the forefront of integration of these services into molecular visualization. Any JSON-based data can be incorporated.

Thank you! Geoff Barton, Jim Proctor, Mungo Carstairs Jmol User Community St. Olaf College Larson-Anderson Endowment Fund

Thank You! Geoff Barton, Jim Procter Mungo Carstairs Jmol User Community St. Olaf College Larson-Anderson Endowment Fund