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Cloud-Based Visualization of Value-Added Model Annotations Using Jmol Bob Hanson St. Olaf College, Northfield, MN http://www.stolaf.edu/people/hansonr University of Dundee Dundee, Scotland 2015.7.20
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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
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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
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Jmol reads 60+ file model file formats, including PyMOL PSE Jaim Prilusky http://ispcsrv.weizmann.ac.il/a2jmolb/browse General Introduction to Jmol
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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.
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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.
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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! http://chemapps.stolaf.edu/jmol/docs
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General Introduction to Jmol Scripting Jmol’s scripting language is extensible function loadPDB(xxxx, ext) { load @{“*“+xxxx + (ext ? “/” + ext : “”)} select protein or nucleic cartoons only; color structure select * } loadpdb “1crn”
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General Introduction to Jmol Configurations: Application
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General Introduction to Jmol Configurations: Java Applet easily added highly customizable highly interactive highly modular signed or unsigned in 20 languages
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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
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Jmol Examples from the Web http://www.rcsb.org
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Jmol Examples from the Web
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Surfaces Using Jmol, we have been experimenting with different ways of creating and using surfaces.
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Surfaces Electron Density Mesh
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Surfaces Van der Waals and “solvent-accessible” representations
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Surfaces Numerical data can be mapped onto atoms and surfaces for visualization
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Surfaces Numerical data can be mapped onto surfaces for visualization, or used to change atom properties, such as displayed atom radius
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Contact Mapping contact {ligand} SURFACE
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Contact Mapping contact {ligand} TRIM
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Contact Mapping contact {ligand} TRIM
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Contact Mapping contact {ligand} HBOND
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Contact Mapping
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Annotations Models are more than atom positions. Approximations Constraints Ambiguity Correlations
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Annotations The future is in combining data from various sources.
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Annotations The future is in combining data from various sources.
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Annotations The future is in combining data from various sources. load =1d66
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Annotations The future is in combining data from various sources. load =1d66 cartoons only
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Annotations The future is in combining data from various sources. load =1d66 cartoons only color structure
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Annotations Visualizing validation data load =4tvj/val cartoons only color structure
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Annotations Visualizing validation data load =4tvj/val cartoons only color structure
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Annotations Visualizing validation data load =4tvj/val
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Annotations Visualizing validation data load =4tvj/val color property_rsrz
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Annotations Visualizing validation data load =4tvj/val {*}.radius = {*}.property_clashes.all
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Annotations Visualizing validation data load =4tvj/val color property_clashes contact {Lys325} {Thr323}
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Annotations Visualizing validation data load =2bxa/val; wireframe only select property_rsrz > 3; wireframe 0.2 Isosurface “=2bxa”
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Annotations JSON format from EBI A simple RESTful call Fully generalizable JSON code (shown here using pretty=true) load =4tvj/val
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Annotations - Domains =xxxx/dom or *xxxx/dom
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Annotations - Domains =xxxx/dom or *xxxx/dom
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Annotations - Domains =xxxx/dom or *xxxx/dom
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Annotations - Domains
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http://www.ebi.ac.uk/pdbe/api/mappings/1lyd?pretty=true&metadata=true
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Annotations – RNA/DNA secondary structure Additional annotations =xxxx/dssr
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Annotations – RNA/DNA secondary structure Additional annotations =xxxx/dssr
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Annotations – RNA/DNA secondary structure Additional annotations =xxxx/dssr
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Annotations – RNA/DNA secondary structure Additional annotations =xxxx/dssr
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Annotations – RNA/DNA secondary structure Additional annotations =xxxx/dssr
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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.
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Thank you! Geoff Barton, Jim Proctor, Mungo Carstairs Jmol User Community St. Olaf College Larson-Anderson Endowment Fund
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Thank You! Geoff Barton, Jim Procter Mungo Carstairs Jmol User Community St. Olaf College Larson-Anderson Endowment Fund
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