Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.
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Transcript of Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.
![Page 1: Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.](https://reader035.fdocuments.us/reader035/viewer/2022081516/551464eb550346b0158b4acf/html5/thumbnails/1.jpg)
Scientific & technical presentation
Structure Visualization with
MarvinSpace
Oct 2006
![Page 2: Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.](https://reader035.fdocuments.us/reader035/viewer/2022081516/551464eb550346b0158b4acf/html5/thumbnails/2.jpg)
Description of MarvinSpace
• high performance 3D molecule visualization tool
• WEB enabled, platform independent
• available as – standalone application with an easy-to-use GUI– Java Applet – developers' toolkit
• visualizes– small molecules, proteins, nucleic acids, crystals,
– molecular surfaces, molecular orbitals, volumetric data
![Page 3: Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.](https://reader035.fdocuments.us/reader035/viewer/2022081516/551464eb550346b0158b4acf/html5/thumbnails/3.jpg)
Features of MarvinSpace
Key features of v5.0
• pure java (all platforms, html integration, applet)
• programmable (via java API)
• scalable rendering quality
• high quality image capturing
• accurate surface representation including Connolly
• property mapping on surface (e.g. electrostatic potential)
• extendable (custom components, calculations can be integrated)
• professional support (24 hour response time, rapid implementation of feature requests etc)
![Page 4: Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.](https://reader035.fdocuments.us/reader035/viewer/2022081516/551464eb550346b0158b4acf/html5/thumbnails/4.jpg)
Features of MarvinSpace
Other features of v5.0• table view (multiple cells)
• multiple molecule view (overlayed ligands; show/hide, add/remove)
• ball, stick, spacefill; cartoon representation
• dynamic surface coloring, transparency
• distance and angle measurement; change of conformation about rotatable bonds
• high quality rendering (depth cueing, perspective projection, anti-aliasing)
• clipping
• atom, bond, residue, molecule, surface component picking
![Page 5: Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.](https://reader035.fdocuments.us/reader035/viewer/2022081516/551464eb550346b0158b4acf/html5/thumbnails/5.jpg)
High quality rendering I
• Three different rendering quality levels
• Line anti-aliasing and full screen option for smooth polygon edges
![Page 6: Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.](https://reader035.fdocuments.us/reader035/viewer/2022081516/551464eb550346b0158b4acf/html5/thumbnails/6.jpg)
High quality rendering II
• Optional and customizable depth cue and clipping planes
• Near and far position setting for both
![Page 7: Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.](https://reader035.fdocuments.us/reader035/viewer/2022081516/551464eb550346b0158b4acf/html5/thumbnails/7.jpg)
Molecule representation I
• wire, ball, stick, spacefill and combinations
• dotted, mesh, solid, transparent drawing types
![Page 8: Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.](https://reader035.fdocuments.us/reader035/viewer/2022081516/551464eb550346b0158b4acf/html5/thumbnails/8.jpg)
Molecule representation II
![Page 9: Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.](https://reader035.fdocuments.us/reader035/viewer/2022081516/551464eb550346b0158b4acf/html5/thumbnails/9.jpg)
Molecular surfaces I
• Smooth and accurate surfaces
• Various surface types: van der Waals, Connolly, solvent accessible, blobby surfaces
![Page 10: Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.](https://reader035.fdocuments.us/reader035/viewer/2022081516/551464eb550346b0158b4acf/html5/thumbnails/10.jpg)
Molecular surfaces II
![Page 11: Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.](https://reader035.fdocuments.us/reader035/viewer/2022081516/551464eb550346b0158b4acf/html5/thumbnails/11.jpg)
Triangle count reduction
• Slightly slower surface generation – Much faster rendering
• Geometric algorithm that preserves surface characteristics
![Page 12: Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.](https://reader035.fdocuments.us/reader035/viewer/2022081516/551464eb550346b0158b4acf/html5/thumbnails/12.jpg)
Surface transparency
![Page 13: Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.](https://reader035.fdocuments.us/reader035/viewer/2022081516/551464eb550346b0158b4acf/html5/thumbnails/13.jpg)
Property mapping I
• Built-in surface coloring options: atom types, residue, chain id, B-factor secondary structure, electrostatic potential
![Page 14: Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.](https://reader035.fdocuments.us/reader035/viewer/2022081516/551464eb550346b0158b4acf/html5/thumbnails/14.jpg)
Property mapping II
• Mapping custom calculated properties
• Fully customizable display via API
![Page 15: Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.](https://reader035.fdocuments.us/reader035/viewer/2022081516/551464eb550346b0158b4acf/html5/thumbnails/15.jpg)
Property mapping III
• Volumetric data, e.g. Gaussian Cube surface and property files
• Interactive change of isosurface threshold value
![Page 16: Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.](https://reader035.fdocuments.us/reader035/viewer/2022081516/551464eb550346b0158b4acf/html5/thumbnails/16.jpg)
Property Mapping IV
• Charmm PDB and grid support
![Page 17: Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.](https://reader035.fdocuments.us/reader035/viewer/2022081516/551464eb550346b0158b4acf/html5/thumbnails/17.jpg)
Large structures
![Page 18: Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.](https://reader035.fdocuments.us/reader035/viewer/2022081516/551464eb550346b0158b4acf/html5/thumbnails/18.jpg)
Large structures
![Page 19: Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.](https://reader035.fdocuments.us/reader035/viewer/2022081516/551464eb550346b0158b4acf/html5/thumbnails/19.jpg)
Secondary structure representation I
![Page 20: Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.](https://reader035.fdocuments.us/reader035/viewer/2022081516/551464eb550346b0158b4acf/html5/thumbnails/20.jpg)
Secondary structure representation II
• Various types: wire, trace, tube, ribbon, cartoon, etc.
• Various colors: residue, chain, structure, rainbow, b-factor
• Customizable
![Page 21: Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.](https://reader035.fdocuments.us/reader035/viewer/2022081516/551464eb550346b0158b4acf/html5/thumbnails/21.jpg)
Ligand binding
• Flexible tool for binding studies
![Page 22: Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.](https://reader035.fdocuments.us/reader035/viewer/2022081516/551464eb550346b0158b4acf/html5/thumbnails/22.jpg)
Labels
• Built-in label types: atom, residue, secondary structrure, molecule
• Customizable types, colors
• Labels can be dragged and edited
![Page 23: Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.](https://reader035.fdocuments.us/reader035/viewer/2022081516/551464eb550346b0158b4acf/html5/thumbnails/23.jpg)
Measurement
•Distance, Bond angle, Dihedral angle
•Interactive torsion tweak
![Page 24: Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.](https://reader035.fdocuments.us/reader035/viewer/2022081516/551464eb550346b0158b4acf/html5/thumbnails/24.jpg)
Pharmacophore modeling
![Page 25: Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.](https://reader035.fdocuments.us/reader035/viewer/2022081516/551464eb550346b0158b4acf/html5/thumbnails/25.jpg)
Future plans
• scripting (Chime)• live content, presentation support• more property calculations (e.g. hydrophobic areas, electron density)• detection of interaction sites• perception and visualization of hydrogen bonds• interactive molecule construction• stereo view• volume rendering• navigation bar• 3d overlay, pharmacophore modeling• share molecular information by labeling and annotating atoms, bonds,
ligands, receptors, complexes, surface regions• protein-ligand binding energy calculation, scoring, boundary clash
![Page 26: Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.](https://reader035.fdocuments.us/reader035/viewer/2022081516/551464eb550346b0158b4acf/html5/thumbnails/26.jpg)
Summary
• 100% java (application, applet)
• High quality rendering
• Fast, hardware accelerated graphics
• Programmable (API)
![Page 27: Scientific & technical presentation Structure Visualization with MarvinSpace Oct 2006.](https://reader035.fdocuments.us/reader035/viewer/2022081516/551464eb550346b0158b4acf/html5/thumbnails/27.jpg)
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