Transcript - ChemAxon
MarvinSpace – live demo Miklós Vargyas, Judit Papp 1 May, 2005 Slide 2 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 • methods for • molecular overlay, • geometry optimization and conformer generation • share molecular information by labeling and annotating atoms, bonds, ligands, receptors, complexes, surface regions MarvinSpace — UGM 2005 2 Slide 3 Features of MarvinSpace Key features of v1.0 • pure java (all platforms, html integration) • programmable (via java API) • extendable (custom components, calculations (e.g. property grids for surface coloring) can be integrated) • professional support (24 hour response time, rapid implementation of feature requests etc) MarvinSpace — UGM 2005 3 Slide 4 Features of MarvinSpace Other features of v1.0 • table view (multiple cells) • multiple molecule view (docked ligands; show/hide, load/remove) • ball, stick, spacefill, cartoon representation • various surface calculations: molecular, solvent accessible, Connolly; blobby • property mapping on surface (e.g. electrostatic potential), dynamic surface coloring, transparency • distance and angle measurement; change of conformation about rotatable bonds • high quality rendering (depth cueing, perspective projection, antialiasing) • dynamic scaling of rendering quality based on actual frame rate • clipping • atom, bond, residue, molecule, surface component picking MarvinSpace — UGM 2005 4 Slide 5 Examples of MarvinSpace • atoms are spheres, not ragged polyhedra. • Proper lights and reflections, not a uniform lit ball placed at every atom position. MarvinSpace — UGM 2005 5 Slide 6 Examples of MarvinSpace • Optional depth cueing (fog effect) MarvinSpace — UGM 2005 6 Slide 7 Examples of MarvinSpace • smooth surfaces • no missing or odd triangles MarvinSpace — UGM 2005 7 Slide 8 Examples of MarvinSpace • fast, novel algorithm, not the common analytic approach • accurate saddle for three and more nearby atoms MarvinSpace — UGM 2005 8 Slide 9 Examples of MarvinSpace • Blobby molecule: a novel approach to surface representation • easy to configure to obtain smooth surfaces MarvinSpace — UGM 2005 9 Slide 10 Examples of MarvinSpace • antialiasing MarvinSpace — UGM 2005 10 Slide 11 Examples of MarvinSpace • surface transparency MarvinSpace — UGM 2005 11 Slide 12 Examples of MarvinSpace • secondary structure representation MarvinSpace — UGM 2005 12 Slide 13 Future plans • protein ribbon view • faster surface drawing (by reduction of surface triangles) • user configurable blobby molecule (potential function and blending characteristic) • more property calculations (e.g. hydrophobic areas) • iso-surfaces • volume rendering • support for volumetric files (Gaussian cube etc) • detection of interaction sites • perception of intra molecular hydrogen bonds • protein-ligand binding energy calculation, scoring • interactive molecule construction • stereo view • navigation bar • 3d overlay • conformational search MarvinSpace — UGM 2005 13 Slide 14 Summary • 100% java 3D molecule viewer • Programmable (API) • High quality rendering • Available from June 2005 MarvinSpace — UGM 2005 14 Slide 15 Thank you for your attention Máramaros köz 3/a Budapest, 1037 Hungary [email protected] www.chemaxon.com MarvinSpace — UGM 2005 15