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Visualization of Complex Molecules - A case study with Chime

Visualization of Complex Molecules - A case study with Chime. Elements of visualization. Rendering Displaying Animation Interaction Simulation. Rendering. To convert graphics from a file into visual form Goal: Visualize something that the user is interested in. Things to take care of:

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Visualization of Complex Molecules - A case study with Chime

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  1. Visualization of Complex Molecules - A case study with Chime

  2. Elements of visualization • Rendering • Displaying • Animation • Interaction • Simulation

  3. Rendering • To convert graphics from a file into visual form • Goal: Visualize something that the user is interested in. Things to take care of: • Parallel projections / schematic views • Perspective projection • Depth cueing • Visible line and surface identification • Surface rendering and illumination model • Ambient light, Diffuse reflection, Specular reflection, Phong reflection model, Intensity attenuation, Transparency, Shadows, Phong shading, Ray-tracing • Exploded and cutaway views • 3D and stereoscopic views

  4. Display technologies • 2 Dimensional • Projection from 3D data to a 2D display • 3 Dimensional • Requirement: Feed different images to both eyes or actually create the 3D object

  5. Display technologies (cont) • Technologies: • with special glasses • Different colors • Different timing / shutters • Different polarization • without special glasses • very dense pixel display (i.e., hologram) • Lenticular display • Gaze-control • Non-gaze-control • 3D interaction HHI

  6. Display technologies (cont) • Recent news from Hitachi (Feb ’04) • Actual floating 3D image, no glasses, viewer can walk around the “picture”, i.e., can be viewed from any direction • 24 video streams, 24 projectors, 15 deg from each other • A see-trough screen rotates and an image is projected when the screen faces the corresponding projector

  7. Animation • Important in visualizing a series of movements or reactions • Movement is important in perceiving the 3D structure of a complex model • Paths based on simulation results, knowledge, or heuristics

  8. Interaction • The following should be intuitive in the User Interface to the model • Rotate / tilt / pitch / yaw • Zoom in/out • Pan up / left / down / right • {Select / grab} {area / object} of interest • Feel / sense item of interest • Peek and focus on objects at will • All this will not be easy to achieve with a mouse and keyboard

  9. Simulation • The tool that you use to visualize the molecules should also interact smoothly with the available simulation tools. • Some common formats support this: • PDB files • The PDB (Protein Data Bank) format is used to store coordinate or velocity data. This is the standard format for coordinate data for most molecular dynamics programs. Specification in: ftp.pdb.bnl.gov:/pub/format.desc.txt. • X-PLOR format PSF files • CHARMm19 and CHARMm22 parameter files • DCD trajectory files • The DCD files are single precision binary FORTRAN files, so are portable between computer architectures. The exact format of these files is said to be very ugly but supported by a wide range of analysis and display programs. • X-PLOR format PSF files • CHARMm19 and CHARMm22 parameter files • DCD trajectory files

  10. Visualization software • PovChem • Protein Explorer • PSI88 • PyMOL • Qmol • QTree • RasMol • Raster3D • Ribbons • RNA Movies • RNA Movies • RnaViz • Spock • Swiss-PdbViewer • Tachyon • VEGA • Viewmol • VMD • WebLab ViewerLite • WebMol • WinMGM • XMol • Jmol • JMV • JMVS • Kinemage • MacMolecule 2 and PCMolecule 2 • Maestro • Marvin Applets and JavaBeans • Mercury • MindTool • Molden • MOLEKEL • MOLMOL • MolPov • MolScript • MolView and MolView Lite • MSP • NIH Image • O • ORTEX • POV-Ray • Pov4Grasp • Biodesigner • CACTVS • Chemdraw net Plugin • Chemical2vmd • Chime • Chimera • Cn3D • CONSCRIPT • Dino • Flex • FlexV • Garlic • Gdis • gOpenMol • GRASP • Hyperactive Molecules Using Chemical MIME • ICMLite • ImageMagick • INTERCHEM modelling software

  11. Chime • Chime is a free program which can display molecular structure in three dimensions for Internet Explorer and Netscape Communicator. Its images look like RasMol but it differs from RasMol in that Chime sits directly on a web page runs inside your browser as a plug-in whereas RasMol is a standalone program that runs outside your browser independently. Chime also differs in that it shows only the molecule(s) provided by the author of the web page you view, whereas RasMol can show any molecule for which you have an atomic coordinate (PDB) file. With knowledge of RasMol or CSML scripting, you can create interactive web pages.

  12. Chime and RasMol • Chime is Built upon RasMol • Tim Maffett, Chime's principal architect at MDLI, used 16,000 lines of RasMol's C source code as part of the infrastructure of Chime. This was possible because Roger Sayle, RasMol's author, had generously placed RasMol's source code into the public domain. For use in Chime, the RasMol source code was converted to C++ and modified to become reentrant (which allows multiple Chime plug-in's to run simultaneously, even on a single web page). Maffett and other programmers at MDLI added over 100,000 lines of original C++ code to create Chime.

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