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Mol3D Products > Mol3D

	Products Overview All Mosaic Vivarium Home Features Animals Matings Colonies Housing Administration Installation Pricing Cheminformatics Library Builder Mol2D Mol3D		The Mol3D component was originally developed as part of VAnimator, VCI's application for 3D molecular viewing and movie creation.  Designed as in-house tools at VCI, VAnimator and the Mol3D control have many unique features, including code for integrating with 3D Studio Max (a standard application for computer generated movies) and code for multiple users to collaborate dynamically and interactively on a 3D model. The Mol3D code is available for source code licensing and can be used directly as an ActiveX control for 3D display in web pages and client applications.  The source code can also serve as a repository of tips, tricks and data models for rendering fully interactive 3D molecular models.  See below for a more complete list of features.   Molecular Graphics Capabilities    Modes Line Mark Ball and Stick Stick CPK size-dependent quality of rendering for improved quality of extreme close-up images use of hemispheres for enhanced performance and quality Ribbon Support 4 different ribbon styles for protein Nucleic acid Labels Atom Bond Monomer Molecule Wide range of properties available for labeling each of these types as well as user properties (see below)    GUI Control Color Widths Specular highlights, etc. Powerful Coloring Capabilities:  color-code all display modes by a wide range of properties including: Element Charge Atom Label Residue Number Residue Type Residue Secondary Structure Any user property    Display Hydrogens May disable hydrogen display for particular display mode    Mouse Control over Graphics Rotation (x, y, z) Translation (x, y, z) Scaling Clipping plane width Field of view (perspective) Stereo angle Docking The ability to move a piece of the molecular system (the selection) with the mouse    Graphics View Capabilities Orthographic or perspective projection Side-by-side stereo Depth cueing Arbitrary position and color of light for solid objects Full control of attributes of camera, etc. Ability to create multiple lights (with different colors) for special effects    Atom Selection Mouse based atom selection Use freeform or rectangular lasso Can extend previous selection with Ctrl key Support for atom, monomer and molecule selection level (picking one atom gets whole molecule, etc.) Can specify different rendering styles for a particular selection May later go back and edit display styles for these selections Allows highlighting of particular pieces of the molecular system Invert selection (make selection equal to all non-selected atoms)    Editing capabilities Cut and paste (parts of the molecular system or the whole molecular system) Delete (delete parts of or whole molecules)    Integration Use of external program, Babel, provides support for reading a very wide range of molecular file formats, e.g.: PDB (Brookhaven) MDL BIOSYM car MSI Quanta/Charmm Tripos Gaussian Spartan Chem3D Mopac Paste From - ability to paste a separate molecular file format (of arbitrary format) into an existing molecular system. Export molecular file output to the same wide range of file formats supported by Babel Export/import of user data Can export all internal molecular properties (atom, monomer or molecule) from the whole system or a subset to an external text file or clipboard Can read any set of data as user properties on atom, monomer or molecule from external text file or clipboard. Can override existing atom properties (such as coordinates or charges) from external text file or clipboard - for instance, allows display of results from external simulation program. This capability provides the ability to cut and paste any data from VAnimator to/from an external program, such as an Excel spreadsheet. This coupled with the ability to color displays by arbitrary user property gives a tremendous facility for displaying a user's data from a wide range of programs. OLE 2 server Can embed a VAnimator document into an external OLE container application such as Microsoft Word. Allows incorporation of molecular display into another presentation or report    Printing High resolution bitmap printing (up to printer resolution of e.g. 360dpi) Provides exceptional quality output even on deskjet printers Automatic scaling of linewidths to appear correctly on the printer Handles display of wide range of font annotations (cannot use e.g. Microsoft Word annotations for very high resolution printing since Word does not print embedded bitmaps at full printer resolution)    Miscellaneous VCI output format stores all program information (including all program state) Register file types - simple registration of many file types so that VAnimator may be used as an external WEB browser application Multi level undo/redo May undo any user interface command Toolbars Palette Facilitates changing mouse modes Main Can easily change rendering styles Also print, undo, cut and paste, etc. Transform Support for center/scale on selection Easy 90 degree x/y/z rotation Continuous rotation mode (x/y/z) Alignment Easy positioning of molecules relative to each other for presentation of results Works much better than simple mouse based docking    Macromolecular support Special support for generation, manipulation, and display of spherical, unilamellar liposomes    Animation Motions can be defined for: cameras lights scene objects Simulation trajectories can be tied into the movie (camera can move through an active simulation) Motion Trajectories: based on user entered points piecewise linear splines based on molecular structure (e.g., camera can be tied to a protein backbone for a fly-along) Output Microsoft AVI files Multiple simultaneous formats and speeds		Getting Started Start using Mol3D Today! Contact Virtual Chemistry to set up a web-based demonstration, to arrange for a trial version, or to have us answer any of your questions. 650.620.0090 (office) info@VirtualChemistry.com contact us

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