Scarlet Line - SOFTWARE DESIGN & DEVELOPMENT Products Molecular Designer Molecular Viewer Browser Plugin Sea Battle Solitaire Syntac Universal Parser Documentation Molecular Viewer Screenshots Installation Test Page User's Guide Usage Add Molecules to your HTML Page Examples Scripting Water Animation Cyclohexane Animation Carbon Dioxide Animation Supported File Formats Alchemy MSI Cartesian ChemDraw Binary ChemDraw XML Chemical Markup Language Chemical Resource Kit 2D Chemical Resource Kit 3D Crystallographic Information File DMol3 Co-ordinates Fasta Sequence GAMESS Input GAMESS Output Gaussian Formatted Checkpoint Gaussian Output GenBank Sequence HyperChem HIN MacroModel Format Macromolecular Crystallographic Information File MDL MOL MDL SD MOPAC Output Protein Data Bank Format NCBI PubChem ShelX Daylight SMILES Mol2 XYZ Cartesian Co-ordinates Troubleshooting Update License Script Reference Sea Battle Solitaire Syntac Universal Parser Description Glossary Contracts Freeware License How To ... Remove ssh Password Create a Boot USB Memory Fob / Stick Locate and Remove Personal Computer Bottlenecks Use HTML and MathML Entities in any XML File Download Molecular Viewer Sea Battle Solitaire Support Molecular Viewer Sea Battle Solitaire About Us Contact Sitemap

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Contents Usage Using the Molecular Viewer Plugin Context Menu How to include molecules in a web page Using the embed Tag Using the Full Browser Window Including the Data Inline How to use Scripting Parameters and Functions Legacy "application/x-spt" Scripts Animation Interesting Example Pages Sites to Visit Add Molecules to your HTML Page How to add molecules to your HTML page Basic Syntax Where to find Chemical Files Protein Molecules Genetic Sequences Small Molecules Reactions and Animation Converting Formats Adding the molecule to your html page Examples Scripting Molecular Viewer Scripting Examples Background Colour Changing Water Animation Molecular Viewer Animation Examples Water Vibration Mode Cyclohexane Animation Cyclohexane Heat of Formation Carbon Dioxide Animation Carbon Dioxide Dissociation Supported File Formats Alchemy Sample of Alchemy chemical/x-alchemy file format MSI Cartesian Sample of Accelrys/MSI Biosym/Insight II chemical/x-msi-car Cartesian Coordinate CAR file format ChemDraw Binary Sample of ChemDraw chemical/x-cdx binary file format ChemDraw XML Sample of ChemDraw chemical/x-cdxml XML file format Chemical Markup Language Sample of Chemical Markup Language chemical/x-cml XML file format Chemical Resource Kit 2D Sample of Chemical Resource Kit diagram chemical/x-crk2d 2D file format Chemical Resource Kit 3D Sample of Chemical Resource Kit diagram chemical/x-crk3d 3D file format Crystallographic Information File Sample of IUCr Crystallographic Information chemical/x-cif file format DMol3 Co-ordinates Sample of DMol chemical/x-dmol coordinates file format Fasta Sequence Sample of NCBI BLAST FASTA chemical/x-fasta sequence file format Referencing the National Center for Biotechnology Information (NCBI) Referencing the Protein Data Bank GAMESS Input Sample of GAMESS chemical/x-gamess-input input file format GAMESS Output Sample of GAMESS chemical/x-gamess-output output file format Gaussian Formatted Checkpoint Sample of Gaussian chemical/x-gaussian-checkpoint formatted checkpoint file format Gaussian Output Sample of Gaussian chemical/x-gaussian-log output file format GenBank Sequence Sample of Gaussian chemical/x-genbank output file format Referencing the National Center for Biotechnology Information HyperChem HIN Sample of HyperChem chemical/x-hin HIN file format MacroModel Format Sample of MacroModel chemical/x-macromodel-input file format Macromolecular Crystallographic Information File Sample of Macromolecular Crystallographic Information chemical/x-mmcif file format Referencing the Protein Data Bank MDL MOL Sample of MDL chemical/x-mdl-molfile MOL file format MDL SD Sample of MDL chemical/x-mdl-sdfile SD file format MOPAC Output Sample of Molecular Orbital PACkage (MOPAC) chemical/x-mopac-out Output file format Protein Data Bank Format Sample of Protein Data Bank chemical/x-pdb file format Referencing the Protein Data Bank NCBI PubChem Sample of National Center for Biotechnology Information chemical/x-ncbi-asn1-xml PubChem file format Referencing the National Center for Biotechnology Information Finding and Downloading Molecules from the PubChem Databases ShelX Sample of University of Göttingen ShelX chemical/x-shelx file format Daylight SMILES Sample of Daylight Chemical Information Systems' SMILES chemical/x-daylight-smiles file format Mol2 Sample of Tripos Sybyl chemical/x-mol2 file format XYZ Cartesian Co-ordinates Sample of chemical/x-xyz file format Chemical MIME Types Supported Troubleshooting Troubleshooting Windows Vista Stuck on "Loading ..." "CML data not recognized" File Not Recognized Long time on "Converting ..." Browser Page Unresponsive Black Horizontal Lines in Shadowing Atoms passing in front of, instead of behind, closer atoms OpenGL Unavailable. ... MacOS X image not refreshing Plugin does not work, having just installed On unix system, plugin does not load after installation Find Install Running on a Sun VirtualBox Guest, stuck or hung Update Molecular Viewer Plugin Update Information License License and Source Code Availability npcml npcmlopen

Sample of Chemical Markup Language chemical/x-cml XML file format <object data="Alanine.cml" type="chemical/x-cml" width="640" height="480" />

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