Give incredible depth to your graphics or focus on specific sections with these features. Screen space ambient occlusion SSAO simulates the occlusion of ambient light in corners and crevasses of 3D objects. If you look in the corner of your room, it will appear slighly darker than the centers of the walls. This technique adds a significant amount of realism to the image and greatly helps with perception of topography. This technique is fully customizable in ChemDoodle 3D.
Outline effects are created by finding significant changes in cached data values from pixel to pixel. You can control colors, thicknesses, sketchiness and more!
A depth of field effect focuses in on a specific portion of your scene, emulating images made with camera lenses. You can define the beginning and ending focus depths as well as the extent of the unfocused blur and dilate effects. After effects are advanced image filters.
ChemDoodle 3D's molecular modeling procedures can be run in real-time using the Minimizer widget so you can interact with molecules while you are building them or easily change between conformations.
Our modeling engine is fast and efficient, allowing you to quickly generate relevant 3D coordinates for your built structures. Define the optimization function used to minimize energies from several built-in search directions including steepest descent, conjugate gradients, and BFGS, with several line search options.
ChemDoodle 3D includes implementations of several published force fields. Our implementations are some of the most accurate and consistent in the industry. The Universal Force Field UFF is excellent for quickly building partial and complete chemical structures for demonstrations and images as it can handle the vast majority of the periodic table. A complete implementation is included in ChemDoodle 3D.
Use this force field to generate experimentally accurate geometries for measurements and calculations. The VSEPR force field is perfect for students and instructors to use and demonstrate why certain atom centers, along with electron pairs, lead to certain shapes in molecular structures. Up to 8 connections on a center and multicenter structures are acceptable. Because the purpose of the VSEPR force field is to generate shapes, energy calculations are irrelevant to the user, as they have no physical significance.
You can also use these charge models to color molecular surfaces. Atom typing is an essential step in the correct application of a force field. You can see what atom types are defined to the atoms in ChemDoodle 3D for the specific force field you are using.
You may even output the atom types for use in other applications. Forces can be rendered to show how the molecule will change given the force field gradient calculations.
In addition to showing you the atom typing and force vector calculations, ChemDoodle 3D will let you know when a structure is not compatible with a specific force field by providing descriptive errors and warnings. Use all of this information for reliability and referencing. Parallel processing allows you to use the power of your multi-core CPU to speed up computations. The force fields in ChemDoodle 3D are specially designed to run in parallel.
This means that your structure, which would normally take x seconds to optimize, will now only take a fraction of x seconds to optimize. Enable parallel processing in ChemDoodle 3D when you want to handle the optimization of a large structure or system. Understanding how parallel processing works and is implemented in ChemDoodle 3D is very important. We have an entire section covering parallel processing in the ChemDoodle 3D user guide.
New to molecular modeling? No worries. We have an entire chapter in the ChemDoodle 3D user guide dedicated to molecular modeling and how it is implemented. You will be optimizing structures in no time. Anaglyphs are a stereoscopy technique used to show images in 3D space to our eyes from a 2D image. It works by rendering the scene for each eye's perspective in a different color space.
Special glasses are then used to filter out each eye's image so one eye cannot see what the other eye sees. Our brain then pieces the two images together to observe the scene in 3D space. Anaglyphs are fully implemented with support for red-cyan, green-magenta, and amber-blue anaglyph glasses, which can be purchased cheaply from online retailers.
The Dubois method has been implemented for the most comfortable anaglyph viewing and you can control both the focal length and eye separation parameters to customize the anaglyph to your preference.
Several models have been exported from ChemDoodle 3D and printed using a 3D printer. These are great for gifts and celebrating your own scientific discoveries! ChemDoodle 3D supports as much of each format as possible, including meshes, normals, materials, transparency, colors and multicolors. Copious visual feedback is provided. There are also many options for customizing the building tools to your preference. Intuitive selection tools allow you to quickly trace, select and edit objects in 3D.
For even more accuracy, use the Selector widget for a comprehensive organization of all the objects in the scene, allowing you to precisely investigate and select content. No other program compares. ChemDoodle 3D renders multiple bonds that are able to orient themselves towards the camera for the most descriptive graphics.
When building 3D structures, ChemDoodle 3D will automatically suggest the best place in three dimensions to add an atom connection. This helps you quickly build molecules. You can then simply turn on the minimizer to optimize physical coordinates. You have full control over how atoms and bonds are rendered, and you can quickly choose from predefined representations, such as van der Waals spheres, ball and stick, stick, wireframe and line.
Use this to show atom labels. Implicit hydrogens are automatically tracked for your structures, but you can also override them as appropriate. Define charges, radicals and isotopic mass values to atoms. These values are also properly read in and written to chemical file formats. Electron pairs and single electron radical objects are rendered on your structure and automatically placed for you you may also manually place them.
Use toruses for aromatic circles or use resonance bonds that automatically orient to the center of rings. Perceive stereochemistry for 3D structures. CIP stereochemistry is determined for chiral centers and double bonds using our advanced and accurate CIP algorithms.
Quickly access powerful functions to help modify your graphics: saturation, Kekulization, ring perception, distance geometry embedding, and more. In addition to creating beautiful graphics for small molecule structures, ChemDoodle 3D will also help you to edit and create graphics for protein and nucleic acid macromolecules. ChemDoodle 3D reads protein and nucleic acid information from PDB files and generates high quality meshes that are superimposed over the atom and bond coordinates.
Beautiful protein ribbons and traces are generated. Copious visual feedback is provided. There are also many options for customizing the drawing tools to your preference, including for accessibility concerns.
ChemDoodle will help guide your drawing to create the most aesthetic figures using a feature we call the "Optimize Zone" for standard bond angles and lengths.
Just move your mouse out of the zone to override it. In addition to the standard elemental labels, you can input any custom label you desire. ChemDoodle will automatically chemically interpret and format labels. You can also directly control text formatting. Labels can be expanded to full atom models and full atom models can be automatically collapsed into concise labels based on your abbreviation library or to a custom label.
Abbreviations and compound labels like "COOH" and "Ph", as well as formulae can be expanded to quickly build and work with complex chemical structures. You can define your own custom abbreviations to be used in ChemDoodle.
If you need to tag atoms or bonds by increments, ChemDoodle provides powerful tools to do this. Simply click on the atom or bond to tag them and the next tag is automatically incremented. Tag by alphabet, number, roman numeral or greek letter.
ChemDoodle will automatically place your charges, radicals, stereocenter labels and other attributes for you in an aesthetic manner. You can override these decisions at any time by holding down and dragging the mouse during placement. In addition to standard ring tools and templates, ChemDoodle provides special arbitrary ring and crown ether tools for quickly building advanced ring systems.
Quickly build structures using our built-in template libraries, or create your own templates. The Templates widget organizes the templates for you. Several tools are provided to help you quickly build complex 3D geometries, including carbon nanotube and prism builders. Armchair, zigzag and chiral nanotubes can be built. Use the Rotate in 3D tool to change the 3D perspective of the drawn structure. Complex algorithms have been implemented to automatically lay out chemical structures aesthetically.
Select only part of a structure to clean only that part, leaving the remaining structure untouched. There are so many tools in ChemDoodle for working with chemical graphics, including alignment and distribution functions, bond adjustment features, action tracking, transforms and more. Our algorithms name molecules naturally and accurately, down to the character and formatting.
If you find any problems, simply contact us with the structure so we can correct it. The majority of the periodic table is handled. Implicit hydrogens will be added for you to your drawings. You have the ability to turn them off for single atoms, globally or override them as appropriate. Detect the aromaticity and anti-aromaticity of your rings and display the number of pi electron contributors.
You can also force aromatic ring recognition using all resonance bonds. This is useful when dealing with large, embedded, aromatic ring systems. Perceive stereochemistry for drawn 2D structures. CIP stereochemistry is determined for chiral centers and double bonds using our advanced and accurate CIP algorithms.
When you draw a stereochemical configuration for a chiral center in ChemDoodle, it is recognized by the software exactly as drawn, being one of two enantiomers. In certain cases, you may wish to define a current chiral center as one configuration or the other, or as a mixture of both and. This can be defined using the enhanced stereochemistry features in ChemDoodle.
You may then output this information into several file formats for use by compatible registration and search engines, for instance. Repeat units aka repeat groups or repeating brackets are used to define linearly repeating substructures in molecules.
A repeat unit consists of a pair of square brackets denoting the substructure to be repeated and a repeat value defining how many times the substructure is repeated. Most conveniently, when properly defined in chemical structures in ChemDoodle, repeat units are automatically recognized, evaluated and expanded so you can quickly draw complex structures and perform cheminformatics tasks such as calculating molecular masses and formulas.
This is very convenient for oligomers and polymers. Calculate dozens of descriptors for structures, including masses, formulae, volumes, physical properties, topological indexes, counts, bioactivity filters and more. Use the Elemental Analysis widget to calculate molecular masses, elemental analysis and isotopic distributions for structures as you draw them. Select entire complexes to calculate bulk properties. ChemDoodle will double check your work for you and notify you when it finds chemistry issues, such as overvalanced atoms, incorrectly drawn stereocenters, or partially intersecting repeat units.
ChemDoodle contains an entire elemental database. Most of the calculations performed by ChemDoodle use this data. The data is kept relevant and referenced and includes many elemental properties such as electronegativites, radii, thermodynamic properties, years of discovery and more. Databases of ionization energies and isotopes are also provided.
You may view this data at any time in the View menu. A fully interactive periodic table is provided for visualization and reference. You can even customize it and print it out! A SciFinder n account is required.
Google Patents searching is integrated. You may perform structure, substructure and similarity searching into the Google Patents and non-patent literature databases at Google using structures drawn in ChemDoodle. All of the resources we use to develop the algorithms in ChemDoodle or the choices we make for the software are documented in the Help menu. This way you can evaluate the quality of our work. Arrows are essential in chemical graphics for many reasons, the most important being for reaction and mechanism diagrams.
Arrows are so important that, in ChemDoodle 2D, they have their own unique toolbar palette. These tools allow you to quickly draw various types of arrows, both straight and in arcs.
Special arrow type templates are also provided, such as bold, equilibrium and retrosynthetic arrows. Other types of paths, such as polylines and bezier curves can also be used for arrows. ChemDoodle 2D provides unique tools to automatically render single electron, electron pair and bond forming pushing arrows based on an starting and ending atom or bond.
Quickly create advanced mechanism drawings. Arrows and arrowheads are completely customizable, just like everything else in ChemDoodle 2D. Change sizes, fills, colors and more. You may also change the arrow stroke to create a wavy photon arrow, or include a no go slash or cross. You can manually define reactants and products, or have ChemDoodle 2D automatically infer reaction components based on their locations around an arrow.
ChemDoodle 2D contains convenient tools for building reactions based on bond breaking and formation. Simply drag the tool over the desired bonds and the appropriate reactions will automatically be generated for you. Reactions can be automatically laid out for you, to achieve the most aesthetic figures. Reactions that are very wide will be stacked appropriately. Complete reactions can be balanced by ChemDoodle 2D, either when drawn using structures and arrows, or typed as a reaction equation.
ChemDoodle 2D will be able to balance any reaction equation that can be balanced. For infinitely irreducible solutions, a proprietary algorithm that minimizes positive integers for coefficients will be determined to balance your equation.
ChemDoodle 2D provides an industry leading stoichiometry table. This stoichiometry table is a form where you input theoretical and experimental values from your experiment and you will get accurate calculations for your input and results. ChemDoodle 2D's stoichiometry tables are fully chemically aware and are self-calculating.
Input reactions are automatically balanced however you can override these stoichiometric ratios with the Equivalents row and the limiting component is automatically inferred based on the input values.
Completely edit the domain and range perspectives for your spectra. Include integration lines and grids. Format titles and then add annotations with shape tools. The NMR SignalSeek widget will also provide you with structure-spectrum correlations and further insight into the simulation. You can completely customize the settings for the simulations. To ensure the continued success of ChemDoodle Web Components , iChemLabs is dedicated to funding and developing this project.
Please also help us by mentioning it to your colleagues and friends and placing a link to us on your webpage. If you really like ChemDoodle Web Components , you may also enjoy ChemDoodle , our advanced and affordable chemical structure environment that works on all operating systems. Download ChemDoodle Web Components v9. Setting up ChemDoodle Web Components for use on your website is very simple and consists of 3 easy steps:.
ChemDoodle Web Components is now installed and ready for you to use! Please refer to the Tutorial menu on the top of this website to begin using the ChemDoodle Web Components.
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