describe the 3d stick drawing
ChemDoodle 3D
3D Chemical Graphics, Animations and Modeling
Click the play button to scout an introduction video
Easily build 3D molecules and quality scientific graphics! Try a Free Trial At present ↗
Main Features
ChemDoodle 3D is a powerhouse for working with chemical science in 3D with industry leading molecular modeling tools and all-time-in-class graphics.
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3D Visualization
A new perspective on chemistry
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Beautiful Scientific Models
We spend a very long fourth dimension scrutinizing the models generated in ChemDoodle 3D. Take a close look at the renderings as you lot are rotating them to sentinel bonds orient towards the photographic camera; every object mesh in the scene is congenital to merge with the others; and our models are some of the most gorgeously crafted by any software in this industry.
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Completely Customizable
All of the rendering in ChemDoodle 3D is controlled by styles defined by you. The styles can use to the entire scene, selected content or individual objects.
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Avant-garde Text System
ChemDoodle 3D'southward advanced 3D graphics engine tin render text beautifully. Use this to testify cantlet labels and more. Yous have full control over font, size and color.
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Custom Chemical element Colour Sets
In improver to the predefined Jmol, Rasmol, PyMOL and CDK color sets, you can as well manually define your ain elemntal color set to employ to molecule rendering.
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Compasses
Include a compass on the bottom left of the graphic, or in the center overlaying the content, to describe orientation.
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Projections
Both orthographic and perspective projections are available and can be switched instantly.
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Mesh Quality
You can apace change between various quality levels to benefit graphics output or to speed up performance.
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Transparency
Transparency effects are just that, they let you run into through objects in the scene. ChemDoodle 3D allows you to render transparent objects with or without back faces.
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Surfaces
ChemDoodle 3D tin generate a number of surface types and color functions for any number of atoms. Visualize the space of your structures in ways other editors cannot.
Y'all can customize mesh algorithms, display types, normals, colors and more.
Different types of surfaces are available, including van der Waals (VDW), solvent accessible surfaces (SAS) and solvent excluded surfaces (SES, Connolly).
Color your surfaces through diverse functions to provide a physical perspective on the structure. Functions include by cantlet color, charges (Gasteiger, QEq, QTPIE), lipophilicity (AlogP98) and tooth refractivity (AMR98).
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Orbitals
View atomic orbital models based on breakthrough numbers with the Orbitals widget. Many options are available for customizing the graphics, which can then be output to an image. A great way to view the different orbital shapes.
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Gamma Correction
Gamma correction alters the brightness model of the graphics to compensate for the non-linear brightness physics of your monitor. ChemDoodle 3D defaults to a standard value of 2.two, only you tin can modify this equally appropriate for your screen.
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Art
Easily create ultra-realistic images, sketches, cartoons, paintings and more than creative illustrations
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Shader Programs
Shader programs are advanced instructions sent to the graphics carte du jour on how 3D graphics are generated. ChemDoodle 3D provides you with several built-in shaders to return your graphics, to create realistic styles like plastic and unrealistic styles like cartoons. Shaders in ChemDoodle 3D also provide boosted features, such as outlining and shadows.
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Lighting
Control the color and direction of the lighting.
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Shading Model
A shading model is the method for converting the scene information into colors implemented past the shader plan. Ambient-Lengthened-Specular (ADS) theory tin can be implemented in many dissimilar ways to create shaders that produce realistic graphics and non-realistic graphics. ChemDoodle 3D implements the following shading model types to cull from, all based on the ADS shading model:
- None
- Flat
- Cartoon
- Gouraud
- Phong
- Blinn-Phong
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Renderers
A renderer is the consummate procedure in which we communicate with the graphics card using ane or more shaders to produce a final paradigm. In the simplest process, a single call is fabricated to the graphics card where we pass in the scene data and produce an image with a unmarried shader programme. This is what we call a forward renderer.
The downside of a forward renderer, is each pixel is calculated in isolation, limiting the techniques we can reach. We can instead concatenation several rendering passes through the graphics carte du jour together, using the output of one consummate pass as input into another. This allows the software to produce some advanced furnishings.
In ChemDoodle 3D, you lot will detect styles for 3 different types of renderers: (1) the forward renderer (2) the deferred renderer and (3) after effects.
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Anti-aliasing
Anti-aliasing smooths out the crude pixel edges in graphics (known as jaggies). ChemDoodle 3D supports both hardware (MSAA) and software (FXAA) anti-aliasing.
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Shadows
Fully customizable, real-time, dynamic shadows add a major sense of realism to your graphics.
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3D Textures
Textures apply a surface styling to the objects rendered in the scene. This is washed by defining some design in three dimensions, similar to how yous would run across 3 dimensional patterns if you were to cut into a block of wood. The objects are and then crafted out of this design to produce the graphics, allowing you to produce a number of interesting styles. Choose from granite textures, wood, stripes and more.
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Fogging
Define fogging using linear, exp1 and exp2 algorithms. Requite incredible depth to your graphics or focus on specific sections with these features.
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Screen Space Ambience Occlusion
Screen space ambience apoplexy (SSAO) simulates the occlusion of ambient calorie-free in corners and crevasses of 3D objects. If you wait 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 paradigm and greatly helps with perception of topography. This technique is fully customizable in ChemDoodle 3D.
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Outlining
Outline effects are created by finding significant changes in cached data values from pixel to pixel. At that place are two types of outline algorithms provided in ChemDoodle 3D: Trace and Creative. You can control colors, thicknesses, sketchiness and more!
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Depth of Field
A depth of field effect focuses in on a specific portion of your scene, emulating images made with camera lenses. You tin can define the outset and catastrophe focus depths as well as the extent of the unfocused blur and dilate effects.
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After Effects
After effects are advanced prototype filters. ChemDoodle 3D includes the post-obit after effects:
- Blur (Gaussian)
- Mistiness (Kuwahara)
- Blur (Median)
- Amplify
- Border Detection
- Pixelize
- Posterize
- Sharpen
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Modeling
Collaborate with your structures in existent-time with advanced physical simulations
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Existent-time Optimization
ChemDoodle 3D's molecular modeling procedures tin be run in existent-time (using the Minimizer widget) so you tin interact with molecules while y'all are edifice them or easily alter betwixt conformations. Our modeling engine is fast and efficient, allowing you to quickly generate relevant 3D coordinates for your built structures.
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The Optimization Function
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.
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Accurate Force Field Implementations
ChemDoodle 3D includes implementations of several published force fields. Our implementations are some of the most authentic and consistent in the manufacture.
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Universal Force Field
The Universal Force Field (UFF) is excellent for chop-chop building partial and consummate chemical structures for demonstrations and images every bit it tin handle the vast majority of the periodic table. A consummate implementation is included in ChemDoodle 3D.
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Merck Molecular Strength Field
The Merck Molecular Force Field (MMFF94) and its static variant (MMFF94s) are both accurately implemented in ChemDoodle 3D. Use this force field to generate experimentally accurate geometries for measurements and calculations.
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General Amber Strength Field
The Full general Bister Strength Field (GAFF) is compatible with the Bister Strength Field for proteins and nucleic acids.
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VSEPR Force Field
The Valence Shell Electron Pair Repulsion (VSEPR) strength field is a very specific Points-On-a-Sphere (POS) force field. The entire purpose of this force field is to produce ideal shapes for VSEPR theory. The VSEPR force field is perfect for students and instructors to use and demonstrate why certain cantlet centers, along with electron pairs, atomic number 82 to certain shapes in molecular structures. Up to 8 connections on a eye 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. When using the VSEPR strength field, the Minimizer widget volition instead brandish the current molecular geometry and VSEPR shape of the atomic centre yous are editing.
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Accuse Models
Several accuse models are implemented in ChemDoodle 3D: Gasteiger-Marsili PEOE, MMFF94, QEq and QTPIE. You can also use these charge models to color molecular surfaces.
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Atom Typing
Atom typing is an essential step in the correct application of a strength field. You can run into what cantlet types are defined to the atoms in ChemDoodle 3D for the specific force field you are using. Y'all may even output the atom types for utilise in other applications.
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Forcefulness Rendering
Forces can be rendered to show how the molecule will change given the force field gradient calculations.
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Algorithm Transparency
In addition to showing you the atom typing and force vector calculations, ChemDoodle 3D will let you lot know when a structure is not compatible with a specific forcefulness field by providing descriptive errors and warnings. Use all of this information for reliability and referencing.
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Parallel Processing
Parallel processing allows y'all to employ the ability of your multi-core CPU to speed up computations. The force fields in ChemDoodle 3D are specially designed to run in parallel. This ways that your structure, which would unremarkably accept x seconds to optimize, volition now merely take a fraction of x seconds to optimize. Enable parallel processing in ChemDoodle 3D when you lot want to handle the optimization of a large structure or organization. Understanding how parallel processing works and is implemented in ChemDoodle 3D is very important. We accept an entire section covering parallel processing in the ChemDoodle 3D user guide.
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Thorough Documentation
New to molecular modeling? No worries. Nosotros have an entire chapter in the ChemDoodle 3D user guide dedicated to molecular modeling and how information technology is implemented. You will be optimizing structures in no time.
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Stereoscopy
Augmented reality on your estimator
Anaglyphs
Anaglyphs are a stereoscopy technique used to show images in 3D space to our optics from a 2D epitome. It works by rendering the scene for each eye'southward perspective in a different color space. Special glasses are and then used to filter out each heart'southward image so one eye cannot run across what the other middle sees. Our brain then pieces the two images together to notice the scene in 3D space.
Hardware
Anaglyphs are fully implemented with back up for red-cyan, dark-green-magenta, and bister-bluish anaglyph spectacles, which tin be purchased cheaply from online retailers.
Customization
The Dubois method has been implemented for the most comfy anaglyph viewing and you can control both the focal length and eye separation parameters to customize the anaglyph to your preference.
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Models & Printing
Several models have been exported from ChemDoodle 3D and printed using a 3D printer. These are bang-up for gifts and celebrating your ain scientific discoveries!
Export the objects you create for 3D printing and other CAD applications
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Model Files
Export your ChemDoodle 3D creations into many pop 3D models file types:
- 3D Manufacturing Format {.3mf}
- Additive Manufacturing File Format {.amf}
- COLLADA Digital Nugget Exchange {.dae}
- Extensible 3D Graphics {.x3d}
- Polygon File Format {.ply}
- STereoLithography {.stl}
- Virtual Reality Modeling Linguistic communication {.wrl}
- Wavefront Object File {.obj}
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Characteristic Back up
ChemDoodle 3D supports as much of each format as possible, including meshes, normals, materials, transparency, colors and multicolors.
Note some formats are less capable. For instance, the STL format cannot store colors, so use a more capable format like the VRML formats to accommodate your application.
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Options
Format specific options are also implemented, such as both binary and ASCII back up for STL and PLY files and caching and compression for VRML files.
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Small-scale Molecules
Build and visualize your molecules in 3D
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Intuitive Controls
ChemDoodle 3D'southward edifice controls are fabricated to conspicuously model the atoms and bonds they manage. Copious visual feedback is provided. There are also many options for customizing the building tools to your preference.
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Advanced Selections
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, assuasive y'all to precisely investigate and select content.
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six Bail Types
6 physically relevant bond types are provided to create any blazon of chemical representation. No other program compares.
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Smart Bonds
ChemDoodle 3D renders multiple bonds that are able to orient themselves towards the camera for the about descriptive graphics.
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Optimize Zone
When building 3D structures, ChemDoodle 3D will automatically propose the best place in three dimensions to add an cantlet connection. This helps you rapidly build molecules. You lot tin then simply turn on the minimizer to optimize physical coordinates. No other program has an optimize zone like ChemDoodle 3D's!
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Assurance and Sticks
Y'all have full control over how atoms and bonds are rendered, and you tin speedily choose from predefined representations, such equally van der Waals spheres, ball and stick, stick, wireframe and line.
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Prove Labels
ChemDoodle 3D's advanced graphics engine can render text beautifully. Use this to show atom labels. Yous have full control over font, size and color.
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Add Hydrogens
Hydrogens volition exist added for you to your structures in appropriate 3D locations.
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Implicit Hydrogens
Implicit hydrogens are automatically tracked for your structures, but you can also override them as appropriate.
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Attributes
Ascertain charges, radicals and isotopic mass values to atoms. These values are also properly read in and written to chemic file formats.
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Electron Pairs
Electron pairs and single electron (radical) objects are rendered on your structure and automatically placed for you (you may also manually place them). Utilize electron pairs in conjunction with the VSEPR force field to model VSEPR shapes.
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Effluvious Representations
Employ toruses for aromatic circles or use resonance bonds that automatically orient to the middle of rings.
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Stereochemistry
Perceive stereochemistry for 3D structures. CIP stereochemistry is adamant for chiral centers, double bonds and allenes/cumulenes using our advanced and authentic CIP algorithms. Mutual cis/trans stereochemistry tin also be adamant for double bonds.
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Optimize Structures
Speedily generate 3D coordinates for your structures using several algorithms.
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Measurements
Measure distances, angles and torsions in your structures.
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Cheminformatics Functions
Quickly admission powerful functions to help modify your graphics: saturation, Kekulization, ring perception, distance geometry embedding, and more.
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Database Lookup
Search databases (PubChem, ChemSpider, ChemExper) for chemical structures and drag them right into your 3D scene using the MolGrabber widget.
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Macromolecules
In addition to creating beautiful graphics for small molecule structures, ChemDoodle 3D will as well help yous to edit and create graphics for protein and nucleic acid macromolecules. The above paradigm was rendered in ChemDoodle 3D of Protein Data Bank entry 5LRS with two solvent accessible surfaces rendered for the poly peptide chains and using the None shader.
3D scientific graphics, large and small!
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Poly peptide Data Banking concern Format
ChemDoodle 3D reads poly peptide and nucleic acrid information from PDB files and generates high quality meshes that are superimposed over the atom and bond coordinates.
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Macromolecular Manual Format
ChemDoodle 3D too fully supports the RCSB Macromolecular Manual Format for incredibly fast input of Protein Data Bank files with full bond order information.
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Protein Ribbon Models
Beautiful protein ribbons and traces are generated. Tubes, cylinder and plank models and cartoon models can also be generated. These models can be segmented, colored and completely controlled through styles. For case, y'all can alter the ribbon thickness or the alpha helix width.
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Nucleic Acid Ladder Models
Accurate nucleic acid ladder models are generated. These models can exist colored and completely controlled through styles. For instance, yous tin can modify the backbone thickness or the platform tiptop.
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Interpolation Algorithms
ChemDoodle 3D can utilise either a B-Spline algorithm or the Catmull-Rom algorithm for generating models. The Catmull-Rom spline creates more authentic models, but the B-Spline algorithm produces smoother and more aesthetic results.
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Balance Atoms and Bonds
Control residual atoms and bonds separately from the residual of the structures for unique graphics.
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Water
Show and hide water atoms divers in PDB files and represent them with stars instead of spheres.
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Periodic Systems
Unit cells are a great way to investigate repeating structures and crystals. The above image was rendered in ChemDoodle 3D of the zeolite Si-O framework, MFI, propagated along the z-axis with exponential fogging using the standard Blinn-Phong shader.
Infinitely repeating chemical science
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Crystallographic Information Format
ChemDoodle 3D reads periodic information from CIF files and can fully resolve point groups and symmetries. Unit of measurement cells for whatever symmetry geometry are extracted.
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Unit Cells and Extrapolated Supercells
Unit cells are rendered and supercells tin can be generated. Use an orthographic projection to get the best view.
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Nanotubes
Build armchair, zigzag and chiral nanotubes with several options. Periodic systems of nanotubes are automatically generated. A great way to output nanotube geometries for other applications.
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Universality
ChemDoodle 3D is designed to perform everywhere for everyone
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Operating Systems
Fully supported on Windows, macOS and Linux.
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High DPI Support
Full support for high resolution displays, such as Retina Macs and the Microsoft Surface Pro.
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Accessibility
Control interface colors, interface font sizes, ascertain cursors and a cursor left-handed and right-handed manner brand it comfy for about users to employ the software. You can too fully define all of the carte item accelerators (except the ones forced past the operating system) and tool shortcuts.
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Mobile Devices
A ChemDoodle license includes access to our ChemDoodle Mobile app companion for iOS (iPod/iPhone/iPad), Android and other mobile devices.
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3rd Party Integration
ChemDoodle 3D works with several partners to assist you improve your workflow. These partners include databases like PubChem, ChemExper and ChemSpider, ELNs such as LabArchives and social networking services similar Twitter.
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Twitter Integration
Chop-chop tweet your selected content from ChemDoodle 3D.
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Continuously Adult
We are always adding new features, and our customers continuously enjoy new updates with peachy new innovative solutions and tools that they have requested. Your license entitles you to all updates.
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Chemical Files
Read and write many popular 3D chemic file types for working with the applications you utilize:
Beilstein ROSDAL (.ros), Crystallographic Data Format (.cif), CHARMM Carte File (.crd), Chemical Markup Language (.cml), Daylight SMILES (.smi, .smiles), ChemDoodle 3D Scenes (.ic3), ChemDoodle Javascript Data (.cwc.js), IUPAC InChI (.inchi), MDL MOLFiles, both V2000 and V3000 connectedness tables (.mol, .mdl), MDL SDFiles (.sdf, .sd), RCSB BinaryCIF (.bcif), RCSB Macromolecular Crystallographic Information File (.cif, .mcif, .mmcif), RCSB MacroMolecular Transmission Format (.mmtf), RCSB Protein Data Bank Files (.pdb, .ent), RCSB Protein Data Bank Markup Language (.xml, .pdbml), Schrödinger MacroModel (.mmd, .mmod), Tripos Mol2 (.mol2, .ml2, .sy2), Tripos Sybyl Line Note (.sln), XYZ Files (.xyz)
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Bitmap (Raster, Pixel) Images
Write a large number of bitmap (also known every bit raster or pixel) images for use with other applications. Some formats have boosted options, such as controlling output resolution in PNG, JPEG, and TIFF images.
- CompuServ Graphics Interchange Format {.gif}
- Joint Photographic Experts Group {.jpg, .jpeg, .jpe, .jfif, .jfi, .jif}
- Microsoft Bitmap {.bmp, .dib}
- Portable Network Graphics {.png}
- Tagged Paradigm File Format {.tiff, .tif}
- UNIX Portable PixMap {.ppm, pnm, pbm, pgm}
- Wireless Bitmap {.wbmp}
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Web Components
Produce 3D ChemDoodle Spider web Components, which are loftier-quality, interactive, HTML5 components for websites and web apps that piece of work in Microsoft Edge, Mozilla Firefox, Google Chrome, Apple Safari and Opera, and even on Mobile Safari on iOS and Chrome for Android.
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References
All of the resources we use to develop the algorithms in ChemDoodle 3D or the choices we make for the software are documented in the Help carte du jour. This way you can evaluate the quality of our piece of work.
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Thorough Documentation
A thorough user transmission is gratuitous to download. Information technology is in PDF format, fully searchable with a fully linked table of contents and index.
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Screenshots
Windows interface
macOS interface
Linux interface
Interface: Building a molecule
Interface: Working with Protein Data Banking company entry 3N4B
Interface: Generating a chiral carbon nanotube
Unlike models rendered for the Poly peptide Data Bank entry 1CRN
Different surface representations for the antibiotic ampicillin
A ball and stick representation of aspirin, with several measurements shown
Various structures (with electron pairs) optimized in ChemDoodle 3D using the VSEPR strength field. Enhanced repulsion was enabled for an accurate bend angle in water. Some angle measurements are shown. ChemDoodle 3D as well deduces molecule geometry and VSEPR shapes.
A close up expect at 3D models printed from ChemDoodle 3D. Starting at the tiptop right, and going clockwise: 3N4B (rainbow tubes), aspirin (Connolly surface, Gasteiger charge function), DDT (ball and stick), 7OVF (Conolly surface, MR function)
Visualizing the internal channels of the zeolite LTA, using a molecular surface on the (-1->1) supercell, with two distances measured and rendered with a Blinn-Phong shader
A MMFF94 optimized model of sildenafil shown with aromatic circles and a Connolly surface (QEq colour function) rendered with the Cartoon shader
The PDB entry 5GZC, showing a ribbon trace through the brawl and stick representation of the poly peptide rendered with the Blinn-Phong shader
PDB entry 2NDO, with a grey background and slight fogging, tubes and stick models for the chain and a vdW model for the small-scale molecule, rendered with the Blinn-Phong shader
PDB entry 3QDU, with 4 solvent accessible surfaces surrounding each concatenation, rendered with the Phong shader
PDB entry 5F60, rendered with a cartoon shader, showing a vdW surface on the largest small molecule, with line and ribbon rendering for the chain, slight fogging and labels shown in an artistic fashion
PDB entry 3N4B with flat ribbons in rainbow color, rendered with a "none" shader, with SSAO on and SSAO mistiness off (to testify a pastel pad texture), and a sketchy outline added to produce a nice hand-drawn consequence
An acetaminophen molecule with Connolly surface, with water molecules in the background blurred with a depth of field technique
PDB entry 2POR, rendered in an creative outline, with soft strokes and increased thickness closer to the camera
PDB entry 3N4B with a Taylor amino acid color set, with a Kuwahara mistiness on top of a depth of field technique, to create a water painting expect where colors bleed into each other
A spacefilling model of PDB entry 3N4B, rendered with SSAO and a Kuwahara blur to produce an oil painting effect
The drug paxil, rendered with a cartoon shader and trace outlines
A realistic looking spacefilling render of PDB entry 6U4V, made to await like a plastic model, with SSAO, shadows and a high shininess value
A brawl and stick model of molecule Ddt, rendered with SSAO and shadows
A spacefilling model of molecule Dichloro-diphenyl-trichloroethane, rendered with SSAO and shadows
Showing how shadows and SSAO greatly benefit topography percecption for PDB model 2POR
A cyclophane is rendered with a Wood texture and SSAO through the Cartoon shader, Pymol colors are used for atoms with a chocolate-brown bond color
A solvent excluded surface of Paxil is colored by accuse value and rendered with a Granite (Marbled) texture using SSAO
The PDB entry 7NER is rendered as a cartoon model using the Cartoon shader, with a Stripes texture practical
An anaglyph (cerise-cyan glasses required) image utilizing the Dubois method of PDB model 3N4B with all residue atoms rendered in wireframe and the poly peptide rendered equally a cylinder and plank model.
ChemDoodle 3D helps you visualize atomic orbitals. Clipping planes are used to amend visualize the f orbitals.
General preferences
Styles Preferences
Advanced preferences
Try ChemDoodle 3D earlier you buy
A free trial for ChemDoodle 3D lasts for xiv days with some features restricted. The trial is not an obligation and we require no identifying or financial information to first a trial. Afterward xiv days, the trial will no longer open. Our free trials are only for evaluation purposes and whatsoever output from the trial will contain a watermark and is copyright of iChemLabs.
To commencement your trial, but download ChemDoodle 3D for your operating organization below, install and open information technology. And so accept the EULA. The next page will ask for a license code, instead click the Free Trial push button to brainstorm.
When yous are set, you may purchase a ChemDoodle license here:
SHA256:
ee91be221fc106e15ba058c6deedcca08550c79ea491baeb8a67a435aa86e61f
SHA256:
0e642a75e10fb4ea6b4d1ab5d3d619c867a83a0b27e370c887925907b1000faf
SHA256:
92618838f050a4e54cf0ccc06cbf273d93bcb9e705959586169ba6bcb508e603
Organisation Requirements
- Windows Vista/7/8/10/11+, macOS ten.11+ (El Capitan, Sierra, High Sierra, Mojave, Catalina, Big Sur, Monterey or more contempo), or Linux.
- A 64 fleck (x86_64 or Apple Silicon) processor is required.
- ChemDoodle 3D requires OpenGL v2.1 drivers.
- A minimum of 1GB of retentiveness.
Exercise you have whatsoever questions?
Source: https://www.chemdoodle.com/3d/
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