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Help

Download PDF: docs/manual.pdf

Click 1 of the subjects below to learn more. You can also watch some videos on YouTube to get started.

Subjects

Drawing structural formulas

MolView consists of ii main parts, a structural formula editor and a 3D model viewer. The structural formula editor is surround past three toolbars which contain the tools y'all can utilise in the editor. Once y'all've fatigued a molecule, yous can click the 2nd to 3D button to convert the molecule into a 3D model which is so displayed in the viewer. Below is a list of all sketch tools.

Tiptop toolbar

• Trash: clear the unabridged canvas
• Eraser: erase atoms, bonds or the current option
• Undo/redo: undo or redo your recent changes
• Selection tools: all these tool can be used to drag the electric current selection or individual atoms and bonds. You tin can add/remove atoms and bonds to the selection by clicking them. If you have selected a separate fragment, you can rotate information technology by dragging an atom in the selection. You can delete the selection using the DEL key or using the eraser tool. Each tool has different behavior for the right mouse button:
  • Drag: move the entire molecule (you can already utilise the left mouse push for this)
  • Rectangle select: select atoms and bonds using a rectangular choice expanse
  • Lasso select: select atoms and bonds past cartoon a freehand selection area
• Color way: brandish atoms and bonds using colors
• Full mode: displays all C and H atoms instead of skeletal display
• Eye: centers the whole molecule
• Clean: cleans the structural formula using an external service
• 2D to 3D: converts the structural formula into a 3D model

Left toolbar

• Bonds: pick i of the bond types (single, double, triple, upwardly, down) and add or modify bonds
• Fragments: pick 1 of the fragments (benzene, cyclopropane, etc.) and add fragments
• Concatenation: create a chain of carbon atoms
• Accuse: increment (+) or decrement (-) the accuse of atoms

Right toolbar

In this toolbar you can select from a number of elements, you can also choice an element from the periodic tabular array using the last button. You can use the element to create new atoms or modify existing atoms.

Finding structures

You can load molecules from big databases like PubChem and RCSB using the search form located on the left side of the menu-bar. Just type what y'all are looking for and a list of available molecules will appear.

You can as well click on the dropdown button next to the search field to select a specific database. This will perform a more extensive search on the selected database. Currently, three big databases are supported:

1. PubChem
2. The RCSB Protein Data Banking concern
3. The Crystallography Open up Database

Tools

The Tools menu contains several utility functions which are listed below.

Link

Yous tin can embed a specific compound, macromolecule or crystal using the provided URL or HTML code. Note that the linked structure is the one which is currently displayed in the model window. You lot can also re-create the URL from the address bar in gild to link to the electric current construction.

Consign

Export options:

• Structural formula image: sketcher snapshot (PNG with alpha channel)
• 3D model paradigm: model snapshot (PNG, alpha channel in Glmol and ChemDoodle)
• MOL file: exports a MDL Molfile from the 3D model (common molecules)
• PDB file: exports a Protein Data Bank file from the 3D model (macromolecules)
• CIF file: exports a Crystallographic Data File from the 3D model (crystal structures)

Information card

This collects and displays information about the structural formula.

Spectroscopy

This shows a new layer where you can view molecular spectra of the current structural formula (loaded from the Sketcher) More details are covered in the Spectroscopy chapter.

3D model resource

This redirects you lot to the web-page for the current 3D model on the website of its source database (except when the model is resolved using the Chemical Identifier Resolver)

Avant-garde search

These functions allow y'all to perform some avant-garde searches through the PubChem database using the structural formula from the sketcher.

1. Similarity search: search for compounds with a similar structural formula
2. Substructure search: search for compounds with the electric current structure every bit subset
3. Superstructure search: search for compounds with the current structure as superset

Spectroscopy

Yous can open the Spectroscopy view via Tools > Spectroscopy. You can view three kinds of molecular spectra.

1. Mass spectrum
2. IR spectrum
3. H1-NMR prediction

Export data

You can also export dissimilar kinds of data from the currently selected spectrum.

• PNG image: snapshot from interactive spectrum
• JCAMP file: JCAMP-DX file of the electric current spectrum

3D model

The Model menu contains some general functions for the 3D model.

Reset

This function sets the model position, zoom and rotation back to default.

Representation

You tin can choose from a list of different molecule representations including; ball and stick, stick, van der Waals spheres, wireframe and lines. Macromolecules are automatically drawn using ribbons.

Groundwork

You can switch between a black, gray or white groundwork. The default background is blackness (exported images from GLmol or ChemDoodle have a transparent background)

Engines

You lot can choose from three different render engines: GLmol, Jmol and ChemDoodle. GLmol is used as default render engine. GLmol and ChemDoodle are based on WebGL, a browser engineering science to support 3D graphics. If WebGL is not available in your browser, Jmol will be used for all rendering.

MolView automatically switches to:

1. Jmol if you execute functions from the Jmol menu
2. GLmol if you lot load macromolecules (due to significant college performance)
3. ChemDoodle if yous load a crystal structure (GLmol cannot render crystal structures)

Yous might want to switch back to GLmol when you practise no longer need Jmol or ChemDoodle since GLmol has a ameliorate functioning.

Annotation that macromolecules are fatigued slightly different in each engine. ChemDoodle provides the finest display. You should, however, avert using ChemDoodle for very large macromolecules.

Model transformation

You tin can rotate, pan and zoom the 3D model. Use the right button for rotation, the heart push for translation (except for ChemDoodle) and the scrollwheel for zooming. On touch on devices, you can rotate the model with i finger and scale the model using two fingers.

Crystallography

You tin load an array of crystal cells (2x2x2 or 1x3x3) or a single unit jail cell when viewing crystal structures.

Fog and clipping

When you are viewing big structures, like proteins, it tin can be useful to hibernate a certain part using fog or a clipping aeroplane. GLmol offers a few options to do this.

1. Fog: you can move the fog forward by dragging the mouse up while property CTRL + SHIFT (elevate in the opposite direction to move the fog backward)
2. Clipping plane: you lot can motility a frontal clipping plane into the structure by dragging the mouse to the left while holding CTRL + SHIFT (elevate in the opposite direction to move the clipping plane back)

Protein display

The Protein menu offers a number of protein brandish settings including different color schemes and unlike concatenation representations.

Bear witness bio assembly

When loading a protein structure, MolView shows the asymmetric unit past default. This function allows you to view the total biological unit instead.

Chain representation

Y'all can cull from four different chain representations. You tin besides view the full concatenation construction past enabling the Bonds option.

1. Ribbon: draws ribbon diagram (default representation)
2. Cylinder and plate: solid cylinders for α-helices and solid plates for β-sheets
3. B-factor tube: tube with B-gene as thickness (thermal motion)
4. C-alpha trace: lines between cardinal carbon atom in amino-acids (very fast rendering)

Chain coloring

You tin choose from vi chain color schemes.

1. Secondary structures: unlike colors for α-helices, β-sheets, etc.
2. Spectrum: color spectrum (rainbow)
3. Chain: each chains gets a different color
4. Remainder: all amino-acid residues are colored differently
5. Polarity: colors polar amino-acids scarlet and not polar amino-acids white
6. B-cistron: blue for low B-factor and red for high B-cistron (if provided)

Advanced Jmol tools

The Jmol bill of fare offers some awesome Jmol-simply functions and calculations.

Clear

Clears all executed calculations and measurements.

High Quality

Enables High Quality rendering in Jmol (enabled by default on fast devices) When turned off, anti-aliasing is disabled and the model is drawn using lines while transforming it.

Calculations

You tin can perform the post-obit Jmol calculations in Jmol:

• MEP surface clear-cut/opaque: calculates and projects molecular electrostatic potential on a translucent or opaque van der Waals surface
• Accuse: calculates and projects diminutive charge as text label and white to atom color gradient
• Bond dipoles: calculates and draws individual bond dipoles
• Overall dipole: calculates and draws net bond dipole
• Energy minimization: executes an interactive MMFF94 energy minimization (note that this function simply executes a maximum of 100 minimization steps at a time)

Measurement

You tin measure out distance, bending and torsion using Jmol. You can actuate and conciliate one of these measurement types via the Jmol menu.

• Distance altitude between two atoms in nm
• Bending angle between two bonds in degrees
• Torsion torsion betwixt four atoms in degrees

Note that in some cases, the resolved 3D model is only an approach of the real molecule, this ways y'all take to execute an Energy minimization in order to exercise reliable measurements.

Embed

Note: the strutural formula is non the same structure equally the 3D model

Width

Summit

HTML lawmaking

You tin can use the HTML lawmaking below to embed the current 3D model in your website.

Embed URL

riveradidepubse.blogspot.com

Source: https://molview.org/

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