3d chemical structure drawing software

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Download PDF: docs/manual.pdf

Click ane of the subjects below to acquire more. You lot can also watch some videos on YouTube to become started.

Subjects

Drawing structural formulas

MolView consists of ii chief parts, a structural formula editor and a 3D model viewer. The structural formula editor is surround by 3 toolbars which comprise the tools you tin use in the editor. In one case you've drawn a molecule, you can click the 2D to 3D push to catechumen the molecule into a 3D model which is then displayed in the viewer. Beneath is a list of all sketch tools.

Pinnacle toolbar

• Trash: clear the entire canvas
• Eraser: erase atoms, bonds or the current pick
• Undo/redo: undo or redo your recent changes
• Selection tools: all these tool can be used to drag the current selection or individual atoms and bonds. You lot can add/remove atoms and bonds to the selection past clicking them. If you take selected a separate fragment, you tin rotate information technology by dragging an atom in the choice. Yous can delete the selection using the DEL key or using the eraser tool. Each tool has different behavior for the right mouse push button:
  • Elevate: movement the entire molecule (you can already use the left mouse push button for this)
  • Rectangle select: select atoms and bonds using a rectangular selection area
  • Lasso select: select atoms and bonds by drawing a freehand selection expanse
• Color mode: display atoms and bonds using colors
• Full mode: displays all C and H atoms instead of skeletal display
• Center: 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: option ane of the bond types (single, double, triple, up, downwards) and add or modify bonds
• Fragments: pick one of the fragments (benzene, cyclopropane, etc.) and add fragments
• Concatenation: create a chain of carbon atoms
• Accuse: increase (+) or decrement (-) the charge of atoms

Right toolbar

In this toolbar y'all tin can select from a number of elements, yous can also option an element from the periodic table using the terminal push button. You can utilize the element to create new atoms or modify existing atoms.

Finding structures

You lot tin load molecules from large databases like PubChem and RCSB using the search form located on the left side of the carte-bar. Just blazon what you are looking for and a list of available molecules will announced.

You can likewise click on the dropdown push button next to the search field to select a specific database. This volition perform a more than all-encompassing search on the selected database. Currently, three big databases are supported:

1. PubChem
2. The RCSB Protein Information Bank
3. The Crystallography Open up Database

Tools

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

Link

You tin can embed a specific chemical 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 copy the URL from the address bar in order to link to the current structure.

Consign

Export options:

• Structural formula image: sketcher snapshot (PNG with alpha channel)
• 3D model image: 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 Information Bank file from the 3D model (macromolecules)
• CIF file: exports a Crystallographic Information File from the 3D model (crystal structures)

Information card

This collects and displays data well-nigh 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-folio 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 you to perform some advanced 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 equally subset
3. Superstructure search: search for compounds with the current structure as superset

Spectroscopy

You can open up the Spectroscopy view via Tools > Spectroscopy. Y'all tin view three kinds of molecular spectra.

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

Export data

You tin also export different kinds of data from the currently selected spectrum.

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

3D model

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

Reset

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

Representation

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

Background

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

Engines

You can cull from three unlike render engines: GLmol, Jmol and ChemDoodle. GLmol is used every bit default return 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 yous execute functions from the Jmol menu
2. GLmol if y'all load macromolecules (due to meaning higher functioning)
3. ChemDoodle if you load a crystal structure (GLmol cannot render crystal structures)

You might want to switch back to GLmol when y'all do no longer demand Jmol or ChemDoodle since GLmol has a meliorate performance.

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

Model transformation

You can rotate, pan and zoom the 3D model. Utilize the right button for rotation, the middle button for translation (except for ChemDoodle) and the scrollwheel for zooming. On bear upon devices, y'all can rotate the model with one finger and calibration the model using ii fingers.

Crystallography

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

Fog and clipping

When you are viewing big structures, similar proteins, it tin can be useful to hide a sure function using fog or a clipping aeroplane. GLmol offers a few options to do this.

1. Fog: you can move the fog forrad past dragging the mouse upwardly while holding CTRL + SHIFT (elevate in the reverse management to move the fog backward)
2. Clipping aeroplane: y'all can move a frontal clipping plane into the structure by dragging the mouse to the left while holding CTRL + SHIFT (elevate in the opposite direction to motion the clipping plane back)

Protein brandish

The Protein carte du jour offers a number of protein display settings including different colour schemes and different chain representations.

Show bio assembly

When loading a protein structure, MolView shows the disproportionate unit of measurement by default. This function allows you to view the full biological unit of measurement instead.

Concatenation representation

You can choose from four different concatenation representations. Y'all can also view the full concatenation structure by enabling the Bonds selection.

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 motility)
4. C-alpha trace: lines between central carbon atom in amino-acids (very fast rendering)

Chain coloring

You lot can choose from six concatenation color schemes.

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

Advanced Jmol tools

The Jmol menu offers some awesome Jmol-only functions and calculations.

Articulate

Clears all executed calculations and measurements.

High Quality

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

Calculations

Yous can perform the following Jmol calculations in Jmol:

• MEP surface lucent/opaque: calculates and projects molecular electrostatic potential on a translucent or opaque van der Waals surface
• Accuse: calculates and projects atomic charge as text label and white to atom color slope
• Bond dipoles: calculates and draws individual bail dipoles
• Overall dipole: calculates and draws cyberspace bond dipole
• Free 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 can mensurate distance, angle and torsion using Jmol. Yous tin actuate and deactivate i of these measurement types via the Jmol carte.

• Distance distance between two atoms in nm
• Angle angle between two bonds in degrees
• Torsion torsion between 4 atoms in degrees

Note that in some cases, the resolved 3D model is only an approach of the existent molecule, this ways you lot have to execute an Free energy minimization in lodge to practice reliable measurements.

Embed

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

Width

Meridian

HTML code

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

Embed URL

maginnisfaile1988.blogspot.com

Source: https://molview.org/

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