MolView is a web application for drawing, searching and viewing chemical structures.
Click one of the subjects below to learn more. You can also watch some videos on YouTube to get started.
You can draw structural formulas using the sketching component.
The top toolbar contains all general editing tools. These tools include a clear all tool, an erase tool, a move atoms tool, an undo and redo tool, two selection tools, a clear selection tool, a center structure tool, a cleanup tool and a resolve tool. The last one converts the structural formula to a 3D molecule displayed in the model window.
In the left toolbar, you can select a tool you want to use in order to modify or extend the structural formula. In order to draw a carbon chain using the chain tool, you have to click a start point or atom and drag a chain.
The right toolbar contains some common elements and a periodic table tool in case you want to use another element. Note that you can only replace existing atoms. So in order to add an atom, you frist have to add a new bond using the tools from the left toolbar.
You can load structures from large databases like PubChem via the search field located on the right side of the menubar. Just type whatever and enter or click the kind of structures you want to find:
It's recommended to use only one or two words for crystal structures search due to database limitations.
You can show or hide search results using the leftmost button. Note that proteins search is absent on mobile browsers which do not support WebGL (because they cannot display proteins fast enough)
You can find the general 3D Model menu in the menubar.
This function sets the model position, zoom and rotation back to default.
You can choose from a list of different molecule representations including; ball and stick, stick, van der Waals spheres, wireframe and lines. Proteins are automatically drawn using ribbons.
You can choose from three different render engines. MolView uses GLmol, Jmol and ChemDoodle Web as render engines. MolView automatically switches to:
You might want to switch back to GLmol after case 2 and 3.
Note that proteins are drawn slightly different in each engine. ChemDoodle Web provides the most sophisticated protein display. You should, however, avoid using ChemDoodle Web for large proteins.
This submenu contains functions to load an array of crystal 'boxes'.
You can find the Tools menu in the menubar. This menu contains several utility functions.
You can link to a specific compound, protein or crystal using URL parameters. This menu gives you two options:
If you only want to link to the current chemical structure, you can also copy the URL from the adress bar. (make sure the URL links to the right structure by reloading the page)
Export options in the Export menu:
Depending on the situation, this function gives you more information about the current molecule.
This method shows a dialog where you can view spectra related to the structural formula from the sketcher. More details are covered in chapter 5.
You can perform three types of advanced search based on the structural formula from the sketcher.
The Spectroscopy menu item is located under Model > Chemical data in the menubar. This menuitem shows the spectroscopy dialog where you can choose from a number of spectra (if available)
The spectroscopy dialog allows you to export two kind of files from the current spectrum:
Jmol provides several advanced functions. Some of these can be accessed via the Jmol menu in the menubar.
Clears all executed calculations and measurements.
You can perform the following Jmol calculations in Jmol:
You can perform the following measurements in Jmol:
In Jmol, you can switch between different render modes in order to speed up performance or to increase quality.
There are three render modes:
If you still have questions, found bugs or want to request new features. You can discuss them with me via social media or send me an email.
make sure to resolve the strutural formula if you want to share the molecule from the sketcher