Contact Site Moderator
Dr. Robert E. Belford
MolView started out as 2D to 3D structure converter where the user can draw a structural formula and view a generated 3D conformer that was generated using the Chemical Identifier Resolver(e). The ability to search by name using the Chemical Identifier Resolver was added later as an experimental feature. This turned out so well I added integrations for PubChem, RCSB and the Crystallography Open Database. Now MolView has become an example of what happens when you bring modern web browser technologies and online scientific data resources together. MolView is available free of charge on molview.org since 1 July 2014. The user base is still rather small (>10k sessions per month) but is growing rapidly.
You might be wondering what you can use MolView for today. The best way to find out is, of course, to visit molview.org and try it out for yourself. To get you started, here is a list of things you might want to try. Each section is also demonstrated in a YouTube video.
You can draw organic molecules in the sketcher on the left side. By default the sketcher shows the structural formula of caffeine. Clear the sketcher by clicking the trash icon in the top-left corner. Then draw a new structure using the sketch tools. You can for example draw a benzene ring, an individual atom or a bond. When you are done drawing the structure, convert the structure to 3D using the '2D to 3D' button in the top-right corner of the sketcher. You can now view and interact with the 3D structure.
Jmol has many powerful computational tools and a few are currently directly accessible in MolView. You can for example render a Molecular Electrostatic Potential surface of the loaded 3D molecule. If you connect a fluorine atom to a hydrogen atom and render a translucent MEP surface, you can clearly see that the fluorine atom attracts electrons much stronger than the hydrogen atom. You can also run an energy minimization via the Jmol menu. This can be useful when the loaded structure is resolved using the Chemical Identifier Resolver. The Chemical Identifier Resolver uses CORINA, a program that splits the molecule into ensembles, looks these ensembles up in a database and assembles them back together.
You can load small crystal structures from the Crystallography Open Database via the search interface. The blue suggestions from the search input are mineral names from the Crystallography Open Database. Additionally you can search trough the entire Crystallography Open Database via the search menu. After you have loaded a crystal structure, you can render a supercell model via the Model menu.
Just like small molecules and crystal structures, macromolecule's can also be loaded into MolView. MolView can retrieve biological macromolecule's from RCSB. You can switch between different color schemes and protein structure representations via the Protein menu.
You can also view certain spectra. To do this, you first have to load or draw a molecule. Then you can open the spectrum viewer via the Tools* menu where you can choose from different spectra. IR and mass spectra are fetched from the NIST Chemistry WebBook. A H1-NMR prediction is calculated using *nmrdb.org. When you select a spectrum, it will be loaded into the interactive spectrum viewer where you can read out the values.
If you write web articles that involve chemistry, the embedding tool from MolView might be just what you need. You can get an embed code for every 3D structure in the viewer by opening the embedding dialog via the Tools menu. You can then paste this embed HTML code into your web page. In future versions you will be able to embed more content such as the spectrum viewer and the sketcher. Below is an example of an embedded caffeine molecule.
Over the past years numerous ideas for new features have come up. I'm now writing a new version with a much higher level of modularity than the current one. This will help me to integrate new exiting stuff. Apart from quite a number of new database integrations, I want to focus on the three other subjects: visualization tools, sketch tools and tools for teachers. The next three sections will explain these subjects in more detail.
Currently MolView uses GLmol, JSmol and ChemDoodle Web for 3D visualization. In the last few years more mature web viewers for molecules have been developed that will replace the current viewers (except for JSmol of course). These viewers include 3Dmol.js (organic molecules, fork of GLmol), PV (simple viewer for proteins) and NGL (advanced viewer for proteins). But viewing 3D models is not the only visualization tool I intend to offer. An interactive NMR viewer like the one on nmrdb.org might finds its way into MolView pretty soon. And perhaps even a DNA sequence viewer/explorer.
The sketcher is the only visualization tool I've actually written myself. I created my own sketcher because it is a very critical component and I was not satisfied with the web-based, open-source sketchers that are currently available. I've added some basic features to the sketcher already and I intend to add quite a number of new features to make it even more powerful. Apart from obvious features such as functional groups, dot structures, reaction arrows and annotations, I've been thinking about a tool for automatically depicting the structural formula using a certain projection such as the Newman projection or the Fisher projection.
I want teachers to use MolView, and therefore making MolView more powerful for teachers is a top priority. In the past year I received quite some requests for new features from teachers who tried MolView. The new architecture will open up the way for quite a number of these features. It have built-in support for embedding any view, anyone will be able to create a step-by-step guide for tutorials in MolView, and it will have mature support for saving and sharing files. I'm especially exited about the step-by-step guides. These can be used to learn new users how to use MolView, but it could for example also be used for a tutorial to explain the difference between geometric isomers.
You can start using MolView today on molview.org. Your feedback is very valuable! don't hesitate to contact me if you have questions or ideas. MolView is growing faster than ever and will require an increasing amount of server resources. A dutch hosting company called PCextreme granted me free access to their infrastructure so I can continue providing this application for free! In the future I want to add more heavy computational tools to MolView. Perhaps we can connect MolView to your computing grid to make this possible!