Bye-Bye GaussView — 3 Free Web Editors to Build/Edit 3D Structure of Small Molecules in Seconds
Intro
While I was a PhD student in the field of quantum chemistry, I used the GaussView software to build the 3D molecule structure models which were then used as input for Gaussian package to conduct ab initio calculations. GaussView was my daily driver since it not only builds 3D structure of molcules, but also visualizes various results of Gaussian calculations (e.g. vibration, density, orbital).
However, after I tranisitioned to the field of drug design & discovery after graduation, I no longer have access to it due to the licensing issue. I have been looking for proper alternatives that are as powerful as GaussView in terms of molecular modeling. Among free softwares, I tried PyMOL, Avogadro and IQmol, but they are just not that good in this regard.
A few things I really miss from GaussView include:
- Wide coverage of elements in the periodic table with predefined hybridization/coordination patterns (e.g. sp3, sp2, sp carbon)
- Large collection of predefined R-group and ring fragments as well as customized fragment support
- Highly flexible control on internal coordinates (i.e. bond, angle and dihedral) which allows user to decide which atom/group are movable or fixed
- Great support for various structure file I/O formats (e.g. SDF, MOL2, PDB)
In this article, I will show you 3 free web apps (yes, I’m not talking about desktop packages!) that can help you to build and edit 3D structures of small molecules with ease just in your browser.
1. MolCalc/MoleCalc
MolCalc has been here for a while when Professor Jan H. Jensen’s research group at University of Copenhagen developed it back in 2013. The latest version of MolCalc is 2.0.
MolCalc (https://molcalc.org/) is a web interface where you can easily build a molecular structure and calculate quantum chemistry properties (with GAMESS). Its backend is JSmol which is originally derived from Jmol project.
To build a molecule from scratch, one quick way is to use its 2D sketchpad and then convert it into 3D structure when you click the ‘3D’ button after drawing your molecule.
If you already have a structure file (for example an SDF file) and just want to edit it using MolCalc, you may right click the canvas of JSmol and load it from your local computer.
After the building work is done, the way to download the structure is not that straightforward. I usually right click the JSmol canvas and jump to its console. Then I will write something like write mol.sdf to download the 3D structure file.
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One thing I really like about MolCalc is that it can assign the formal charge of certain atoms which is quite necessary for SDF/MOL2 format. Furthermore, MolCalc will automatically ‘clean up’ the structure with force field to eliminate steric clashes.
The MolCalc project is fully open-source on GitHub (https://github.com/jensengroup/molcalc).
Following MolCalc, Professor Jeffery L. Yarger at Arizona State University developed MoleCalc (https://molecalc.cloud/) which is a fork of the former. However, it does not contain the 2D interface like MolCalc. MoleCalc is also open-source on GitHub (https://github.com/mscloudlab/molecalc).
2. Qbics Mol*
You may have heard about Mol* (molstar) which is nowadays a popular library (https://github.com/molstar/molstar) for visualizing molecular structures (especially macromolecules). It is nowadays the default visualization engine on the RCSB PDB website.
Qbic-Molstar (https://zhjun-sci.com/qmolstar.html) is one Mol* fork developed by Professor Jun Zhang’s research group at Shenzhen Bay Laboratory. It is a very powerful platform where users can easily build different molecular structures with various elements and fragments. In addition, its internal coordinate editing function is also flexible.
To load an existing structure file, one can first navigate to the home panel and upload a structure file. After building a molecule, one can download the structure by exporting it with various formats.
Qbic-Molstar supports local deployment and the developers provide a Windows build on their website.
3. Rowan
I came across Rowan’s 3D structure editor (https://labs.rowansci.com/editor) in their recent LinkedIn post. It is accessible for all visitors.
The coverage of elements is quite wide and it also has a library of fragments. Furthermore, it allows user to add fragments by entering the SMILES string of that fragment. The internal coordinate manipulation function is also powerful, but it assumes that the last selected atom is movable.
When saving the 3D structure file, currently Rowan’s structure editor only supports the XYZ format since the bond order information is not retained.
Noteworthy is that Rowan’s 3D structure editor is being improved constantly and this article might not reflect all its features when you read it.
Comparison
------------------------+----------+------------+-------
Item | MolCalc | Qbics-Mol* | Rowan
------------------------+----------+------------+-------
2D drawing support | Y | N | Y
Element coverage | Limited | Wide | Wide
Element hybridization | N | Y | Y
Predefined fragments | N | Y | Y
Customized fragment | 2D sketch| N | SMILES
Assigning formal charge | Y | N | N
Bond order adjustment | Y | Y | N
Internal coordinate | N | Y | Y
Export structure format | Many | Many | .xyz
Quantum chemistry calc. | Y | N | N
Local deployment | Y | Y | N
Open-source | Y | N | N
------------------------+----------+------------+-------Outro
I hope this article would be helpful if you are exploring the free tools for building 3D structure of molecules.
