Simple Molecular Structure Analysis

Hermann Staudinger, the Nobel prize laureate that discovered the existence of macromolecules, considered them to be high molecular compounds that contained over 1000 atoms. The term remains one of the most important concepts in science related fields, and is generally accepted that it designates large molecules. CueMol is an application that allows you to visualize the macromolecular structure in detail.

Molecules are small group of atoms tied by various chemical bounds, and they are seen as the basic structure for most elements or objects. Macromolecules are compounds that can contain hundreds or thousands of atoms.

While there are a lot of molecular viewers, most of them available free of charge, there aren't that many macromolecular viewers. CueMol is one of the macromolecules viewers that not only lets you explore the molecular structure, but will also allow you to measure distances, angles and even torsion within a molecular structure.

The Looks

When you open CueMol for the first time, the interface might seem a little complex, mainly because of all the tabs placed on the visualization window's left side.

If you start using the application though, you will realize that the panels are placed in an intuitive way and will help you study the molecule a lot easier. The application allows you to open more than one file at a time by creating a new tab for each molecule.

The largest area of the main window is reserved for the macromolecule visualization, where you can view the graphic representation for each selected molecule file. Here you can zoom, rotate and visualize the changes made from the left panel in real time.

The Works

The first thing you need to do after opening the application is choose/download a macromolecule file. CueMol does not come with sample files, but they can be downloaded for free from the developer's website. Or, if you have access to a Protein Data Bank (PDB), you can download molecule files by inserting their ID, a feature that I found to be quite useful if you're not a scientist and you don't have molecular files on your Mac.

When opening the molecule, you can choose one of the available rendering types, and also the way you want to visualize the molecule. Depending on the file type, one can choose the centered view or the freeform view, which is a lot more useful, mainly because it allows you to move and zoom anywhere inside the molecular structure.

For mtz files, users can also change the desired amplitude, resolution or grid spacing, in order to customize their experience. After pressing OK, the molecule can be viewed in the central panel, and a lot of actions will appear on the left, allowing you to analyze the molecular structure, or change density and symmetry parameters.

The first panel here is Scene, which lets you edit/save camera positions, and some object properties depending on the type of molecule file. The next panel (Molecular structure) allows users to select focus and zooming tools, as well as some properties, thus helping you visualize the position of a molecule inside the compound.

In the selection panel one can focus on various areas inside the molecule. Users can add hierarchical, terminal or around/expand areas that will allow them to center the image on a precise point inside the molecule.

The coloring menu should allow users to change colors inside the macromolecule, allowing one to differentiate various areas inside it. This feature can be very useful if you want to differentiate molecules or groups of molecules inside the compound.

An user can also study the symmetry of the molecule, by adding a unit cell in the middle of the visualization window. This will allow the comparison of two molecule areas and is feature targeted towards scientists.

The density map lets a user change the molecule color, as well as the transparency, extent and atom size inside the molecule. The View panel allows you to rotate the molecule, change the position of your current view, or access some manual zoom actions.

A useful feature can be found in the Render menu, accessible from the menubar. Here you can access the POV-Ray rendering option, that allows one to create a stereoscopic image, change the projection mode and save the file after the rendering process is complete. Or, you can export the non-rendered scene in PNG and POV formats.

From the tools menu the user can access various tools, like molecular superposition, surface generation, elepot calculation, and even a tool that should allow one to cut various areas from the molecule.

You may also want to customize the application preferences, in order to suit your needs. They are pretty basic, allowing you to change the atom label fonts and their sizes.

The interesting thing here is that you can enable multi-touch trackpads, which can be helpful if you want to use your trackpad to easily zoom or explore the molecule. Unfortunately, I could not see if the application really provides support for such a device, since I did not have one available while testing CueMol.

The Good

The Bad

The Truth