CueMol

CueMol is an advanced application whose purpose is to help you visualize macromolecule models. It can be deployed on Windows, Mac OS X and Linux.

The program gives you the possibility to import information from molecular coordinates (PDB format), electron density (CCP4, CNS , and MTZ formats), MSMS surface data, and APBS electrostatic potential map (OpenDX format).

The GUI looks and feels a bit overwhelming at a first glance because the program comes packed with a wide range of customization options. You can find out more about the tool’s capabilities on its official website.

There’s support for a multi-tabbed environment which helps you analyze different molecular models and switch between them. Plus, it allows you to copy and paste objects across different scenes.

CueMol gives you the possibility to undo or redo you actions, rotate objects to different angles, and set up a comprehensive suite of parameters which are related to scene, molecule structure, selection, symmetry, density map, view, and animation.

Animation functions include support for simple spin, camera motion, fading in/out effects, and structure morphing options. The program comes bundled with several measurement tools which are specialized in performing calculations related to distance, angle and torsion.

You are allowed to play or stop the animation, activate the loop mode and save scenes to a file on your computer so you can easily import data for future adjustments.

You can work with different display modes, namely basic molecular functions (e.g. ball-and-stick model, CPK model), cartoon model, edge rendering, solvent-excluded molecular surface, electron density rendering via GPU shader, and geometric object (solid or dashed lines).

You are given the freedom to activate various macromolecule module-related tasks, such as molecular superposition, molecular bond editor, interaction analysis, protein secondary structure tool, solvent-excluded creation mode, molecular surface cutting utility, as well as electrostatic potential by APBS.

CueMol provides an advanced set of features for helping you analyze macromolecular structures, and is suitable especially for professional users. The GUI looks a bit intimidating and difficult to decode, so you may need to invest extra time in the configuration process.