JmolC

JmolC is a Java applet and standalone application designed for interactive visualization and exploration of three-dimensional molecular structures. It is commonly used in chemistry, biochemistry, and related scientific fields. JmolC allows users to load and display molecular data from various file formats, including PDB, MOL, and XYZ.

Key features of JmolC include the ability to rotate, zoom, and translate molecules to examine them from different perspectives. Users can also manipulate the representation of the molecule, switching between wireframe, ball-and-stick, space-filling, and cartoon models. Color schemes can be customized based on atom type, residue, or other properties. JmolC supports the display of molecular surfaces, such as van der Waals surfaces and solvent-accessible surfaces, which can aid in understanding molecular shape and interactions.

Beyond basic visualization, JmolC offers tools for analyzing molecular properties. It can display bond lengths, angles, and torsion angles. Users can select specific atoms, residues, or chains to highlight and measure distances between them. JmolC also has capabilities for animating molecular dynamics trajectories and displaying conformational changes. The application can be controlled through a graphical user interface or via scripting, allowing for automated tasks and the creation of custom visualizations. JmolC is open-source software, which has contributed to its widespread adoption and development within the scientific community.