Computer software, visualization RasMol

Visualization software allows the user to display molecular structures imported from databases or other software programs. Chime, RasMol, and Protein Explorer programs are available at the websites listed below for Windows operating PCs and Macintosh PowerPC computers. 

Structural visualization Computer graphics is the most effective means for visualization and interactive manipulation of molecules and molecular systems. Numerous software programs (e.g., Cn3D, RasMol and KineMage, Chapter 4) are available for visualization, management, and manipulation of molecular structures. 

Due to the nature of MD simulations, one of the most productive forms of analysis of a simulation is to be able to visualize the trajectory of the molecules of interest. This is particularly useful since experimental techniques are not able to produce visual pictures of atomistic interactions and therefore it is something that only simulations (at this point) are able to provide. In order to visualize a simulation trajectory there are several different very powerful computer packages that are commonly used. These software packages include VMD (2009), PyMol (2010), RasMol (2008), and several others (Free Molecular Visualization Software 2008). O Figure 7-5 shows an example of the type of pictures that can be made using the visualization software. 

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