Dynamanal

Dynamanal is a visualization tool for simulation analysis whose primary purpose is to make it easy to communicate with the Dynameomics database. The database contains information about the RMSD, SASA, Phi-Psi, and Contact analyses, each of which can be viewed with Dynamanal. Additionally, Dynamanal can communicate with Jmol to allow easy visualization of the structures of the proteins at various time points.

When Dynamanal is first started, it will display the phi-psi analysis window. Additionally, the Jmol window will display the structure of the first picosecond of the simulation. The Jmol window can be interacted with in the same way as any Jmol window. For more information, see the Jmol documentation . The structure in the Jmol window can be changed in either of two ways. The first is to type the picosecond of the simulation that you want to see into the box beneath the Jmol window and push the display button. This will load the new structure from the database shortly (load times can be fairly lengthy for structures). The other method is to click on the graph for SASA, RMSD, or Contract analyses. This will draw a line on the point at which you clicked and reload the structure at that time.

The phi-psi analysis window consists of two subwindows and contains a residue list. The residue list can simply be used to select the residue whose phi-psi data you wish to view. Obviously, the phi-psi data for the first and last residues are null. The top plot contains a histogram of the proportion of time the phi and psi angles spend at each measurement. The bottom plot is a traditional Ramachandran plot of the distribution of the angles of that particular residue.

The SASA (Solvent Accessible Surface Area) analysis tab contains a residue list similar to the phi-psi tab's residue list and a line plotting interface. When zoomed out, the SASA line is actually an approximation based on the whole of the data encapsulated at any given point. To see actual data points, one can zoom in by holding the left mouse button and dragging it. By default, the SASA plot contains a maximum and minimum line as well; these show the greatest and smallest point that is hidden by the zoom. Because SASA has many subcomponents, the advanced button can be clicked to select specific parts of the SASA data that you wish to view as well or to change the options for the plot overall.

The Contact tab displays the number of native or non-native contacts that the protein retains through the simulation. The RMSD tab displays the root mean square deviation over the simulation. Both of these are protein specific rather than residue specific thus do not have a residue list. Otherwise, they behave in a nearly identical manner to the SASA tab.

All of the plot windows have an additional submenu that can be accessed by right clicking. This window allows you to save a PNG file of the graph, reset your zoom, or find the X and Y values at that particular point. Additionally, for the SASA, RMSD, and Contact plots, you can save a PDB file of the structure at the time specified in the submenu (at the X value).