The first step in creating electrostatic potential maps in Iqmol is to determine the ionic composition of the molecule and create a model from it. The model is then used to generate a profile map of the molecule, which can be plotted on a graph to plot ion concentrations. This profile map is then used to create an electrostatic potential map of the molecule in Iqmol.
As with all molecular modeling, Iqmol allows you to control the accuracy of the map by selecting the correct ion model, or model distribution, for your molecule. You can also use Iqmol’s ion modeling tools for creating and correcting profiles. If you do not have a model to plot, you can enter your sample molecule and use Iqmol’s template generator tool to create one. It will then spit out a model of the molecule in Iqmol. The model can also be adjusted based on its density, ionization state, and charge.
Once you have determined the proper ion model for your molecular sample in Iqmol, you are ready to plot the profile map. In this step, you simply use Iqmol’s Plotter tool to plot the profile map on the plot surface of your choice. You can also select an Iqmol plot wizard to assist you with plotting, or you can choose to plot the profile map by hand.
The reason for choosing Iqmol’s plotter tool is that it allows you to control the accuracy of your map by altering the size of the molecules in the sample, while maintaining ion distributions and electrode placements. As an example, the ion model for a small molecule is less accurate, so Iqmol allows you to plot the profile map for a molecule on a smaller scale to keep the accuracy of the molecular model constant throughout the entire model map.
After you have created your profile map in Iqmol, you are ready to plot it in Iqmol using the Iqmol plotter. by clicking on the “plot” button at the lower left of the toolbar. If the grid is too large, the plotter will automatically expand the grid to provide more surface area to plot on. If the grid is too small, the plotter will automatically reduce the grid to provide more surface area to plot on.
To begin your plotting, choose a molecular ion model in Iqmol and then click on the “plot” button on the plotter toolbar. Use the mouse wheel or mouse to drag the model across the plot surface to change the plot view. Click on “view” to view the plot in a graphical format. You can click on the “label” button to mark labels, and click on a label to toggle between “marker”range” views of the model in the plot view.
When you are satisfied with the results of your plot, select “mark” to mark the model with a label, and click on the “draw” button in order to place your marker on the molecular ion. If you want to reset the label, select “reset” and click on the label. To erase a marker, select the “reset” and select the label.
You can also use Iqmol’s “scatter plot” to plot multiple ion locations simultaneously. Click on “plot” to view the scatter plot. When you select a grid and plot, the plotter will automatically expand the grid to provide more surface area for the scatter plot in order to display more ion locations in the plot.
After you have finished your plot, select “mark” to mark the location of your marker with a label, and select “reset” to reset the marker label to the default location. To erase a marker, select the “mark” and select the “reset” button. To view the plot again, select “view” and repeat the step two or three times.
By using Iqmol’s Iqmol plotter, you can easily plot your molecular ion profiles on the molecular ion model. You can create a full map in just minutes and create a unique profile map every time.