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Chapter 9. Versus
Plot Experimental Versus MoKa Predicted pKa values. By importing an SD file containing experimental pKa data, your pKa values are automatically plotted versus predicted pKa using the Kibitzer recognition system embedded in Versus. Because assignments in the presence of multiple pKa values can be challenging, the plot differentiates between pKas belonging to multiprotic molecules, with each pKa being labeled by a different color showing the overall number of pKas of the molecule of interest. All molecules represented in unstable tautomeric forms are colored in red. Correlation coefficient values are computed by considering the overall pKas - R2 (tot) - , pKas from monoprotic - R2 (1) -, diprotic - R2 (2), and multiprotic - R2 (3) - molecules.
9.1. The Interface
Here is a quick guide to the elements of the Interface.
Objects - You can quickly scroll upward and downward through the molecules in the SD file and whenever you choose an object the molecule is displayed in the Molecule view window
Molecule view - Displays the molecule currently selected. You can select a molecule by clicking on a point in the plot or an object in the Objects pane
pKa values - Displays the atom number of the selected molecule, as well as its type (A = acid, B = base), its experimental pKa (from the SD file) and its MoKa predicted pKa
Plot Controls - You can zoom in and out on the plot using the mouse scroll wheel. You can select points in the plot to display the corresponding molecule, which is a function set by default. You can navigate by left-clicking on the plot and move across it. Reset View resets the plot view, while Screenshot lets you save an image of the current plot
Plot - Plots Predicted Versus Experimental pKas. The molecule corresponding to the selected point is displayed in the Molecule view window. You can select multiple points by left-clicking and lasso selecting and selected points can be deleted by right-clicking and choosing remove selected.
9.2. The Menus
Here are the menus you will see displayed on the Versus menu bar (left to right), and the commands you will find in each.
File menu
New - Creates an empty working file
Open - Opens a .vs file to import into Versus
Save - Saves your current workSave as - Exports your current work as a .vs file
Import SD files - Imports an SD fileExport database as CSV - Exports the current file in a comma delimited file containing name objects, atom numbers, type (A or B), experimental pKa, and predicted pKa
Exit - Quits Versus
Tools menu
Load custom model - Selects the Custom Model (.mkd file) to use for pKa prediction obtained using Kibitzer
Restore standard model - Selects the MoKa standard Internal Model for pKa prediction
Note: It is possible to load a custom model at program startup by using the
--load-modeloption, like this: versus --load-model=modelname
View menu
Optimize 3D view - Rotates the structure in the
Molecule view pane for better visualization
Toggle log window - Opens the log window
9.3. Working with Versus
Import your SD file to plot experimental versus predicted pKa values. If you have an SD file with experimental pKa values, use Versus to plot MoKa predicted pKa values versus experimental pKa values. Versus automatically assigns each pKa to its corresponding ionizable site. The procedure evaluates MoKa performance quickly, but it is not error-free because pKa values are assigned according to MoKa predictions.
Use the SD file generated by Kibitzer to automatically read pKa values that you have already checked and assigned correctly. To avoid incorrect assignments, load an SD file with pre-assigned pKa values. You can generate an SD file with pre-assigned pKa values using Kibitzer. If you have previously checked your Kibitzer project file, using this option means you will avoid any incorrect assignments.
Evaluate the benefits of the training. If you have already generated a custom model, the benefits of the training can be evaluated (Tools > Load custom model). Now using your custom model you can see experimental pKa plotted versus predicted pKa.
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