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Molecules can be saved by choosing the ``Save" option in the File menu. This will then launch a dialog (see Figure 4.2) which will allow specification of the desired filename and file format. This dialog is very similar to the dialog described in the Opening Files section above (see section 4.1). For the basic details about the dialog, please refer to that section. However, there is an additional feature unique to saving which is the ability to save only the Marked conformations of a molecule by checking on the ``Marked Conformations Only" check box seen on the bottom of the dialog (see Figure 4.2).
VIDA supports writing multiple molecular file formats including:
Once the desired output file has been selected, another dialog will appear which will prompt for the actual molecules to save. An example of this dialog can be seen in Figure 4.3. In this dialog, lists are represented by folder icons and molecules are represented by molecule icons. Selecting a list icon, will save the entire list of molecules. Selecting individual molecule icons will save only the molecules selected.
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There are multiple buttons in the upper right hand corner which control the way in which molecules are displayed in this dialog. In addition, the button in the upper right hand corner controls whether or not a 2D preview of the selected molecule is shown. Furthermore, there is a pulldown menu which allows filtering of which molecules are listed in the window. Filters include: All, Marked, and Visible.
To expedite the saving process, right-clicking on a molecule or a list of molecules and selecting the ``Save" option will save just those molecules associated with the right-click event. This will result in the appearance of the first dialog discussed above (see Figure 4.2) to specify the desired output file, but will bypass the second dialog just discussed.
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