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Multiple mechanisms of selection were discussed in the user interaction section above (see section 5.1.6). In addition to the mechanisms discussed above, there are additional modalities which are unique to molecules. These modalities are accessed through the buttons in the Selection section of the Molecules page of the Style Window (see Figure 5.3).
This section contains two rows of buttons and controls. In the first row, the first button selects all of the currently Visible molecules. The second button, prompts the user for a substructure query (can be SMARTS, SMILES, IUPAC or common name) and then performs a search over the molecules in the specified scope, selecting those that match the query. If the resulting selection, is sufficiently large, the user will be prompted with the option to Mark (see section 3.1.4) the results instead of selecting them.
The third button inverts the current selection. The fourth button selects all the atoms and bonds within a specified distance from the current selected set. The selection distance is controlled by the slider bar in the second row and the actual value is displayed in the text display next to the slider bar. As a visual aid, when there is a selected set and the selection distance is greater than zero, a transparent white surface with a radius equal to the selection distance is displayed around the selected set. The button to the left of the slider bar toggles whether or not the selection distance should also control the visibility of atoms and bonds in the display (i.e. only atoms and bonds within the specified distance of the selected set will be displayed). When the ``distance controls visibility" button is set on and a visible atom or bond is in a residue, all of the other atoms and bonds in that residue will also be made visible to maintain complete residues.
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