Find Toolbar

The Find toolbar allows you to find collections of atoms in the Workspace. The found object becomes the Workspace selection.

To display this toolbar, do one of the following:
  • in the Maestro main window, choose Select → Find
  • press Ctrl+F (⌘F).
  • Features
  • Additional Resources

Find Toolbar Features

Find option menu

Choose the structural unit type that you want to find from this option menu. Some of the tools on the toolbar are only present for certain choices from this option menu.

Search box

Enter or select the information for the particular structural unit to be found in this text box. For some structural units, you can type in the information; for others, a menu is shown in the search box; for yet others, tools are displayed to the right for defining the structural unit. For information entered into the search box, clicking the X button clears the information from the search box.

Once the information is provided, click the search button or press Enter to do the search. For Residue Type and Secondary Structure, choosing a different type automatically starts the search.

  • For Atom Number, Molecule Number, or Residue Number, enter the number in the text box.

  • For Element, enter the element symbol.

  • For PDB Atom Name, enter the atom name.

  • For Sequence, enter the 1-letter residue sequence.

  • For Residue Type, choose the type from the menu.

  • For Secondary Structure, choose the structure from the menu.

  • For SMARTS, enter the SMARTS pattern, or select a substructure in the Workspace and click Load, or click the 2D sketch button and draw the structure in the 2D sketcher.

  • For ASL, enter the ASL expression, or click Define to set up the expression in the Atom Selection Dialog Box.

Load button

Load the SMARTS string to use for the search from the Workspace selection. This button is only present when SMARTS is chosen from the Find option menu.

Define button

Define the atoms to search for. Opens the Atom Selection Dialog Box, in which you can select the atoms. The ASL expression is entered into the text box when you click OK. This button is only present when ASL is chosen from the Find option menu.

2D sketch button

Sketch the structure to find in the Search for Structure - Sketch Structure dialog box. The option menu is populated from the residue types that are present in the Workspace. This option menu is only present when Residue type is chosen from the Find option menu.

Search settings button menu

This button menu provides options for viewing and selecting matches.

Fit to Matches

Center the atoms in the current match in the Workspace and zoom in to those atoms (i.e. fit the match to the Workspace). When the search is first performed, the Workspace view is fitted to all matches. If unselected, no fitting of the Workspace view to all or individual matches is done.

Select All Results

Select this option to add all the matches to the atom selection. If unselected, the atom selection includes only the atoms from the current match.

Arrow buttons

Click these buttons to select the next or previous occurrence of the search object. These buttons are disabled if there is only one match. In this case, if you want to find the match again, click in the text box and press Enter. The atoms of the match are selected in the Workspace. Matching sequences are selected in the sequence viewer, if open. If you change the Workspace and click one of these buttons, the search is applied to the changed Workspace before selecting the next or previous occurrence.

If you specified the atom, molecule, or residue number, stepping through the instances does not step to the atom, molecule or residue with the next number. Rather, it steps through instances of the specified atom, molecule, or residue number. For example if you have three chains, A, B, and C, and searched for residue 53, stepping through the instances first selects residue 53 in chain A, then residue 53 in chain B, then residue 53 in chain C. Atom and molecule numbers are unique within the Workspace, so there is only ever one instance of an atom or molecule number.

Status display

This area displays the number of objects found, and the index of the occurrence of the object that is currently selected and displayed.

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