Toggle Table Panel

This panel provides a means of interacting with the Workspace and the project that is similar to PyMOL.

To open this panel, in the Maestro main window, choose Window → Toggle Table.

  • Using
  • Features
  • Additional Resources

Using the Toggle Table Panel

The Toggle Table provides easy ways to manipulate the Workspace. Either the entire Workspace or individual entries can operated on. Menus provide easy ways to change the color, representation style, and labeling of entries. Various chemical features can be displayed or hidden, groups of atoms can be selected, and simple properties can be calculated.

The central section of the Toggle Table lists all entries in the Workspace. Clicking on the name of an entry toggles the visibility of that entry. However, it is important to note that even if an entry is not visible, it is still in the Workspace as long as it is listed in the Toggle Table. This means that all Workspace operations will be applied to this entry. Panels that offer to "Analyze the Workspace" or "Import from Workspace" will operate on these entries, even if they are not visible and the entry name is grayed out. To remove (exclude) an entry from the Workspace, use the Remove from Workspace command under the A menu for that entry, or exclude it using the Project Table.

In addition to the docked panel, the Toggle Table also provides a right-click context menu in the Workspace for easy access to many of its features. This menu is available by right-clicking and holding anywhere in the Workspace. The contents of the context menu depend on whether the click occurs on an atom (which selects the atom) or empty space.

Toggle Table Panel Features

Quick Access Buttons

This set of buttons provides quick access to a number of actions, some of which are also on the menus.

Reset button

Resets the view to its default view, in which the view axes are aligned with the coordinate axes of the structure.

Zoom button

Changes the view of the Workspace so that all atoms fit inside the workspace view.

Orient button

Provides an optimal view of the Workspace structures. This is accomplished by translating and rotating the structure in the Workspace so that the center of mass is at the origin, the largest principal axis lies on the x axis, and the second-largest principal axis lies on the y axis. When you apply this operation to the selection, it is the center of mass and principal axes of the selection that are used, but the entire structure is reoriented.

Note: This operation changes the coordinates of the structures, not just the coordinates of the view (the camera angle).

Draw button

Save an image of the Workspace to a file in TIFF, JPEG, or PNG format.

Help button

Shows this help document in your browser.

Ray button

Uses PyMOL to draw a ray-traced image of the Workspace.

This feature requires PyMOL to be installed, and either the PYMOL4MAESTRO or PYMOL_PATH environment variable must point to the directory where the PyMOL executable file resides.

Deselect button

Clears the current Workspace selection.

Rock button

Rotate the Workspace back and forth smoothly.

This button functions as a toggle. Click it when it is in the selected state to stop the Workspace from rotating.

Fullscreen button

Switch Maestro to full screen mode. To exit full screen mode, press the Escape key or click on this button again.

Entries in the Workspace Section

This section of the Toggle Table has a row for each entry in the Workspace, plus additional types of objects. The buttons in these rows open menus that operate on the objects for that row.

There are three distinct types of rows in this table:

  • Entry rows: These rows apply to a single entry that is currently in the workspace. The name of the row is the Title of the entry that its menu items apply to. Entry rows are deleted when the entry is excluded from the Workspace, and a new row is added when an entry is added to the Workspace
  • The All row: This row applies to all atoms in the Workspace.
  • Selection rows: When a group of atoms is selected, a Selection row is added to the Entry Region. Actions in this row apply to the group of atoms that was selected to create this row and even apply after those atoms are no longer selected. The Selection row named (Selection) always refers to the most recent group of selected atoms. Selection rows can be renamed: renamed Selection rows always refer to the same set of atoms regardless of subsequent Workspace selections. Selection rows are deleted when any atoms they refer to are removed from the Workspace. Only one selection can be active at a time.

Some operations or menu items change based on whether they are being applied to the All row, an Entry row, or a Selection row. The descriptions below describe the behavior for Entry rows. When a behavior changes for the All row or a Selection row, the change is noted after the description.

Any Entry row in this table refers to an entry that is currently in the Workspace whether that entry is visible or not. This means that the entry it refers to is affected by actions in the All row, and also that it will be analyzed or imported by panels that operate on the Workspace.

Name

Clicking on the name of an All or an Entry row toggles the visibility of that object in the Workspace. When the object's visibility is off, the name is greyed out.

However, it is important to note that even if an entry is not visible, it is still in the Workspace as long as it is listed in the Toggle Table. This means that all Workspace operations are applied to this entry. Panels that offer to "Analyze the Workspace" or "Import from Workspace" will operate on these entries, even if they are not visible and the entry name is greyed out.

Note: the interactions between toggling visibility by clicking on the Name, hiding atoms with the various Hide menu commands, and including/excluding entries from the Workspace can result in a situation where the name is not greyed out but no atoms are visible. Should this occur, simply choose to show the atoms using one of the commands in the Show menu.

Clicking the name of a Selection row toggles the selection state of the atom group that row refers to. Any currently selected atoms that are not part of this atom group are deselected. Clicking the name of any other selection row selects the atom group that the row refers to, and any currently selected atoms that are not part of this atom group are deselected.

A button

Opens the Action menu, also referred to as the A menu.

  • Delete Selection—For a Selection row, remove the row from the Toggle Table. The atoms in this selection group are deselected but otherwise remain unaltered.

  • Rename Selection—For a Selection row, the renamed row persistently refers to the same set of atoms even after a new group of atoms is selected, so it is a way of storing a selection.

  • Zoom—Zoom the workspace view to fit this entry on screen. In the All row, this action is equivalent to clicking the Zoom button at the top of the panel.

  • Orient—Orient this entry for optimal viewing.

  • Center—Center this entry in the Workspace.

  • Origin—Set the center of the entry as the center of Workspace rotation.

  • Clean—Minimize the energy of the Workspace or the selected atoms using the OPLS_2005 force field. The current selection is updated (or a new selection created) to refer to the minimized atoms. To avoid starting a lengthy calculation that is better performed in the background, Clean is limited to structures of fewer than 1000 atoms.

  • Preset—Change the workspace display in a specific manner, as chosen from the submenu. Some of these representations take a little time to set up, and a progress bar is displayed at the bottom of the table.

    • Simple—Show proteins as ribbons colored by chain (C alpha trace), ligands and bound receptor as sticks, and solvent, disulphides and ions as lines.
    • Simple (no solvent)—Same as Simple, but no waters are shown.
    • Ball and Stick—Show everything in Ball and Stick, with no protein ribbons.
    • B-Factor—Show the protein as tubes with residues colored by the B-factors of the residues, in a relative scheme that ranges from shades of blue, through green and yellow to red.
    • Technical—Show atoms as sticks, colored with rainbow colors by residue position, and show polar contacts (hydrogen bonds) as yellow dotted lines.
    • Ligand—Show proteins as ribbons colored with rainbow colors by residue position, and ligands as lines. All protein atoms within 5 Å of the ligand are shown as lines, with carbons colored with rainbow colors by residue position. Waters are shown as sticks, polar contacts are shown as yellow dotted lines, and the view is zoomed in to the atoms shown.
    • Ligand Sites—Similar to Ligand
      • Cartoon—Show proteins as cartoons rather than ribbons.
      • Solid surface—Show the molecular surface of the protein around the ligand as an opaque surface, colored by the nearest non-hydrogen atom.
      • Transparent surface—Show the molecular surface of the protein around the ligand as a semi-transparent surface, colored by the nearest non-hydrogen atom; show atoms and bonds as sticks.
      • Dot surface—Show the molecular surface of the protein around the ligand as a dot surface, colored by the nearest non-hydrogen atom; show atoms and bonds as sticks.
      • Mesh surface—Show the molecular surface of the protein around the ligand as a mesh surface, colored by the nearest non-hydrogen atom; show atoms and bonds as sticks.
    • Pretty—Show proteins as cartoons colored with rainbow colors by residue position and ligands as sticks.
    • Pretty (with solvent)—Same as Pretty but waters are shown as ball and stick.
    • Publication—Same as Pretty, but protein helices are two-sided.
    • Publication (with solvent)—Same as Pretty (with solvent), but protein helices are two-sided.
    • Protein Interface: Color ribbons and carbons by chain, show anything not at a protein interface as cartoon ribbons and interface residues as ball and stick. . Non-carbon atoms retain their previous coloring. Interface residues are residues in a chain with more than 300 atoms that are within 4.5 Å of another chain with more than 300 atoms.
    • Antibody Presets—Show everything as cartoon ribbons colored by antibody structure according to the numbering scheme chosen from the submenu. The light chain is colored in red hues, the heavy chain is colored in blue hues, and everything else is colored green. Constant regions are dark hues and the CDR regions are bright hues. The light chain L1-L3 loops are shaded orange to brown, while the heavy chain H1-H3 are shaded grey-blue to cyan.
    • Default—Show everything as lines with default colors (colored by element with green carbons).

  • Polar Contacts—Turn on and off display of hydrogen bonds between chosen groups of atoms with this submenu. The display is turned on with Find; it is turned off with Remove All. Each menu choice clears any previous choice before applying the new choice. The atom groupings you can choose are:

    • Within Object
    • Involving Side Chains
    • Involving Solvent
    • Excluding Solvent
    • Excluding Main Chain
    • Excluding Intra-Main Chain
    • Just Intra-Side Chain
    • Just Intra-Main Chain
    • To Other Atoms In Entry
    • To Other Atoms In Entry Excluding Solvent
    • To Any Atoms
    • To Any Atoms Excluding Solvent

    If you want more flexibility in choosing the atom groups between which polar contacts are shown, you can use the Interactions Toolbox.

  • Generate—(not available for the All or Selection rows)

    • Selection—Select various groups of atoms. You can also select groups of atoms with the Workspace tools—see Selecting Atoms.
      • All—All atoms.
      • Polymer—Backbone and side-chain atoms.
      • Organic—Ligand atoms.
      • Solvent—Water atoms.
      • Surface Residues—All residues with solvent-exposed surface area greater than 10 Å2.
      • Protein Interface—Residues in a chain of more than 300 atoms that are within 4.5 Å of another chain of more than 300 atoms.
    • Symmetry Mates—Create and show nearest-neighbor crystal symmetry mates. This requires crystal symmetry information to be preset for this structure. Submenu items control the cutoff distance from the original structure for which symmetry mate atoms should be displayed. Note that no matter how far the cutoff is placed from the original structure, only the nearest-neighbor mates are created and shown. The symmetry mates are created as separate, temporary entries and are shown in the toggle table. Symmetry Mates can also be removed using this submenu.
      Since this command is a Workspace-wide setting, it affects all entries in the Workspace, not just the entry for the Toggle Table row that it was selected for.

  • Modify— Alter the group of selected atoms to include or exclude other atoms. After a Modify action, the selection row applies to the new group of atoms. Available for selection rows only, and replaces Generate.

    • Around—Deselect the current set of atoms and select all atoms or residues within a given distance from the current set of atoms. The distance is chosen from the submenu, and can encompass atoms only or be filled to entire residues that have any atoms within the chosen distance.
    • Expand—Expand the current selection to include all atoms or residues within a given distance from the current set of atoms.
    • Extend—Expand the current selection to include all atoms or residues within a given number of bonds from the current set of atoms.
    • Invert
      • Within Objects—All atoms in the entry that are not part of the Selection group are selected.
      • Within Chains—For the chains that contain at least one atom in the Selection group, all atoms that are not part of the Selection group are selected.
      • Within Residues: For the residues that contain at least one atom in the Selection group, all atoms that are not part of the Selection group are selected.
      • Within Molecules: For the molecules that contain at least one atom in the Selection group, all atoms that are not part of the Selection group are selected.
      • Within Any—All atoms in the entire Workspace that are not part of the Selection group are selected.
    • Complete
      • Residues—All atoms in the residues that contain at least one atom in the Selection group are selected.
      • Chains—All atoms in the chains that contain at least one atom in the Selection group are selected.
      • Object—All atoms in the entries that contain at least one atom in the Selection group are selected.
      • Molecules—All atoms in the molecules that the Selection group is part of are selected.
      • C-alphas—All alpha carbons within the Selection group are selected. All other atoms, including non-alpha carbon atoms in the Selection group are deselected.
    • Restrict to
      • Object—Restrict the selection to atoms in a specific entry, chosen from the submenu.
      • Selection—Restrict the selection to atoms in a specific Selection group, chosen from the submenu.
      • Visible—Restrict the selection to atoms that are visible.
      • Polymer—Restrict the selection to backbone and side-chain atoms.
      • Organic—Restrict the selection to ligand atoms.
      • Solvent—Restrict the selection to water atoms.
      • Inorganic—Restrict the selection to atoms with element other than H, C, N, O, F, P, S, Cl, Br, or I.
    • Include
      • Object—Include atoms in a specific entry, chosen from the submenu.
      • Selection—Include atoms in a specific Selection group, chosen from the submenu.
      • Visible—Include all visible workspace atoms.
    • Exclude
      • Object—Exclude atoms in a specific entry, chosen from the submenu.
      • Selection—Exclude atoms in a specific Selection group, chosen from the submenu.
      • Visible—Exclude atoms that are visible.
      • Polymer—Exclude backbone and side-chain atoms.
      • Organic—Exclude ligand atoms.
      • Solvent—Exclude water atoms.
      • Inorganic—Exclude atoms with element other than H, C, N, O, F, P, S, Cl, Br, or I.

  • Rename—Change the name of the entry. This changes the name displayed in the Toggle Table and also the Title property of the structure. If you decide you do not want to change the name after all, press Esc.
    This command is only available for Entry rows.

  • Duplicate—For Entry rows, create a new project entry that is the duplicate of this entry. Both structures remain in the Workspace.
    This command is not available for the All row.
    For Selection rows, this merely creates a duplicate Selection row in the Toggle Table, which you can use as the basis for another selection. No project entry is created.

  • Remove from Workspace—Remove (exclude) this entry from the Workspace. The entry remains in the Project Table and can be returned (included) to the Workspace by using the Include in Workspace button or the Project Table.
    This command is not available for Selection rows.

  • Remove Everything from Workspace—Remove (exclude) everything from the Workspace, i.e. clear the Workspace. The entry remains in the Project Table and can be returned (included) to the Workspace by using the Include in Workspace button or the Project Table.
    This command is only available for the All row.

  • Delete from Project—Remove this structure from the Workspace and the Project. It no longer appear in the Project Table.

  • Delete Selections—Remove any Selection rows from the Toggle Table. All atoms deselected but are otherwise unaltered. Only available for the All row.

  • Copy to New Project Entry—Create a new project entry by copying the selected atoms or entries. The new entry is added to the Workspace. For individual entries, this command is the same as Duplicate

  • Extract to New Project Entry—(Selection rows only) Create a new project entry that contains the atom group only. The atoms are deleted from their current structure.

  • Hydrogens—Add or remove hydrogen atoms: The scope of the addition or removal is defined by the row: all entries, the current entry, or the selection. Atoms are removed, not just hidden. You can also add or remove hydrogen with the 3D Builder (see Building and Editing Structures).

  • Remove Waters—Remove water molecules. The scope of the addition or removal is defined by the row: all entries, the current entry, or the selection. Atoms are removed, not just hidden.

  • Compute—Compute simple properties of the object (selection or entry):

    • Atom Count—The number of atoms.
    • Formal Charge Sum—Sum of atom formal charges.
    • Partial Charge Sum—Sum of atom partial charges.
    • Surface Areas—Compute surface areas. Solvent-Accessible surface area (SASA) uses a solvent radius of 1.4 Å while Molecular Surface Area uses the same algorithm but with no solvent to expand the atomic radii. The surface area is computed for the object in the context of the visible atoms in the Workspace.
S button

Opens the Show menu, also referred to as the S menu.

The Show menu contains commands that alter the display of structures in the Workspace. There are three different types of display for structures:

  • Atomic representations such as lines, sticks, ball and sticks or spheres
  • Ribbon representations such as ribbons and cartoons
  • Surface representations such as solid or mesh surfaces

Each atom may have one of each representation type active at once, but cannot have multiple representations of the same type active. For instance, an atom can be shown simultaneously with lines, cartoon ribbons and a mesh surface. However, an atom cannot be shown simultaneously by both ball and stick and sphere representations because they are both atomic representations. If an action is chosen to show an atom with a representation in the same category as an existing representation for that atom, the existing representation is removed and the atom is shown with the new representation. For instance, if an atom is shown as Lines, and the ball and stick menu item is chosen, the Lines representation is removed and the atom is shown with ball and stick representation.

  • As—This submenu contains menu items that appear to be duplicates of those described below. However, selecting them from the As submenu removes any current representation of any of the three types for that atom and replaces them all with the selected representation. For instance, an atom shown with lines and cartoon ribbons is shown as only ball and stick if Show → As → Ball and Stick is chosen, but are shown as cartoon and ball and stick if Show → Ball and Stick is chosen.
  • Lines—Set atomic representation to lines (wire frame).
  • Sticks—Set atomic representation to sticks (tube).
  • Ball and Stick—Set atomic representation to ball and stick.
  • Ribbon—Set ribbon representation to ribbon. This is the Maestro ribbon style known as calphatube or CA trace tube.
  • Cartoon—Set ribbon representation to cartoons.
  • Label—Show any labels defined for this structure.
  • Nonbonded—Set the atomic representation of any atom with 0 attachments to Lines (wire frame). These atoms appear as small stars.
  • Spheres—Set the atomic representation to Spheres (CPK). The sphere radii are the van der Waals radii of the atoms.
  • Nonbonded Spheres—Set the atomic representation of any atom with 0 attachments to spheres (CPK).

The above items appear on both the Show menu itself and on the As submenu. When you choose from the Show menu, the representation is added to the display. When you choose from the As submenu, the previous representation is replaced by the new choice. For instance, a residue shown with lines and cartoon ribbons is shown as only ball and stick if S → As → Ball and Stick is chosen, but is shown as cartoon and ball and stick if S → Ball and Stick is chosen.

  • Mesh—Set the surface representation to mesh colored by current atom color.
    This command is not available for Selection rows.
  • Surface—Set the surface representation to solid colored by current atom color. This command is not available for Selection rows.
  • Organic—Set the atomic representation of backbone and side-chain atoms to lines, sticks or spheres.
  • Main Chain—Set the atomic representation of backbone atoms to lines, sticks or spheres.
  • Side Chain—Set the atomic representation of side-chain atoms to lines, sticks or spheres.
  • Disulfides—Set the atomic representation of disulfide atoms to lines, sticks or spheres.
H button

Opens the Hide menu, also referred to as the H menu.

The Hide menu contains commands that hide features in the Workspace. To redisplay these features, use the Show menu. Each item hides only the particular feature for the row, and leaves any other features as they are. Hiding atoms also hides any representation of the bonds to those atoms.

  • Everything—Hides atomic, ribbon, and surface representations and labels.
  • Atoms—Hides atomic representations.
  • Ribbon—Hides ribbon representations.
  • Cartoon—Hides ribbon representations.
  • Label—Hides labels. The labels remain defined and can be re-shown with the S → Label menu command.
  • Nonbonded Atoms—Hides atomic representation for atoms with 0 attachments.
  • Mesh—Hides surface representations.
  • Surface—Hides surface representations.
  • Main Chain—Hides atomic representations for backbone atoms.
  • Side Chain—Hides atomic representations for side-chain atoms.
  • Waters—Hides atomic representations for water atoms.
  • Hydrogens—Hides atomic representations for nonpolar or all hydrogens, as chosen from the submenu.
  • Symmetry Mates—Removes all crystal symmetry mates from the Workspace. This is a Workspace setting, so affects all symmetry mates in the Workspace.
  • Polar Contacts—Removes hydrogen bond markers.
  • All Others—Hides atomic, ribbon, and surface representations and labels for all atoms in the Workspace other than the atoms this row applies to.
L button

Opens the Label menu, also referred to as the L menu.

The Label menu contains commands that label features in the Workspace. Unless otherwise specified, labels are created for every atom the row applies to. Atom labels created by these commands are not cumulative. Any existing atom labels are removed when new ones are created.

Labels can be cleared from the Workspace with L → Clear. They can be hidden with H → Label. In the latter case, they can be re-shown with S → Label, while in the former the labels need to be created (usually by other Label menu commands) before they can be shown again.

  • Clear—Clears all labels.
  • Residues—Label the first carbon atom in each residue with the three-letter PDB code and residue number.
  • Chains—Label the first and last residue in each chain with the chain name.
  • Atom Name—Label each atom with its PDB atom name.
  • Element Symbol—Label each atom with its element symbol.
  • Residue Name—Label each atom with the three letter PDB code of the residue it is part of.
  • Residue Identifier—Label each atom with the residue number of the residue it is part of.
  • Chain Identifier—Label each atom with the name of the chain it is part of.
  • B-factor—Label each atom with its PDB B-factor value if it exists.
  • Occupancy—Label each atom with its partial occupancy data if it exists.
  • VDW Radius—Label each atom with its van der Waals radius.
  • Other Properties:
    • Formal Charge—Label each atom with its formal charge.
    • Partial Charge (0.00)—Label each atom with its partial charge to two decimal places.
    • Partial Charge (0.0000)—Label each atom with its partial charge to four decimal places.
    • MacroModel Text Type—Label each atom with its MacroModel atom type.
    • MacroModel Numeric Type—Label each atom with its numerical MacroModel atom type.
    • Stereochemistry—Label each atom with E,Z and R,S stereochemistry.
  • Atom Identifiers—Submenu of atom identifiers that can be used for labels.
C button

Opens the Color menu, also referred to as the L menu.

The color menu contains commands to color the atom representations by various coloring schemes including by element, chain, substructure, B-factor and entry.

  • Color by Element—Color H, C, N, O and S atoms. Default colors are white for H, green for C, blue for N, red for O and yellow for S.
    • Reset HNOS—Set H, N, O and S atoms to their default color. Carbon atoms remain their current color.
    • Custom Color {C}HNOS—Pick the color for carbon atoms and set H, N, O, and S atoms to their default color. Clicking on the menu item opens a palette of colors to choose from for carbon atoms, while selecting Recent Color Choices lists the most recent colors chosen by this command.
    • Custom Color {H}CNOS—Pick the color for hydrogen atoms and set C, N, O, and S atoms to their default color. Clicking on the menu item opens a palette of colors to choose from for hydrogen atoms, while selecting Recent Color Choices lists the most recent colors chosen by this command.
  • Color by Chain—Color atoms by chain:
    • by Chain (Carbons)—Change the color of carbon atoms only.
    • by Chain (Calpha)—Change the color of alpha carbon atoms only.
    • by Chain—Change the color of all atoms.
    • Chainbows—Each chain is colored like a rainbow.
  • Color by Substructure—Helices, sheets and loops are colored by the chosen color scheme. All other atoms retain their current color.
  • Color by Spectrum
    • Rainbow (Carbons)—Color carbon atoms only with rainbow colors by residue position. The chain is divided into segments, each of which has residues of the same color.
    • Rainbow (Calpha)—Color alpha carbon atoms only with rainbow colors by residue position.
    • Rainbow—Color all atoms with rainbow colors by residue position.
    • B Factors—Color atoms by the residue B factor.
    • B Factors (Calpha)—Color alpha carbon atoms only by the residue B factor.
  • Auto—Color groups of atoms via a cycle of colors:
    • Carbons—Each time this is selected, carbon atoms are colored by the next color in the cycle.
    • All Atoms—Each time this is selected, all atoms are colored by the next color in the cycle.
    • Carbons by Object—Each entry the row applies to gets carbon atoms colored a different color.
    • All Atoms by Object—Each entry the row applies to gets all atoms colored a different color.
  • Custom Color All Atoms—Change the color of all atoms. Clicking on the menu item opens a palette of colors to choose from, while selecting Recent Color Choices lists the most recent colors chosen by this command.

Include in Workspace Button

This button opens a dialog box that can be used to include one or more additional project entries in the Workspace. Entries already in the Workspace are marked in the dialog with "(Included)" in front of their name. One or more entries can be selected by clicking on a single entry or control- or shift-clicking on multiple entries, and then clicking OK. Double-clicking a single entry selects that entry and closes the dialog box.

Empty Space Context Menu

Actions in this context menu (opened by a right-click and hold in an empty part of the Workspace) apply to either all atoms or to all visible atoms for those commands labeled with Visible, unless otherwise specified. Most context menu commands are described elsewhere under other menus.

Selected Atom Context Menu

Right-clicking and holding on an atom selects that atom and opens a context menu that acts on the current selection. Shift- and control-right-click and holding adds the atom to the currently selected atoms and opens the context menu.

Related Topics