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1. Selection Toolbar Maestro 11 Beta Reference Guide This document provides an illustrated high-level description of the new and significantly changed features available in the Maestro 11 Beta release. The Maestro11 Beta can be enabled by choosing Try Maestro 11 from the Welcome screen, or by selecting Switch to Maestro 11 from the Maestro menu and restarting Maestro. To switch back, choose Return to Maestro Classic from the Maestro menu and restart Maestro. Contents 1. Selection Toolbar 1. Picking 2. Picking Level 3. Predictive Highlighting 4. Quick Select 5. More Selection Actions 6. Fitting 7. Style Toolbox 8. Preset Styles 9. Builder 10. Task Tool 2. Workspace Navigator 3. Footer Bar 1. Status Bar 2. Workspace Toggles 3. Workspace Configuration Panel 4. Interactions Tool 5. Measurements Tool 6. Workspace Gadgets 1. 2D Overlay 2. Workspace Properties 4. Miscellaneous 1. Banners 2. Hierarchical Project Table 3. Special Workspace Interactions 4. Menus 1. Structure Hierarchy 2. Navigator Panel

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1. Selection Toolbar

Maestro 11 Beta Reference Guide This document provides an illustrated high-level description of the new and significantly changed

features available in the Maestro 11 Beta release.

The Maestro11 Beta can be enabled by choosing Try Maestro 11 from the Welcome screen, or by selecting Switch to Maestro 11 from the Maestro menu and restarting Maestro. To switch back, choose Return to Maestro Classic from the Maestro menu and restart Maestro.

Contents

1. Selection Toolbar1. Picking2. Picking Level3. Predictive Highlighting4. Quick Select5. More Selection Actions6. Fitting7. Style Toolbox8. Preset Styles9. Builder

10. Task Tool2. Workspace Navigator

3. Footer Bar1. Status Bar2. Workspace Toggles3. Workspace Configuration Panel4. Interactions Tool5. Measurements Tool6. Workspace Gadgets

1. 2D Overlay2. Workspace Properties

4. Miscellaneous1. Banners2. Hierarchical Project Table3. Special Workspace Interactions4. Menus

1. Structure Hierarchy2. Navigator Panel

1. Selection Toolbar

1.1 Picking

1.2 Picking Level

The Selection Toolbar is the main tool of Maestro 11. It allows the user to easily select atoms in

the Workspace and act on them.

The Selection Toolbar provides two ways of selecting atoms in the Workspace: direct picking or quickobject selection. In direct picking, the user can click on atoms in the Workspace or marquee over an areato select them. In quick object selection, the user can choose from a list of common structure objects ortheir own defined sets.

The Picking tool is the primary selection mode of the Maestro11 Workspace.

The picking tool is located at the top left of the window. When active, the arrow

turns blue, and clicking on or dragging across atoms in the Workspace changes

the active selection.

In addition to standard picking, we have added two new modes: additive andsubtractive picking.

button action button action

Additive Picking. While in thismode, any object you click inthe Workspace or on the SelectToolbar is added to yourcurrent selection.

Subtractive Picking.Subtractive Picking. While inthis mode, any object you clickin the Workspace or on theSelect Toolbar is removed fromyour current selection.

Tip - In standard picking, Shift key still adds to selection and Cntrl/Cmd still invertsselection state. Tip - Click the arrow to return to the standard picking mode from any another mode. Tip - Double-click the arrow to select all atoms in the Workspace. Tip - Use additive and subtractive picking along with the quick selection objects tocreate complex selections within the workspace (see below).

1.2 Picking Level

1.3 Predictive HighlightingPredictive highlighting indicates which atoms will be selected when you click. Put your mouse over anatom to see which atoms "light up". Note that even undisplayed atoms will appear if you hover over arelated atom while in residue-picking mode or higher.

The Picking Level menu determines what you are picking in the Workspace. By default, the level is atom selection. At a higher level, clicking a single atom selects all its related atoms - the associated residue, chain, molecule, or entry.

The menu includes:

Atom (A)Residue (R)Chain (C)Molecule (M)Entry (E)

NEW - In atom selection level, clicking on a bond will select the two bonded atoms. This is especially useful when editing or building out the structure.

NEW - Using the left mouse button, double-click an atom in the Workspace to expandthe selection to the next level.

1.4 Quick SelectThe Quick Select buttons offer one-click selection for certain

types of common objects in the Workspace.

button action button action

P. Selects all proteinatoms in the Workspace.

All. Selects all atoms in the Workspace(displayed or not).

L. Selects all ligandatoms in the Workspace.

S. Selects all solvents orwaters in the Workspace.

Deselect. Clearsthe currentselection.

More Objects. Additional common objects for quick selection.

Common Objects Menu. Thefollowing objects are included in thecommon objects menu:

Displayed AtomsBinding SitesBinding Sites + Ligands Proteins

All ProteinsBinding Site ResiduesBackboneSide ChainsC-alpha AtomsProtein-protein interface

HydrogensAll Hydrogen AtomsAll NonpolarNonpolar LigandNonpolar ProteinPolar

LigandMembrane

1.5 More Selection Actions

1.6 Fitting

Nucleic acidsWatersSolventsIonsMetal AtomsHeavy AtomsCustom Sets. Save and restoresets of atoms for custom quickselection.

button action button action

Invert. Invert the Workspaceselection. Selects all atomsnot currently selected;deselects those alreadyselected.

Expand. Offers options forexpanding current selection by aparticular radial distance inAngstroms, or by including atomswith a matching quality.

Previous. Restores the lastWorkspace selection.

Define... Opens the AtomSelection Dialog panel, allowingthe user to define a customWorkspace selection.

1.6 Fitting

1.7 Style Toolbox

button action button action

Auto-Fit. Toggles setting to automatically fit the view to to all displayed atoms or to the ligand when entry inclusion is changed.

Fit to Workspace. Fits theWorkspace viewport to alldisplayed atoms.

Fit to Selection. Fits theWorkspace viewport to thecurrently selected atoms.

Fit to Ligand. Fits theWorkspace viewport to anindividual ligand. When multipleligands are present, repeatedclicks move to the next ligand insequence.

1.7 Style ToolboxThe Style Toolbox applies formatting to the selected atoms. (If none are

selected when the toolbox is opened, all will be selected temporarily.)

The options include visibility, color, representation style, atom labels,

surfaces, and residue ribbons.

button action button action

Display/Undisplay Atoms. Makes selected atoms visible or invisible in the Workspace (toggle).

Display Only. Displays theselected atoms andundisplays any unselectedatoms.

Create Quick Surface. Creates a surface from the selected atoms (one per entry).

Wireframe. Displays selected atoms in wireframe representation.

Thin Tube. Displays selected atoms in thin tube representation.

Thick Tube. Displays selected atoms in thick tube representation.

Ball and Stick. Displaysselected atoms in balland stick representation.

CPK. Displays selectedatoms in CPKrepresentation.

button action button action

Color Scheme. Applies acolor scheme to theselected atoms. The left-side of the button re-applies the last used colorscheme, and the arrow onthe right opens a dropdownfor selecting and applyinganother color scheme.

Singlecolor.Opens adropdownofpossiblecolors.Applies asinglecolor totheselected

Show Only Polar Hydrogens. Undisplays nonpolar H associated with selected atoms & displays polar H. Arrow offers other hydrogen options: Hide All, Show All.

1.8 Preset Styles

1.9 Builder

atoms.

Add Labels. Opens adropdown of label schemesto apply to any selectedatoms.

RemoveLabels.Removeslabelsfromselectedatoms.

Add Ribbons. Adds and updates ribbons for any selected residues (four minimum), using the default color scheme and ribbon style from Preferences. (Tip: Right-click ribbon to edit properties.)

RemoveRibbons.Removesribbonsfromselectedatoms.

The left side of the Preset Styles split button applies the custom preset.

The arrow on the right opens a dropdown containing pre-populated

PyMOL presets. The 'Reapply preset when WS changes' setting

applies the custom preset anytime an entry is included in the

Workspace.

Tip - Double-click on the left side of the button to toggle on 'Reapply presetwhen WS changes'.

1.9 BuilderThe 3D Builder palette is the primary structure-editing and building tool

of Maestro 11. It allows the user to work directly in the 3D Workspace,

selecting atoms and bonds to delete them, add to them, or change

their properties.

This palette is opened by clicking the BUILD toggle button above theWorkspace. The pane will remain open until manually closed, and alwaysfloats above the main window.

Creating New Entries

button action button action

Create New Entry.Creates a new blankentry.

Duplicate Entry. Duplicates allentries currently in theWorkspace (Duplicate In Place).Each new entry is named for itsoriginal entry, with a suffixadded.

Copy SelectedAtoms. Creates anew entry by copyingthe atoms selected inthe Workspace.

Extract Selected Atoms.Creates a new entry byextracting the selected atomsfrom the entry or entries in theWorkspace.

Basic Edits

button action button action

Delete Atoms. Deletes all selectedatoms and their bonds.

Increment BondOrder. Increasesbond order of allselected bonds by1, up to 3.

Delete Bonds. Deletes all bondsdefined by selected atoms. Leavesatoms.

Decrement BondOrder. Decreasesbond order of allselected bonds by1, down to 0.

Add Bond. Adds a bond to theselected pair of atoms.

Increase Charge.Increases charge

of all selectedatoms by 1.

Set Element. Button changeselement of all selected atoms towhat is shown on label. Arrowopens Element palette (see below).

DecreaseCharge.Decreases chargeof all selectedatoms by 1.

Selecting the Element

Moving and Building

button action button action

Move Atoms. Initiates amode that allows user tomove selected atoms in avariety of ways:

Rotate / Translate SculptQuick Adjust

Mode banner includes instructions, choice of quick adjustment, and an option for auto-minimization, as well as other settings.

Adjust Only Menu.Clicking the arrowbutton next to MoveAtoms opens a menu ofadjust-only options:

Rotate Dihedrals Adjust Length or Distance Adjust Angle or Dihedral Rotate Peptide PlaneRotate Carbonyl PlaneEach initiates a special picking mode with banner.

Add Fragments. Opens a Fragments pane.

Click the arrow beside the Set Element button to openthis palette. Choosing an element changes the selectedatoms and sets the main button to use this element. The“...” button opens another pane with the full periodictable. Recently-used elements that are not already shownare preserved in the two empty slots.

palette for adding fragmentsto selected atoms or bonds.Fragments offered include:

RingsOrganic functionalgroupsMetal CentersOther (full fragmentlibrary)

The Organic and MetalCenter tabs include extraslots for recently-used itemswithin these categories. Thecorresponding More... buttonbrings up the library dialogshowing more of the samecategory.

Clicking a ring or otherstructure adds thefragment to the selectedatoms or bonds in theWorkspace, if possible.Each new fragment istemporarilyaccompanied by aFragment Menu icon(see below).

Draw Structure. Still in development, currently disabled. Initiates a mode that allows the user to draw or erase bonds and atoms in the Workspace and change the element of existing atoms. The mode banner offers instructions and a set of tools:

PencilEraser Element Palette

Banner tools. The Pencil tool may be used with the Element palette to:

Add a bonded atom Add a detached atom Add or increment a bondSet the element of an atom or set of atoms

The Eraser tool may be used to:

Delete an atom or set of atoms Delete or decrement a bond

Add Hydrogens. Adds anymissing hydrogens to theselected atoms.

Minimize. Minimizesselected atoms (only).Maps to Ctrl-M onkeyboard.

Fragment Menu

More Editing Options

button action

2D Sketcher. Brings up the 2D Workspace dialog. If there is asingle small molecule entry in the Workspace, the dialogprovides 2D editing functionality.

Other Edits. Displays a menu of additional edit actions thatcan be applied to the selected atoms or bonds:

Invert ChiralityConvert Cis/TransSelect Rotamer (or Find Torsions)Switch Alternate PositionsCreate Zero-Order Bonds to MetalsChange IsotopeMutate ResidueSet Residue NumbersChange Other Properties

Invert Chirality. Inverts chirality of any chiral atoms found among selectedatoms.

This small icon appears alongside each newly addedfragment and persists in the Workspace until an unrelatedaction is taken. Clicking the icon opens a menu of actionsthat are available for the new fragment. These actionsvary with the fragment type and its connection, but mayinclude:

Flip to Alternate H / Flip OrientationChange Connection Point / Change Connection SideRotate DihedralSelect FragmentDelete Fragment

Note: Fragments created by selecting a single atomacross a set of overlaid structures will have just oneFragment Menu that operates on all the overlaidfragments. Only Select and Delete will be offered in thesecircumstances (for now).

Note: This feature is still in development and may not handle all conditionsas expected.

Convert Cis/Trans. Flips each bond of the correct type by 180 degrees.Enables only if at least one of these types is selected:

peptide bonddouble-bond not in a ring

Select Rotamer(s). Allows the user to step through available rotamers forthe selected residue. If the selected atoms represent a single residue, abanner with arrows and other controls is offered in the Workspace. If theatoms represent more than one residue, the Rotamers dialog is brought upinstead. (This dialog can also be brought up from the single-residue bannerby clicking the 'i' icon.)

Find Torsions. Allows the user to step through torsions of the selecteddihedral bond on a ligand or other non-protein structure. Opens a bannersimilar to the Select Rotamer banner described above. The 'i' opens theRapid Torsion Scan dialog.

Switch Alternate Positions. Allows the user to switch to the alternatepositions (if any) of the residues represented by the selected atoms.Remains disabled if no alternate positions are found in the selection.

Create Zero-Order Bonds to Metals. Creates zero-order bonds fromsurrounding atoms to selected metal atoms.

Change Isotope. Pops a small dialog allowing the user to specify theisotope number for the selected atoms. Remains disabled if the selectedatoms are not all the same element.

Mutate Residue. Opens a palette of possible residue types, allowing the user to change the type of the selected residues. Includes a secondary palette of “variant” types; the two most recently selected of these are added to the main palette.

Set Residue Numbers. Opens a dialog that allows the user to renumberthe set of selected residues.

Change Other Properties. Opens a dialog with options to change other properties for the selected atoms. This includes Chain Name and Residue Name, as well as Partial Occupancy values.

Note: This feature currently handles true cis-trans bonds only (E/Z).

Note: This feature is still in development; some variants are not functional.

1.10 Task ToolThe Task Tool is a searchable grid of applications and

commonly used tools in Maestro. Recently used items are listed for one-click access, and users can mark any action as a "Favorite" to add it to a special Workspace toolbar.

Search text field. This will initially have the keyboard focus after you open the tool, so that you can immediately start typing. Browse. You can click on this to browse through all the actions (similar to using a menu).Recent actions. Your recently-used actions appear here. Stars indicate "Favorite" items.

The "Browse" menu item

launches a palette with a grid

of Workspace tools and

Applications.

Tip - When hovering over an item, use the Star icon to add or remove it from the Favorites bar.

Tip - When hovering over an item, categories are grey, actions are blue.

The Favorites bar appears across the top of the Workspace, just below the Selection Toolbar. Several actions appear here by default, as shown.

Tip - To add your own favorite action, click the star outline beside the item in the Task Tool. Press and drag items on the toolbar to reorder them, right-click to delete.

2. Workspace NavigatorThe Workspace Navigator is used for managing entries and interacting with structures in the Workspace. It is a single panel with two parts: the Entry List and the Structure Hierarchy.

The Entry List is a subset of the Project Table, and as such it offers:Inclusion of structures in the WorkspaceSelection of entry rows for management or science tasks New entry creation through duplication, splitting, and merging Grouping and ungrouping of entriesDeleting entries

The Structure Hierarchy organizes and represents the structures and substructures included in the Workspace, providing various ways to act on them.

Note: For information about the new features of the Entry List, see section 4.2 Hierarchical Project Table, below.

2.1 Structure HierarchyThe Structure Hierarchy provides a hierarchical view of the entries currently included in the Workspace. It allows the user to work with the structure at each level, offering a visibility toggle, a styling toolbox, and atom selection for each row of the tree.

Content OrganizationEach entry in the Workspace is represented as a folder in the Structure Hierarchy. Depending on the entry, this folder may contain a single Ligands folder and/or folders for Protein, RNA, DNA, Solvents, and Other. The Ligands folder contains all the ligands found in the entry, while the Protein folder contains a subfolder for each Chain, which in turn contains the list of residues. The Solvents folder contains subfolders for Waters and other Solvents. The Other folder contains subfolders for Metals/Ions, etc. as appropriate. In most cases, the type of object is indicated by the icon displayed on the row.

button status button status

Displayed. All children aredisplayed. For lowest items, atleast one atom is displayed.

Undisplayed. Allatoms in thesubstructure areundisplayed.

Partially Displayed. Substructurecontains both displayed andundisplayed children.

Arrow. Indicates afolder. Togglesopen substructuretree.

Row Selection. Click on a row in the tree to select all theatoms in the specified structure. Selection modifiers (Shiftor Ctrl/Cmd) may be used to build up more complexselections. Selections made outside of the tree will bereflected in the tree and may be combined with the treeselections.

Toolbox Button. Hover over a row to bring up the toolbox“+” button, then click the button to open the toolbox forthat row.

Tip - Double click on an item to Fit the Workspace to it.

2.2 Navigator PanelAdjust pane heights. The dark line above the Structure Hierarchy header is a splitter that can be dragged to adjust the relative heights of the panes. When the cursor changes as shown, press and drag, or double-click to set the height of both sections to 50%.

Collapse pane. To close one of the two sections of the panel, click on the flattened rectangle at the right edge of the header. The other section will expand to fill the available space.

Expand pane. To restore a collapsed section to its previous height, click the open rectangle that appears at the same location.

Search. To search the contents of either pane, click the magnifying glass icon on the the corresponding header. A search field will open below it. On the Entry List, the filtering options will also be shown (funnel icon).

3. Footer Bar

3.1 Status Bar

The footer at the bottom of the Workspace contains the Status Bar and the Workspace Configuration toolbar.

The Status Bar provides information about the structures in the Workspace. The Workspace Configurationtoolbar allows the user to determine what sorts of auxiliary objects are shown and also provides access tothe various gadgets and tools that enhance the Workspace.

The fixed left-most area of the status bar shows the selected,

displayed, and total residues within the Workspace. These

values update as selection changes.

When the mouse is not over an atom, the right-area

summarizes the Workspace contents by the total number of

atoms, residues, chains, molecules, entries and formal charge.

When the mouse is over an atom, the right area offers

information about the hovered atom, such as the element,

PDB name, charge, and location within the structure.

3.2 Workspace TogglesThe Workspace Configuration Toggles allow the user to

temporarily mute any auxiliary objects currently available in the

Workspace.

Objects will appear blue when they are available and visible withinthe Workspace; they have a transparent background when availablebut muted; and they appear disabled when not available. Thoseobjects include:

button action button action

Annotations.Toggles the displayof Labels, Captions,and Highlights.

Measurements.Toggles the display ofDistance, Angle,Dihedral, and 1H NMRCoupling. Use the [...]to open theMeasurements panel.

Surfaces. Togglesthe display ofsurfaces in theWorkspace.

Ribbons. Togglesdisplay of Ribbons inthe Workspace

Interactions.Toggles display ofInteractions inWorkspace. Use the[...] to open theInteractions panel.

More Configuration.Opens the WorkspaceConfiguration panel.

3.3 Workspace Configuration PanelThe Workspace Configuration Panel consolidates options for

laying out the Workspace and additional features of Maestro.

Each item can be toggled, and some (when toggled on) offer

additional options.

WorkspaceToggles

AlternatePositionsCoordinateAxisUnit CellCrystalMatesDipoleMoment

Workspace GadgetsClipping PlanesWorkspaceNavigator2D OverlayWorkspacePropertiesCommandInput AreaSequenceViewer

BackgroundTileWorkspaceStereoBackgroundColor

3.4 Interactions Tool

3.5 Measurements Tool

Hovering over the Interactions toggle in the Workspace

Configuration toolbar displays a “...” button that can be clicked

to bring up the Interactions Settings panel.

This panel offers show/hide toggles for three types of non-bondedinteractions, each of which has subtypes that can also be toggledindependently. The user can thus hide any of the basic interactiontypes while preserving the state of the subtypes. Each of theseinteraction types also has an atom sets setting; in all cases, thedefault is Ligand-receptor. The types and subtypes are as follows:

Non-covalent bondsHydrogen bondsHalogen bonds

Pi InteractionsPi-pi stackingPi-cation

Contacts/ClashesGoodBadUgly

Hovering over the Measurements toggle in the Workspace

Configuration toolbar displays a “...” button that can be clicked

to bring up the Measurements panel. This panel includes tabs

for each type of measurement currently found in the

Workspace.

Double-click on a measurement row in the panel to fit the Workspace to that measurement, or right-click for more actions.

The arrow in the top right corner of the panel offers Delete All Measurements as well as Delete and Export actions for the measurements in the currently viewed tab. The icon button to the left of the arrow puts the Workspace in measurement mode.

Tip - Right-click a measurement label in the Workspace to change the measurement value, delete the measurement, or move the labels.

3.6 Workspace Gadgets3.6.1 2D OverlayThis optional Workspace Gadget displays a 2D version of any ligands or other

small molecules in the Workspace. Right-click on the pane to bring up a menu;

if only a single structure is shown, this includes the option to open the structure

in the 2D Sketcher.

Note: if the 2D Overlay is hidden, it can be displayed again via a toggle in theWorkspace Configuration panel.

3.6.2 Workspace PropertiesThis Workspace gadget appears in the top left corner and displays the selected property information for the “target” entry in the Workspace. Click on the text to change the properties shown, or right-click to bring up a menu with hide and edit options. When this text is hidden, moving the mouse into the corner of the screen displays a faded version of it; click on the text to make it visible again.

Note: An entry is defined as the “target” if it is the only entry in the Workspace, or the only entry that is both included and selected.

4.1 BannersNotification BannersNotification banners report on the success or

failure of background processes such as

imports and jobs. If appropriate, they also

include links to common “next steps”. These

banners will close automatically after a brief

delay if the user is working in Maestro;

otherwise, they will remain until manually

dismissed. If multiple notifications are

received, they will be stacked up in sequence,

and a summary banner will appear, as shown.

Mode BannersSome actions - for instance, measurement and adjustment - require the user to pick atoms in the Workspace in a particular sequence or otherwise use the mouse in a special way. When the user chooses such an action, the Workspace enters a special

“mode.”

Modes are indicated by a mode banner, which remains open as long as the user is working in that mode. The banner displays prompts or instructions and sometimes additional options.

Closing the banner ends the mode. Canceling typically discards the most recent changes; selecting OK or Done keeps the changes. The Esc and Enter keys are usually available as shortcuts for these actions.

4. Miscellaneous

4.2 Hierarchical Project TableThe new Hierarchical Project Table offers the ability to organize entries in a more flexible way by enabling the creation of groups within groups.

Major features:

Nested groupsInterspersed groups and entries (no special 'ungrouped' area)Group header shows how many entries are in the group Shortcut rows can be used to 'mirror' one or more rows at the top of the table, so they can't be scrolled out of view.

4.3 Special Workspace InteractionsRibbons and the Ribbon EditorLeft-clicking on a ribbon segment selects the CA atom for the corresponding residue, whether or not that atom is displayed. The selection expands appropriately for higher picking levels.

Right-clicking on a ribbon brings up the Ribbon Editor palette shown at the left. This editor applies to all ribbons found within the selected atoms, or all ribbons if there is no selection. Options include deleting the ribbon, changing the color scheme, changing the ribbon style, and hiding or showing some or all of the associated residue atoms.

Surface MenuRight-clicking on a surface in the Workspace brings up this menu. Display Options... opens an editor dialog for renaming and changing the appearance of the surface. Manage Surfaces... opens a dialog showing all the surfaces currently included in the Workspace, whether visible or not. Tip: To bring up this menu, move the mouse pointer to a point on the surface where there are no atoms underneath. The cursor will change to a plain arrow.

4.4 Menusmenu description

Maestro Mac: standard application menu. All platforms: customization options.

File Formerly “Project”. All project and structure actions. Includes Quit.

Edit Actions related to changing structures and entries. Includes Preferences.

Select Actions related to selection.

Workspace Actions related to Workspace contents. Also includes appearance settings.

Scripts Access point for user-defined scripts.

View Actions for changing camera view, saving views, changing screen display.

Window Access point for floating windows, pane and gadget toggles. Also includes deprecated menus.

Help Access to Help, Keyboard Shortcuts, Tutorials, etc. Also includes access to new ContactTechnical Support and Configure Licensing and Hosts dialogs.

Measurement MenuRight-clicking on a measurement value in the Workspace brings up this menu. Move Measures initiates a mode for dragging any measurement label in the Workspace. The Adjust and Set options offer two ways to change the current value - by dragging atoms or by entering a specific number. The last two options also act on the current measurement only.

Heads-up Display (HUD)Holding down spacebar on the keyboard displays this special translucent panel in the Workspace. Press and drag with your left mouse button on one of the three actions to change your camera view. The HUD is especially useful in Move Atoms mode, when normal mouse actions change the selected atoms rather than the view, but it can be used at any time.