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Using the Drop-Down Menus

All of BioLuminates functionality can beaccessed via the drop-down menus.

File -For import/export and le saving

Edit-For selecting and editing structures

in the Workspace

Style-For applying molecular styles tothe Workspace contents

View-For adjusting global Workspacedisplay settings

Tools-For performing various analyses,and accessing superposition andalignment tools

Tasks-For running calculations

Window-For raising and closingapplication windows

Help-Links to various Help resources

Using the Toolbars

Show and hide the toolbars:Click onthe respective toolbar title to toggle thattoolbar between being shown and beinghidden.

For example, toggle on the Project toolbar,and click the button to bring up theProject Table.

Buttons can be added and removed to anytoolbar by right-clicking on a toolbar andselecting Customize.

BioLuminate 2014 User Interface

Mouse Controls

Rotate xy: Left button

Rotate z: Shift+middle and right buttons

Translate: Click and hold the middlebutton while moving the mouse

Select Multiple Atoms: Shift+left button

Zoom: Hold the right buttonwhile movingthe mouse

Customize Mouse Buttons:Edit > Settings > Mouse Actions, fromthis menu the mouse buttons can becustomized for PyMOL, 2-button, 3-button,and track pad mouse congurations.

Display right-click contextual menus:Right-click and holdin an empty portionof the Workspace, or on a structure orselection in the Workspaceor SequenceViewer.

For example, go to Edit > Pick Mode >Residues and select a residue in theWorkspace. Right-click and holdover theselected residue, and a menu of options willappear. From the menu, selectActions > Expand 5 to expand theselection to include atoms within 5 of theinitial selected residue.

Monitoring Calculation Jobs

Click the button in the lower leftof the interface to open the Job Monitorpanel.

This button appears green when jobs arerunning and appears grey when all jobs arecomplete. The numbers displayed indicatehow many jobs are currently running.

Using the Toggle Table

The Toggle Table includes a number ofshortcut buttons atop a list of entries(rows) currently in the BioLuminateWorkspace.

Entries can be hidden and made visible bytoggling the entry name.

Use the buttons to the right of the entryname to act on the corresponding entry:

- Actions - Show - Hide- Label - Color

All entries in the Toggle Table are includedin the Workspace. Before performing acalculation, place only those structures

you wish to perform the calculation on inthe Workspace.

Remove structures from the Workspace:To remove a specic entry from theWorkspace, select > Remove fromWorkspace. To clear the Workspace, select

in the All row and choose RemoveEverything from Workspace.

Note:Clearing the Workspace does notdelete structures (entries) from the

project le; it only excludes them from theWorkspace.

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Working with Projects

Create a new project: File > New Project or Ctrl+N

Save a project: File > Save Project As; subsequent work issaved automatically to the project le

Open an existing project: File > Open Project or Ctrl+O

Close a project: File > Close Project or Ctrl+W

Undo/Redo:Edit > Undo, Ctrl+Z,or use the /buttons in the Edit toolbar

Working with Multiple Structures

Import single or multiple structures: File > ImportStructures or Ctrl+I

Import a PDB structure:File > Get PDB or click thebutton in the Project toolbar

Clear the workspace: Select > Remove Everythingfrom Workspace in the All row of the Toggle Table o r clickthe button in the Workspace Toolbar. Clearing theWorkspace does not delete your structures (entries); itonly excludes them from the Workspace.

Superimpose two proteins: Include two proteins in theWorkspace, then go to Tools > Protein Structure Alignment

Working with Proteins

Generate a 2D diagram of a ligand in a binding pocket:

With a protein-ligand complex in the Workspace, selectTools > Ligand Interaction Diagram. Here, select View > LIDLegend for a diagram legend.

Analyze protein quality:Select in the ProteinsToolbar to view Protein Reports of potential problems withthe structure in the Workspace

Adjust torsions: Select in the Proteins Toolbar andthen select a bond in the Workspace; click and dragtheleft mouse button to manually adjust the torsional angle

View Ramachandran plot:Select in the ProteinsToolbar

Changing Molecular Representation

Change atom and bond appearance for a given entry:

> Preset, or > As > Lines, Sticks, Balls, etc.

Change molecular color scheme: > Color by Element,Color by Chain, etc.

Modifying and Measuring Structures

Adjust distances, angles, and torsions: Edit > Adjust

Distances and Angles or click the button in the EditToolbar.

Structure sculpting:Edit > Structure Sculpting, or click

the sculpting button in the Build or Proteins toolbar,then click and dragon an atom in the Workspace.

Measurements: Style > Measurements > Pick to Measure

to measure a distance. Alternately, press and hold the

button in the Labels Toolbar to select to measure adistance, angle, dihedral, or 1H NMR coupling. Then, clickon appropriate structures in the Workspace.

Using Workspace Styles

Apply Workspace Style to a given entry: Style > ApplyPredened Style, or click the button in the Styletoobar

Edit Workspace Style settings: Style > Predened StyleSettings > Style Settings or click and hold the buttonin the Style toolbar and select Settings to dene visual

styles

Automatically re-apply style when contents ofWorkspace change: Style > Auto Apply Predened Style

or Click the button in the Style toolbar

Saving Images

Save an image: File > Save Image or select thebutton in the Toggle Table

Save a ray-traced image: Select the button in theToggle Table

Finding and Selecting Structures

Find structures or entries: Ctrl+Fwill display the Findtoolbar in the Workspace; use the and buttons inthe Find toolbar to traverse matches.

Select atoms in the Workspace: Click and hold inthe Edit toolbar or go to Edit > Pick Mode and select fromAtoms, Residues, Molecules, Chains, or Entries the typeof structure you wish to select. Click in the Workspace toselect a structure. An entry titled (Selection) is enabled inthe Toggle Table.

Select atoms in the Sequence Viewer: ChooseEdit > Settings > Show Sequence Viewer to turn on theSequence Viewer. Hover over a residue letter to view the3-letter residue code and residue number. Select multipleresidues using Shift+Clickand Ctrl+Click . An entry titled(Selection) is enabled in the Toggle Table.

Note: The contents of an entry titled (Selection) are

overwritten by the most recent selection. (Selection)entries are also not saved with a project le. In the(Selection) row, choose > Copy to New Project Entry tocreate a new entry that will be saved with the project le.

Customizing BioLuminate

Many global settings can be adjusted by the menu optionsat Edit > Settings. Some recommended settings to explorehere include Show Sequence Viewer, Preferences, MouseActions, and View > Workspace Appearance.

Any changes you make to settings are automatically savedfor your next BioLuminate session.

Getting Help

All of our help documentation can be found in the Helpdrop-down menu.

Help: Search our software documentation using a webbrowser

Knowledge Base:A database of questions that havealready been solved by our technical support team

Training Videos:Visitwww.schrodinger.com/supporttraining/18/32/

Performing Common Operations in BioLuminate 2014