Using the Drop-Down Menus

All of BioLuminates functionality can be

accessed via the drop-down menus.
File - For import/export and fle saving
Edit - For selecting and editing structures
in the Workspace
Style - For applying molecular styles to
the Workspace contents
View - For adjusting global Workspace
display settings
Tools - For performing various analyses,
and accessing superposition and
alignment tools
Tasks - For running calculations

Window - For raising and closing
application windows
Help - Links to various Help resources
Using the Toolbars
Show and hide the toolbars: Click on
the respective toolbar title to toggle that
toolbar between being shown and being
hidden.
For example, toggle on the Project toolbar,
and click the button to bring up the
Project Table.
Buttons can be added and removed to any
toolbar by right-clicking on a toolbar and
selecting Customize.
BioLuminate 2014 User Interface
Mouse Controls
Rotate xy: Left button

Rotate z: Shift+middle and right buttons

Translate: Click and hold the middle
button while moving the mouse

Select Multiple Atoms: Shift+left button

Zoom: Hold the right button while moving
the mouse
Customize Mouse Buttons:
Edit > Settings > Mouse Actions, from
this menu the mouse buttons can be
customized for PyMOL, 2-button, 3-button,
and track pad mouse confgurations.
Display right-click contextual menus:
Right-click and hold in an empty portion
of the Workspace, or on a structure or
selection in the Workspace or Sequence
Viewer.
For example, go to Edit > Pick Mode >
Residues and select a residue in the
Workspace. Right-click and hold over the
selected residue, and a menu of options will
appear. From the menu, select
Actions > Expand 5 to expand the
selection to include atoms within 5 of the
initial selected residue.
Monitoring Calculation Jobs
Click the button in the lower left
of the interface to open the Job Monitor
panel.
This button appears green when jobs are
running and appears grey when all jobs are
complete. The numbers displayed indicate
how many jobs are currently running.
Using the Toggle Table
The Toggle Table includes a number of
shortcut buttons atop a list of entries
(rows) currently in the BioLuminate
Workspace.
Entries can be hidden and made visible by
toggling the entry name.
Use the buttons to the right of the entry
name to act on the corresponding entry:
- Actions - Show - Hide
- Label - Color
All entries in the Toggle Table are included
in the Workspace. Before performing a
calculation, place only those structures
you wish to perform the calculation on in
the Workspace.
Remove structures from the Workspace:
To remove a specifc entry from the
Workspace, select > Remove from
Workspace. To clear the Workspace, select
in the All row and choose Remove
Everything from Workspace.
Note: Clearing the Workspace does not
delete structures (entries) from the
project fle; it only excludes them from the
Workspace.
Working with Projects
Create a new project: File > New Project or Ctrl+N
Save a project: File > Save Project As; subsequent work is
saved automatically to the project fle
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 > Import
Structures or Ctrl+I
Import a PDB structure: File > Get PDB or click the
button in the Project toolbar
Clear the workspace: Select > Remove Everything
from Workspace in the All row of the Toggle Table or click
the

button in the Workspace Toolbar. Clearing the
Workspace does not delete your structures (entries); it
only excludes them from the Workspace.
Superimpose two proteins: Include two proteins in the
Workspace, 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, select
Tools > Ligand Interaction Diagram. Here, select View > LID
Legend for a diagram legend.
Analyze protein quality: Select in the Proteins
Toolbar to view Protein Reports of potential problems with
the structure in the Workspace
Adjust torsions: Select in the Proteins Toolbar and
then select a bond in the Workspace; click and drag the
left mouse button to manually adjust the torsional angle
View Ramachandran plot: Select in the Proteins
Toolbar
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 Edit
Toolbar.
Structure sculpting: Edit > Structure Sculpting, or click
the sculpting button in the Build or Proteins toolbar,
then click and drag on 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 a
distance, angle, dihedral, or 1H NMR coupling. Then, click
on appropriate structures in the Workspace.
Using Workspace Styles
Apply Workspace Style to a given entry: Style > Apply
Predefned Style, or click the button in the Style
toobar
Edit Workspace Style settings: Style > Predefned Style
Settings > Style Settings or click and hold the button
in the Style toolbar and select Settings to defne visual
styles
Automatically re-apply style when contents of
Workspace change: Style > Auto Apply Predefned Style
or Click the button in the Style toolbar
Saving Images
Save an image: File > Save Image or select the
button in the Toggle Table
Save a ray-traced image: Select the button in the
Toggle Table
Finding and Selecting Structures
Find structures or entries: Ctrl+F will display the Find
toolbar in the Workspace; use the and buttons in
the Find toolbar to traverse matches.
Select atoms in the Workspace: Click and hold in
the Edit toolbar or go to Edit > Pick Mode and select from
Atoms, Residues, Molecules, Chains, or Entries the type
of structure you wish to select. Click in the Workspace to
select a structure. An entry titled (Selection) is enabled in
the Toggle Table.
Select atoms in the Sequence Viewer: Choose
Edit > Settings > Show Sequence Viewer to turn on the
Sequence Viewer. Hover over a residue letter to view the
3-letter residue code and residue number. Select multiple
residues using Shift+Click and 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 fle. In the
(Selection) row, choose > Copy to New Project Entry to
create a new entry that will be saved with the project fle.
Customizing BioLuminate
Many global settings can be adjusted by the menu options
at Edit > Settings. Some recommended settings to explore
here include Show Sequence Viewer, Preferences, Mouse
Actions, and View > Workspace Appearance.
Any changes you make to settings are automatically saved
for your next BioLuminate session.
Getting Help
All of our help documentation can be found in the Help
drop-down menu.

Help: Search our software documentation using a web
browser
Knowledge Base: A database of questions that have
already been solved by our technical support team
Training Videos: Visit
www.schrodinger.com/supporttraining/18/32/
Performing Common Operations in BioLuminate 2014