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Materials Science Suite Interface

Using the Toolbars

Show and hide the toolbars: Click on the respectivetoolbar title to toggle that toolbar between being shown

and being hidden. For example, toggle on the View Toolbar,

and click the button to t the Workspace contents tothe Workspace.

Entry List and Project Table

After importing a set of les (File > Import Structures),the list of structures can be viewed in the Entry List or

the Project Table. All data relevant to the structure can be

found in the Project Table.

Open Project Table: File > Project Table or click in theProject Toolbar

Using the Drop-Down Menus

All of the Materials Science Suites functionality can beaccessed via the drop-down menus.

File: Import/export and le savingEdit:Selecting and editing structures in the WorkspaceStyle: Applying molecular styles to the Workspace contentsView: Adjusting global Workspace display settingsTools: Performing analyses, building complexes, andenumerating libraries

Tasks: Running various calculationsWorkows: Installing, creating, and managing KNIMEworkowsWindow: Raising and closing application windowsHelp: Links to various Help resources

Mouse controls

Rotate xy:Left buttonRotate z:Shift+middle+right buttonTranslate xy:Middle buttonTranslate z:Middle+right button

Zoom:Right buttonSelect:Shift + Left buttonChange Mouse Settings:Edit > Settings > MouseActionsDisplay right-click contextual menus:Right-clickand hold in an empty portion of the Workspace, or on astructure or selection in the Workspace.

Monitoring calculation jobs

Click the button in the lower left of the interface

to open the Mini Job Monitor panel. Double-clicking

on a current job listed in the panel or clicking on the

Monitor button will open the Job Monitor panel with more

information.

The button appears green when jobs are

running. The numbers displayed on the button indicate how

many jobs are currently running out of a total number of

jobs submitted.

Status Bar

Place the mouse cursor over a specic atom in theWorkspace. The status bar at the bottom of the Workspacewill turn yellow and provide information about that specicatom.

Include/display a structure in the Workspace: Click onthe square in the In column. The square will be lled in toshow that it is now included in the Workspace.

Select a structure:Click anywhere in the row that isoutside the In column square and the row will turn yellowto signify that its selected.

Include/select multiple structures in the Workspace:Same as above but simply hold Shift or Ctrl when selectingor including structures. This is useful for running jobs on

multiple structures.

Search for an entry by name:In the Project Table, click

Tools > Find/Replace and type in the search eld. In theEntry List, type in the search eld. Search results aredynamically updated.

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Materials Science Suite 2014 - Common Tasks

Working with projects

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

Save a project:File > Save Project As; subsequent workis saved automatically.

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

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

Change default directory for saving les:File > ChangeDirectory

Save an image:File > Save Image

Editing structures in Workspace

Turn on Build and Fragments Toolbar: Edit > 3D Builder> Show Build Toolbar/Show Fragments Toolbar or clickthe Build and Fragments Toolbar button.

Draw in 3D:Hold and select an atom type. Click onan existing atom to start adding to the structure or click

in an empty portion of the Workspace to start a newstructure. Double clicking will end the drawing session.

Change atoms:Hold , select atom type, then selectan atom in the Workspace to replace it with the selectedatom type.

Note: You can select any atom type in the periodic tableby selecting Other from the drop-down menu.

Clean up geometry:Click to run a quick minimizationof the all structures in the Workspace. If a set of atomsare selected then only those atoms will be minimized

(this feature can be turned off in Edit > Settings >Preferences under Builder > Geometry cleanup).

Add fragments:Select a fragment in the FragmentsToolbar and click on an atom to attach it to that atom;click in the empty Workspace to make a separatestructure.

Use metal templates:Metal templates can be accessed

from the Fragments Toolbar by clicking , which will

open a list of metal templates to add to the structure.

Edit structures in 2D:Edit > 2D Sketcher. After editing,click Create New Entry on the bottom of the window toadd it to your project.

Symmetrize Workspace: Edit > Symmetrize Workspace

Add new structure to Project Table:Edit > CreateProject Entry from Workspace

Working with structures

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

Clear the Workspace: Edit > Clear Workspace or click

the button in the Workspace Toolbar. Clearing theWorkspace does not delete your structures (entries); itonly excludes them from the Workspace.

Select atoms in the Workspace:Click and holdin the Edit Toolbar or go to Edit > Pick Mode and selectfrom Atoms, Molecules, or Entries. Shift + Click in the

Workspace to select.

Modifying and measuring structures

Adjust distances, angles, and torsions:Edit > Adjust

Distances and Angles > Pick to Adjust or click thebutton in the Edit Toolbar.

Structure sculpting:Edit > Structure Sculpting, or click

the sculpting button in the Build Toolbar, then clickand drag on an atom in the Workspace.

Measurements: Style > Measurements > Pick to Measureto measure a distance. Alternately, press and hold the

button in the Labels Toolbar to select to measure a

distance, angle, dihedral, 1H NMR coupling, or reposition.Then, click on appropriate structures in the Workspace.

Perform local transformation:Edit > Transform > Pick to

Transform or click the button in Edit Toolbar. Selecta set of atoms and then rotate the set around the newly

created sphere using the left mouse button or move

along the xy plane with the middle mouse button.

Align structure to axis or plane:Edit > Align

Dene Centroids:Edit > Dene Centroids

Displaying Surfaces

Create a surface for a given entry:Navigate to Tools >Create and Manage Surfaces and select a surface typefrom the list.

Modify surface settings:Tools > Create and ManageSurfaces > Surface Manager or click in the ProjectTable. In the Manage Surfaces panel, select DisplayOptions to edit transparency, style, and color scheme.

Changing Molecular Representation

Change atom and bond appearance:Style > Atom andBond Representation will open a new panel to changethe atom and bond appearance. Alternatively, click

and hold the desired appearance in the Representation

Toolbar and select the group that you want to apply the

representation to.

Change molecular color scheme: Style > Atom andBond Coloring will open a new panel to change the color

scheme. Alternatively, click the in the Representation

Toolbar to select a coloring scheme.

Clipping Planes WindowOrange lines:Signies the clipping planes of theWorkspace. Increase or decrease the range of theclipping planes with the scroll wheel or click and drag the

orange lines in the window.

Green lines:Signies the view area of the Workspace.Zoom in and out with the mouse controls (see otherside).

Getting Help

All of our help documentation can be found in the Help

menu.

Help documentation:Search our softwaredocumentation through the web browser

Knowledge Base:A database of questions that havebeen answered by our technical support team

Contact Schrdinger technical support: An onlineform to contact technical support