Introduction to Cerius2

and Material Studio

Yuk Sham
Supercomputing Institute Consultant
Phone: (612) 627-7472
Email: shamy@msi.umn.edu
 Outline
Introduction to Cerius2
What is Cerius2
How to run Cerius2
Overview of GUI
Examples of usage

Introduction to MaterialStudio
What is MaterialStudio
How to run MaterialStudio
Overview of GUI
 What is Cerius2 and Material Studio

Commercially available from Accelrys, Inc.

(formerly know as Molecular Simulation, Inc.)
Software for research in Life and Material
Sciences
Cerius2 for the SGI platform
Molecular visualization software
Graphic User Interface (GUI) for other stand
alone software (modules)
Some of Cerius2 features

Molecular Visualization
Structure Editing and
Optimization
Crystal and amorphous crystal
building
Powder Diffraction Studies
Molecular simulation
Properties Calculations
Morphology predictions
 Current
licenses

http://www.msi.umn.edu/software/cerius2/
 Current Availability

Floating Licenses setup

Available on all SGI workstations at

BSCL, SDVL and VWL
 How to run Cerius2

Running Cerius2 on a SGI machine

source /usr/local/cerius/cshrc

cerius2

(***sometimes: cerius2 unlock)

 How to run Cerius2
To run cerius2 without sourcing the cshrc file,
modify .cshrc in your home directoy.

cd
pico .cshrc

Add the following to the .cshrc file.

source /usr/local/cerius/cshrc

(Dont do this if you are doing this for insightII)

 Porting Display to another unix
workstation
ssh X sgimachine.msi.umn.edu

source /usr/local/cerius/cshrc

cerius2

SGI machines:

For SDVL: e.g. i2, i3, i6, i8 etc

For VWL: vi1, vi2, vi4
For bscl: bi1, bi2, bi4, bi7 etc
Cerius2 the viewer
Viewer toolbar

Module toolbar

Viewer Window
Selecting a module

Module selector

Card selector
 Examples
Graphical User Interface
Building/Editing small molecules
Assigning forcefield
Minimization and Dynamics
Sketching a molecule
with 3D Sketcher
Sketching a molecule
Select desire atom type
and click Sketch
Left click to draw the
first atom, move to a new
position and left click to
draw the second bonded
atom
Left click on the same
atom to end the sketch
Click selection button then
click H Adjust to add
missing hydrogen
Click Undo for mistakes
 Finding your molecule in
Cambridge Structure Database

Cambridge Structural Database

Available on all SGI and Sun workstation at
BSCL and VWL

module load cambridge

cq

Save your search as a single entry in a

standard file format
Loading a molecule
Loading Model
Loading Model
Saving and Restoring your session
 Viewing your models

Panel Display

Add and
Delete Model

Model Selector
Unbuilding a crystal
 Add Hydrogen to crystal

Click Unbuild Crystal in Builders/Crystal Builder

window

(This will convert your crystal to give you your lowest number
of molecular component in your crystal)

Click H Adjust in Build/3-D Sketcher to add

missing hydrogens

Click build Crystal in Builders/Crystal Builder

window

(This will convert molecule back into the unit cell)

Rebuilding a crystal
 Rendering
Rendering
options
Rendering Images
Crystal visualization
Viewing your models
Combining structures
Create a new model by
clicking the + button
Left mouse click on the
background of the
molecule you want to copy
and drag to the new model
window
Repeat for the another
molecule so you have a
model with both molecules
Selection fragment or groups of atoms
Click on Atom to select
method of atoms selection.
To select an individual
molecules, click Frag
Point and click on molecule
to select all atoms in the
molecule
 You and your mouse

Right mouse click to rotate

Ctrl-Right mouse click to rotate selected atoms
Middle mouse click to translate
Ctril-Middle mouse click to translate selected
atoms
Left mouse click and drag to select
Mouse point at atom or bond and left mouse
click to select atom or bond
Middle and right mouse click (together) to zoom
in and out
Combining structures
Calculating free volume
Assigning Forcefield and Charges
Assigning Charges
 Minimization and Dynamics

Click run in OFF Method/Minimizer/Run window

Click Charges in OFF Setup/Charges window, the

Charges Window will pop up. Click Calculate to
assign charges.
Minimization
Exporting Images
Printing with lpr command in UNIX

lpr P printer_name CERIUS.ps

 cerius2 Examples

Cerius2 step through examples

Help/examples

Training workbooks is available

 cerius2 Documentation

http://www.accelrys.com/doc/life/index.html

Username: msi
Passwd: msi-doc
 What is Material Studio

Commercially available from Accelrys, Inc.

(formerly know as Molecular Simulation, Inc.)
Software for research in Life and Material
Sciences
Material Studio is for the Windows platform
Molecular visualization software
Graphic User Interface (GUI) for other stand
alone software (modules)
Some of Material Studio features

Molecular Visualization
Structure Editing and
Optimization
Crystal and amorphous crystal
building
Powder Diffraction Studies
Molecular simulation
Polymorph predictions
 Material Studio
modules

http://www.msi.umn.edu/software/materialstudio
 Current Availability

Floating Licenses setup

Availability:

Remotely on sdvlapp1 using citrix clients

PCs at VWL
 Getting
citrix clients
 Setting up
Connection:
Local Area Network citrix clients
Network protocol:
TCP/IP

ICA Connection:
sdvlapp1.msi.umn.edu

encryption level:
128 Bit

Window Colors: your choice:

True color (24 bit)

Windows Size: your choice:

640x480, 800x600, 1024x768

http://www.msi.umn.edu/sdvl/sdvlapp1/qswin.html
 Running Material Studio

Click

Goto

Start/All Programs/Accelrys MS Modeling 3.0/MSModeling

Material Studio viewer
Material Studio viewer
Sketch Molecule
Measure
 You and your mouse

Right mouse click to rotate

Middle mouse click to translate
Left mouse click on atoms to select atoms.
Mouse point at atom or bond and left
mouse click to select atom or bond
Left and right mouse click (together) to
zoom in and out
Importing
Rebuilding
Crystal
Rebuilding
Crystal
 Display Style

Right mouse click

on background to
view options
Click Display
Style to view
options
Display Style
Lattice
 Crystal
Maniputation
Cleaning
your
Molecule
MS Modules
MS IO
and
printing
Local Disk and printing inside citrix
MS Documentation
 To get help

By mail help@msi.umn.edu
Web www.msi.umn.edu
Phone 612 626 0802

Yuk Sham
Computational Biology/Biochemistry Consultant
Phone: (612) 624 7427 (Walter Library)
Phone: (612) 624 0783 (VWL)
Email: shamy@msi.umn.edu