Cerius² Notes

• Introduction
• Licensed modules
• Format of this document
• Starting and Stopping the program
• Outline of the program
• Menu bar
• Supported file format
• Tutorial (for C637 Spring 2001)

Cerius² is a comprehensive molecular modeling and simulation package used for materials science and life science. It offers a broad range of application modules for various molecular environment, including organic molecules, biomolecules, drugs, polymers, organometallic catalysts, inorganic solids, surfaces, etc.. Cerius² version 3.5 is currently available at the IU MolViz facility with the following licensed modules:

This is a beginner's guide to general molecular modeling practices using Cerius² (some images and contents in this page came from the MSI's Cerius² documents). Refer to the Cerius² manuals for a more complete description of each individual module. The hardcopies of the manuals are located in room A701. The online Cerius² manuals are also available at the MSI web site (contact the MolViz staff for user ID & password).

Visualizer

The core module of the Cerius² software package, which provides a comprehensive modeling environment for building, editing and visualizing models of molecular structure.

 

Crystal Builder

Build and visualize 3D periodic crystal structures.

 

Polymer Builder

Construct polymer chains from monomers that are either taken from a fragment library or user-defined.

 

Surface Builder

Build 2D periodic structures by cleaving a plane from a crystal or by placing atoms and fragments within a suitable 2D-surface cell.

 

Interface Builder

Construct and visualize an interface between two different crystals or a twin or defect within a crystal.

 

Crystal Packer

A computational module which assists in the estimation of sublimation energies and the packing of molecular crystals.

 

Open Force Field

Provides a molecular mechanics force field database covering organics, polymers, zeolites, organometallics, etc.

 

Force Field Editor

A graphical user interface which allows user to choose force fields from the database or create and customize user's own force fields.

 

Morphology

Predicts and analyzes the external morphology of crystals from their internal crystal structure.

 

Diffraction-Amorphous

A computational instrument for the simulation of X-ray, electron, and neutron diffraction patterns from models of non-crystalline and disordered materials.

 

Diffraction-Crystal

Another computational instrument for the simulation of X-ray, electron, and neutron diffraction patterns from crystalline models.

 

Minimizer

Minimize the energy of molecular or periodic structures using molecular mechanics calculations.

 

Dynamics

Performs molecular dynamics simulations to investigate time-dependant behavior of materials.

 

Discover

A molecular simulation program which provides a wide range of simulation methods, enabling studies of many more molecular systems and materials types than you could using conventional simulations methods.

Menus and sub-menus are described as main menu / sub-menu. For example, File/Load Model specifies the Load Model menu under the File pull-down in the menu bar. All mouse-accessible selections are made by positioning the mouse cursor and clicking the LEFT mouse button. Keys that must be pressed simultaneously, or function keys, are listed in "<>" (e.g., <control-D> or <F9>).

1. Log into a departmental SGI workstation.
2. Open a UNIX shell by clicking Desktop/Unix Shell (on the toolchest in the upper left corner of the screen).
3. In the new UNIX shell, type cerius2. The program takes about 30 seconds to generate windows and graphics.
4. To exit from the program, click File/Exit in Cerius², then confirm that you want to exit.
5. DON'T forget to log out of the SGI workstation (click Desktop/Log Out, then confirm that you want to log out) if you are completely finished.

The Cerius² program has three main windows:  the model window where models are displayed, the main control panel which provides access to various Visualizer tools, and the text window in which text messages are displayed.

The main control panel consists of the menu bar, the toolbar, the model manager, and the deck of cards menu as shown below:

The menu bar contains a group of pull-down menus that provide fully access to all Visualizer tools. A brief description of these menus is given in the next section. The toolbar offers a shortcut to the frequently used Visualizer tools:

The model manager enables you to manage (select, edit, save) your models. In the deck of cards menu, the application modules are grouped into card decks for easy access.

The program is operated by the mouse. In general, the three mouse buttons perform different functions. The left button is used to click a control panel button, drag a slider, select an option from a pull-down menu or popup, and so on. The middle button is used by the system's native window manager and also for certain model-manipulation activities. The right button is used to obtain help text for GUI controls.

The Cerius² on-screen help facility enables you to obtain information about each control and menu item by right-clicking on the control or menu item. A window containing the requested help text appears on the screen. Click the help window to close it, or right-click on another item to obtain the help text for the new item.

The menu card search tool on the main control panel's toolbar enables you to search for a keyword used anywhere in the menu card deck or in menu items of the menu bar. The search is not case sensitive, and wildcards can be used.

File Menu

• New Session

  Reinitialize Cerius². All unsaved models and data are lost.

• Load Session

  Load molecules and data from a previously saved session. All display options, etc. are recalled.

• Save Session

  Save molecules and data from the current session. All display options, etc. are saved.

• Load Model

  Load coordinate file. Default display options, etc. are used.

• Save Model

  Save molecule as coordinate file. Display options, etc., are NOT saved. The following coordiante file formats are supported: MSI, CAR, XTL, BGF, MSF, CSSR, MACCS, MolEN, CAMBRIDGE, MOPAC, PDB, ShelX.

• Print
• Exit

Edit Menu (most of these menus are self-explanatory)

• Cut
• Copy
• Paste
• Delete
• Duplicate
• Select All
• Selection

  Select atoms.

• Groups

  Define a group of atoms.

Build Menu (menus are self-explanatory)

• 3D-Sketcher
• Add Atom
• Annotation
• Edit Atoms
• Edit Bonds
• Edit H-Bonds
• Element Defaults
• Disorder

View Menu (most of these menus are self-explanatory)

• Reset View
• Set Origin
• Center
• Fill Window
• Display Attributes

  Change style (stick, ball & stick, cylinder, etc.) or label.

• Colors
• Atom Visibility
• Dials

  Pan and magnify via software dials.

• Orient

  Set origin and reset view.

• Options

  Display annotations, scales, axes; set mouse-controlled movement or constant motion.

• Graphics

  Z-clipping, lighting, depth-cueueing, projection, stereo.

• Animation

  Show "frames" of a movie.

• Rendering

  Choose Psycho or RayTrace rendering modes.

Move Menu

• Model Move

  Move model via software dials & sliders.

• Atoms Translate
• Atoms Rotate
• Atoms Align

  Align atoms along an axis.

• Atoms Position

  Move atoms to a defined position.

• Atoms Match

  Superimpose atoms.

• Bond Geometry

  Change bond length, bond angles, bond torsion angles.

Geometry Menu

• Measurements

  Measure distance, angle, torsion angle, chirality.

• Close Contacts

  Measure ven der Waals contacts.

• Connolly Surface

  Generates Connolly "dot" surface.

• Free Volumes

  Calculate total, occupied, and accessible volumes in molecule or crystal lattice.

• Vector Properties

  Display vectors indicating FORCE, VELOCITY, ELECTRON SPIN, and SHELL OFFSET.

Utilities menu

• Record Commands

  Generate a log of commands during your session.

• Playback Script

  Run a log of commands.

• Panel Manager

  Display, hide, move menu panels.

• Application Licensing

  Show license information.

• Command Tracing

  Display extra information in information window when you activate a menu command.

• External Processes

  Run process outside of Cerius² environment.

• Customize

  Customize your Cerius² environment.

MSI (default file extension .msi)

Molecular Simulations Inc. (MSI) native Cerius² format (the default).

XTL (.xtl)

MSI file format.

CAR (.car, .mdf)

MSI native Insight II format for Cartesian coordinate file (.car) and molecular data file (.mdf).

ARC (.arc)

MSI native Insight II format for Cartesian coordinate archive file.

BGF (.bgf, .xtl)

MSI BIOGRAF (BGF) file format used by the BIOGRAF, POLYGRAF, and NMRgraf programs.

MSF (.msf)

MSI QUANTA structure file format.

CAMBRIDGE (.dat, .fdat)

Cambridge Structure Database (CSD) FDAT format (read only).

CIF (.cif)

Crystallographic Information File (CIF) format -- International Union of Crystallography format for crystal structure data. The Cerius² version 3.5 (the current version installed in the MolViz facility) can only read the CIF files generated by the Cambridge Structural Database which contain additional CSD-specific information. The generic CIF files (i.e., exactly meet the IUCr format rules) are supported by Cerius² 3.7 and newer version.

CSSR (.cssr)

SERC Daresbury Laboratory's Cambridge Structure Search and Retrieval (CSSR) file format.

ICSD (.icsd)

Inorganic Crystal Structure Database ICSD format (read only).

MACCS (.mol, .mdl)

MDL's MACCS file format.

MOPAC (.pac)

MOPAC/AMPAC Z-matrix file format, the data input standard for the MOPAC and AMPAC quantum mechanical programs.

MolEN (.xyz)

Enraf-Nonius' MolEN file format. Only MolEN users can load and save files of this type.

PDB (.pdb)

Protein Data Bank format for 3D molecules.

SHELX (.res, .ins)

SHELX structure file format used by the SHELXTL program, the standard for X-ray single-crystal structure determination.