Cerius2 Modeling Environment

Contents

Release 4.5, June 2000

1. How To Use This Guide

Who should use this guide

Additional information sources

Other Cerius2 documentation

Typographical conventions

2. Introducing Cerius2

Starting Cerius2

Building a model--caffeine

Saving a model

What you can do with a model display

Building another model--ferrocene

Reading in additional models

Managing multiple models

Printing a model

Controlling the 3D display

Exploring Cerius2 on your own

Summary--Some of what you've learned

3. Tutorials

Basic GUI Functions

Before you begin

Step-by-step tutorial

A. Loading and displaying a molecular model

B. Viewing and labeling a model

C. Selecting atoms

D. Manipulating control panels

Review

Related material

Using the 3D Sketcher

Before you begin

Step-by-step tutorial

A. Building cyclohexane and saving the structure to file

B. Converting cyclohexane into the boat conformation

C. Editing cyclohexane to make benzene

D. Editing benzene to make phenol

E. Building xylene from template fragments

Review

Managing Models and More

Before you begin

Step-by-step tutorial

A. Using the model manager

B. Making picric acid from phenol (transferring data between model spaces)

C. Building a model of indigo

D. Measuring the indigo model

E. Generating hard copy

Review

Related material

Managing and Modifying Graphs

Before you begin

Cerius2 Graphs terminology

Summary of tutorial

Step-by-step tutorial

A. Loading graphs and using the Gallery Manager

B. Using the Graph Manager and setting plotting attributes

C. Scaling graphs

D. Annotating graphs

E. Saving graph files

F. Creating new graphs and using expert functions

Checklist review

Related material

Basic Molecular Simulation: Minimization & Dynamics

A. Build a model of the glucose molecule

B. Minimize the glucose energy

C. Add water to the system

D. Simulating the behavior of the glucose/water system

What to do next

4. The Cerius2 Interface

Starting Cerius2

Initial layout of the Cerius2 screen

Main control panel

Model window

Text window

Using the mouse--the basics

Mouse buttons

Mouse activities

Using the main control panel

The menu bar

The toolbar

The model manager

Deck of cards menu

Controls and control panels

Types of controls

Managing control panels

Information sources

On-screen help

Menu card searching

Messages and status information

Other windows

5. Building Models

Basic building

Starting to construct a new model

Strategy

The 3D-Sketcher

Other basic building tools

Adding atoms and bonds

Selecting the element type

Adding atoms and single bonds

Adding templates (groups of atoms)

Selecting templates

Adding templates to a model

Custom templates

Fusing and connecting fragments

Adding hydrogens

Selecting atoms and groups of atoms

Selecting and deselecting individual atoms

Selecting atoms in several models

Selecting and deselecting collections of atoms

Selecting according to properties

Defining and selecting groups

Customized atom selection

Basic editing

Changing atoms and their bonding types

Changing the element type

Changing the formal charge

Changing the bond type

Changing the hybridization and adjusting the valence

Editing the structure

Deleting atoms and bonds

Duplicating parts of a model

Examining and changing bond lengths

Examining and changing angles

Examining and changing torsions

Inverting about an atomic center

Translating and rotating atoms

Aligning and positioning atoms

Refining the conformation

Advanced building and editing

Editing element and bond attributes

Element properties

Bond properties

Hydrogen bonds

Introducing substitutional disorder

Introducing positional disorder

Temperature factors

Specifying temperature factors

Editing temperature factors

Loading and saving temperature factors

Control of the model-cleaning function

Other builders

6. Managing Models and Sessions

Loading model structure files

Handling multiple models

Basic model management tasks

Creating, clearing, and deleting model spaces

Specifying the current model

Selecting model spaces

Controlling model visibility and the display mode

Renaming models

Sorting model table entries

Moving models between model spaces

Copying whole models from one model space to another

Moving parts of models from one model space to another

Copying models to and from other applications

Saving model structure files

Saving individual models

Saving all models

Working with Cerius2 sessions

Starting a new session

Saving the current session

Loading a previously saved session

Using saved sessions as preferences settings

7. Geometry Analysis

Measuring models

Distances

Angles

Planes

Torsions

Inversions

Calculating close contacts

Model surfaces

Connolly surfaces

Vector properties

8. Viewing and Displaying Models

Moving models on the screen

Basic tasks and methods

Translating models

Rotating models

Changing the view magnification

Setting position and orientation

Moving models relative to one another

Superimposing models

Storing and retrieving views

Animating models

Labeling and annotating models

Labels

NO LABEL

NUMBERS

SYM/NUM

ELEMENTS

CHARGES

FORMAL CHARGE

OCCUPANCY

ISOTROPIC

FFYTPE

HYBRID

NAME

MASS

CHIRALITY

Default annotation

Custom annotations

Model display style

Atom and bond display styles

Bonds as sticks

Bond order display

Bonds as cylinders

Lone atoms

Atoms as balls

Ball and stick models

Cations as polyhedra

Thermal ellipsoids

Structure traces

Cross sections of models

Apparent depth effects

Depth cueing

Projection

Resolution and graphical quality

Printing models and graphs

9. Enhancing Model Display

Model display colors

Default element colors

Coloring selected objects

Coloring atoms by properties

Background color in model window

Customizing display colors

Drawing colors

Color ranges

Creating and editing a new color range

Editing a color range

Property-color mapping

Creating and editing a binary property color map

Creating and editing a continuous property color map

Editing a property color map

Surfaces--style and transparency

Lighting control

Adjusting global light settings

Defining discrete light sources

Color and components

Directional lights

Positional lights

Spotlights

Light attenuation

Rendering and ray-tracing

Stereo viewing

10. Working with Graphs

Creating graphs

Starting a new, empty graph

Specifying the type of graph

Selecting data to plot

Loading graphs

Displaying and editing graphs

Selecting and displaying graphs

Selecting which data sets to display and edit

Labeling and annotating graphs

Changing graph axes and scale

Changing plotting style and color

Managing graphs

Controlling default display format

Preventing replacement of old graphs

Removing graphs and data from a Cerius2 session

Saving graphs

11. Working with Tables

Introduction to Cerius2 tables

The table window

Keeping track of the current table

Managing and editing tables

Creating a new table

Loading and reloading tables

Importing an ASCII text file into a new table

Specifying the current table

Entering values and editing individual cells

Copying, moving, and clearing information

Inserting and deleting entire rows or columns

Table expansion and cursor control

Saving a table

Closing a table

Table style and display

Aligning information within columns

Assigning data types

Setting display formats

Specifying headings and banners

Changing row, column, and heading sizes

Values and mathematical expressions

Applying mathematical expressions to cells or columns

Entering mathematical expressions

Using numbers

Cross references

Calculations on models

Manipulating text

Table and command operations

Recalculating table values

Models in tables

Copying models into columns

Setting up calculations on models

Saving tables containing models

Grouping table information

Creating a named group

Editing a group definition

Selecting named groups

Deleting a group definition

Searching for information in a table

Viewing subsets of a table

Viewing named groups

Viewing search results

Sorting table information

Graphing table information

Exporting table information

12. Working with Isosurfaces

Analyzing 3D grid properties

Mapping a property onto a surface

Editing and displaying slices

13. Scripts and Licensing

Command logging and scripting

Recording commands

Command tracing

Controlling Cerius2 from scripts

Playing back scripts and log files

Starting Cerius2 with a command script file

Managing licenses

Running application modules externally

14. Customizing the Interface

Interface configuration

Deck of cards menu configuration

Control panel management

Interface look and feel

Interface colors

Miscellaneous environment customizations

A. References

B. Definitions

Models, fragments, and templates

Glossary

C. Mouse and Keyboard Actions

Mouse actions

Control panels

Any control

File browser

Model table

Graph window

Model window

Table window

Cursor over individual cell

Cursor over row or column heading

Keyboard shortcuts

Graph window

Model window

Table window

D. File Formats

Structure files

MSI

MSF

BGF

CAMBRIDGE (read only)

CIF (read only)

CSSR

ICSD (read only)

MACCS/Molfile

MolEN

MOPAC

PDB

SHELX

Loading and saving temperature factors in structure files

.Grf

Header record

Comments

Object definition blocks

X-Y data set ODB

2D data set ODB

X-Y plotting attribute ODB

2D plotting attribute ODB

X-Y graph ODB

2D graph ODB

Gallery ODB

Termination record

.Xy and .con files

File documentation at our website