Cerius2 Modeling Environment

B       Definitions

Models, fragments, and templates

It is easy to get the terms fragment, model, template, and molecule confused. We have tried to be consistent in this documentation.

Definitions

• A fragment is a set of covalently bonded atoms.

• A model is the entire contents of a Cerius² model space. The visible part(s) of a model may include:

A single atom.

One fragment, for example, a model of caffeine.

Several fragments that interact by noncovalent bonds or that do not interact, for example, a large solute fragment and many small solvent fragments.

A protein consisting of many residues and one or more subunits.

A receptor-ligand complex.

A 1D periodic structure such as polyethylene or DNA.

A 2D periodic structure such as a regular surface.

A 3D periodic structure such as a crystal.

• A template is a model or fragment that is used in building models.

• Strictly speaking, molecules exist only in the real world, not in the simulated world of computational chemical modeling.

word	meaning	additional information
ambient light	Light impinging on a scene from all directions.	Concepts
balloon help	Small explanatory text boxes displayed when the cursor lingers over a control.	Balloon help
bitmap resolution	Number of dots per inch (used in printing graphs).	Bitmap resolution for printing graphs
bond type	Associated with the nature and number of shared electrons between atoms (e.g., single, double, partial bond types).	Changing the bond type
charge	The overall partial charge on an atom.	--
cleaning a model	Optimizing the model conformation.	Refining the conformation
color map	Defined correlation of properties with a color range.	Editing a property color map
color range	Defined sets of colors.	Creating and editing a new color range
command script	A file of Cerius2 commands that can be used to control future Cerius2 sessions.	Recording commands
data set	A set of related points in a graph, for example, all the points belong to one curve.	Selecting data to plot
data type	Real numbers, Booleans, text, etc., in a table.	Assigning data types
depth cueing	Representation of aerial perspective.	Apparent depth effects
derivation	Mathematical expression in table cells.	Applying mathematical expressions to cells or columns
diffuse lighe	Light scattered from an object in all directions.	Concepts
display style	Display of atoms and/or bonds as sticks, balls, etc.	Ball and stick models
dummy atoms	Nonstandard "elements" with defined properties.	Dummy atoms
enter	Type some characters, then press <Enter> or click anywhere else in the control panel.	Type a C in the sketch...
formal charge	The difference between the number of electrons possessed by the neutral isolated atom and that formally possessed by the atom within the molecule, assuming that electrons in covalent bonds are shared equally between participating atoms and that no sharing of core and lone pair electrons occurs.	--
fractional bond order	A quantitative measure of the order of a bond, which may, for example, be related to overlap integrals in the molecular-orbital description of the system.	--
gallery	The graph window.	Displaying and editing graphs
graphics quality	Related to the color interpolation between facets used to draw curved surfaces.	Graphics quality
graphics resolution	Related to the number of facets used to draw curved surfaces.	Object resolution
group	A named set of atoms.	Defining and selecting groups
group	A named set of table cells.	Grouping table information
initialization script	A command script that is run automatically when Cerius2 is started.	Starting Cerius2 with an automatic script
mixture elements	Special "elements" whose properties are definable as proportional mixtures of those of real elements.	"Mixture" elements
model manager	Set of tools in the main control panel for managing models and model spaces.	Using the main control panel
model space	A virtual "space" in the model manager environment that may or may not contain a model.	Creating, clearing, and deleting model spaces
pen colors	Individually defined drawing colors.	Creating and editing a new color range
projection	Representation of linear perspective.	Superimposing models
rendering	The production of high-quality 3D images.	Rendering and ray-tracing
residue ID	Alphanumeric representation of the location of a residue within a sequence.	--
residue type	Standard chemical name for an amino acid residue.	--
session	Lasts from when you start or reinitialize Cerius2 until you quit or reinitialize Cerius2.	Working with Cerius2 sessions
specular light	Highlights reflected from an object.	Concepts
temperature factors	Used to describe the effect of thermal vibration on crystal structures.	Temperature factors
thermal ellipsoids	Used to represent the thermal motion of atoms.	Thermal ellipsoids
value	The information actually displayed in a table cell.	Applying mathematical expressions to cells or columns
Visualizer	The core components and main control panel of Cerius2.	The Cerius2 Interface