Energy in hartrees	See Properties menu, energy in hartrees)
Energy in kcal/mol	See Properties menu, energy in kcal/mol)
Energy in kJ/mol	See Properties menu, energy in kJ/mol)
Excited states, semi-empirical models	See CI,CIS,CID keywords)
Expert	See Help menu (spreadsheet), expert)

Expert modes, access to

3.4

Export

See File menu, export); See Sheet menu, export)

Export dialog

4.10

External	See Setup menu, external
External menu		8.6
	Gaussian	8.6.1
Extract As	See Molecule menu (spreadsheet), extract as

-- F --

FDAT (Crystal) files, import of		4.9
File browser		4.0

File menu
	close	4.3
	delete	4.8
	export	4.10
	group as	4.7
	import	4.9
	merge as	4.6
	new	4.1
	open	4.2
	print	4.11
	quit
		4.12 7.1.7.2 7.2.2.2 7.3.2.2 7.4.2.2 7.5.2.2 7.6.2.2
	save
		4.4 7.1.7.2 7.2.2.2 7.3.2.2 7.4.2.2 7.5.2.2 7.6.2.2
	save as
		4.5 7.1.7.2 7.2.2.2 7.3.2.2 7.4.2.2 7.5.2.2 7.6.2.2
File menu (monitor)		3.5.1.2
	quit	3.5.1.2
File system
	close SPARTAN files	4.3
	delete SPARTAN files	4.8
	export MACROMODEL files	4.10
	export PDB files	4.10
	export SYBYL MOL and MOL2 files	4.10
	export VRML files	4.10
	group SPARTAN files	4.7
	import SPARTAN files	4.9
	import SPARTAN Exchange files	4.9
	import SPARTAN Collection files	4.9
	import MACROMODEL files	4.9
	import PDB files	4.9
	import Crystal FDAT files	4.9
	import SYBYL MOL and MOL2 files	4.9
	merge SPARTAN files	4.6
	open SPARTAN files	4.2
	save SPARTAN files	4.4
Filters	See View menu (monitors), filters

Folding, in peptide builder		7.1.3
Freeze Center	See Geometry menu, freeze center

Freeze center dialog

6.4

Frequency calculations	See Vibrational frequencies
Frozen-core applications	See MP2 keyword

-- G --
Gaussian 94	See External menu, Gaussian 94
Gaussian 94
	access to via SPARTAN	8.6.1
	availability	8.6.1
	capabilities	8.6.1
	limitations of SPARTAN's interface	8.6.1

Gaussian 94 dialog

8.6.1

Generate

See Edit menu, (transition search) generate

Generate dialog

7.3.2

Generate Monosubstituted

See Edit menu, (combinatorial study) generate monosubstituted

Generate Polysubstituted

See Edit menu, (combinatorial study) generate polysubstituted

Generating transition state guess	See Transition search dialog, generating transition state guess
Geometry, constraining
	angle; SeeGeometry menu, constrain angle
	dihedral angle; SeeGeometry menu, constrain dihedral
	distance; SeeGeometry menu, constrain distance
Geometry, measurement of
	angle	6.2
	angle with plane	6.2
	dihedral angle	6.3
	distance	6.1
	distance to plane	6.1
Geometry menu	angle	6.2 7.1.7.5 7.2.2.4 7.3.2.4 7.4.2.4 7.5.2.4 7.6.2.4
	constraint angle	6.6 7.1.7.5
	constraint dihedral	6.7 7.1.7.5
	constraint distance	6.5 7.1.7.5
	define ligand point	7.1.7.5
	define plane
		6.9 7.1.7.5 7.2.2.4 7.3.2.4 7.4.2.4 7.5.2.4 7.6.2.4
	define point
		6.8 7.1.7.5 7.2.2.4 7.3.2.4 7.4.2.4 7.5.2.4 7.6.2.4
	dihedral
		6.3 7.1.7.5 7.2.2.4 7.3.2.4 7.4.2.4 7.5.2.4 7.6.2.4
	distance
		6.1 7.1.7.5 7.2.2.4 7.3.2.4 7.4.2.4 7.5.2.4 7.6.2.4
	freeze center	6.4 7.1.7.5
	report chirality	6.13
	report symmetry
		6.12 7.1.7.5 7.2.2.4 7.3.2.4 7.4.2.4 7.5.2.4 7.6.2.4
	surface area	6.10
	volume	6.11
	Geometry optimization
		changing convergence requirements; SeeConvergence difficulties
constrained optimization
		8.2 8.3 8.4 8.5
increasing number of cycles; SeeOPTCYCLE keyword
restart with Hessian
		8.2 8.3 8.4
Geometry, setting of
	angle; SeeGeometry menu (builders), angle
	dihedral angle; SeeGeometry menu (builders), dihedral
	distance; SeeGeometry menu (builders), distance

Global rotate		3.3
Graphics Options	See Help menu, graphics options
Group As	See File menu, group as

-- H --

Hardware, machines supported

1.4

Helix, in nucleotide builder

7.1.4

Help files associated with SPARTAN
Help menu
	ab initio options	10.3
	available elements	10.10
	conformer options	10.9
	density functional options	10.4
	graphics options	10.8
	keystroke equivalents	10.2
	mechanics options	10.6
	properties options	10.7
	semi-empirical options	10.5
	use of the mouse	10.1
Help menu (monitor)		3.5.1.5
	monitor overview	3.5.1.5
Edit menu (spreadsheet)		11.2.5
	column	11.2.5
	expert	11.2.5
	molecule	11.2.5
	plot	11.2.5
	sheet	11.2.5
	spreadsheet overview	11.2.5
Hide	See Model menu, hide
Hydrogens	See Model menu, hydrogens

-- I --

Iconifying SPARTAN

2.9

Import	See File menu, import
Infrared intensities	See INTENSITY keyword
in hartrees	See Add Energy menu (spreadsheet), in hartrees; See Add Rel. Energy menu (spreadsheet), in hartrees
in kcal/mol	See Add Energy menu (spreadsheet), in kcal/mol; See Add Rel. Energy menu (spreadsheet), in kcal/mol
in kJ/mol	See Add Energy menu (spreadsheet), in kJ/mol; See Add Rel. Energy menu (spreadsheet), in kJ/mol
Inorganic molecules, building	See Molecule builders in SPARTAN, expert
Insert	See Molecule menu (spreadsheet), insert
Intensities	See INTENSITY keyword

Intermolecular reations, transition states for

7.3.3

Isosurfaces

See Display menu, isosurfaces

Isosurfaces dialog

9.5.1

Isosurfaces menu		9.5
	create	9.5.1
	delete	9.5.3
	edit	9.5.2
Isotopes	See Build menu, isotopes

-- K --
Keyboard functions		2.5
Keyboard equivalents		2.5
Keystroke Equivalents	See Help menu, keystroke equivalents
Kill	See Actions menu (monitor), kill
Killing SPARTAN jobs	See Actions menu (monitor), kill, kill now!!
Kill Now!!	See Actions menu (monitor), kill now!!

-- L --
Labels	See Model menu, labels
Library		7.1.5
Library dialog		7.1.5
Linear synchronous transition method	See transition states, linear synchronous transit method
Lists	See Setup menu, lists

Lists dialog

8.1

Logo menu
	about SPARTAN
		3.1 7.1.7.1 7.2.2.1 7.3.2.1 7.4.2.1 7.5.2.1 7.6.2.1
	calculator	3.7
	colors
		3.2 7.1.7.1 7.2.2.1 7.3.2.1 7.4.2.1 7.5.2.1
	monitor	3.5
	preferences
		3.3 7.1.7.1 7.2.2.1 7.3.2.1 7.4.2.1 7.5.2.1
	Periodic Table	3.6
	print setup	3.4
Logo menu (monitor)		3.5.1.1
	about monitor	3.5.1
	preferences	3.5.1.1
LogP, available models		8.7

-- M --
MACROMODEL files
	export Seefile system, export MACROMODEL files
	import Seefile system, import MACROMODEL files

Mechanics

See Setup menu, mechanics

Mechanics dialog		8.5
Mechanics methods
	MMFF	1.3.4
	range of application	1.3.4
	SYBYL	1.3.4

Mechanics module

See SPARTAN, mechanics module

Mechanics Options	See Help menu, mechanics options
Memory requirements
	ab initio calculations	1.3.1
	density functional calculations	1.3.2
	semi-empirical calculations	1.3.3

Merck molecular force field

See mechanics methods, MMFF

Merge As

See File menu, merge as

Minimize

See Edit menu (builders), minimize

Minimize dialog

7.0

MMFF

See See mechanics methods, MMFF

MNDO

See semi-empirical methods, available models

MNDO/d

See semi-empirical methods, available models

MNDOaq

See solvation methods, available models

MNDOhd	See solvation methods, available models
Model menu		5.2 7.1.7.4 7.4.2.3
	annotate	5.9.5
	ball and spoke	5.4 7.4.2.3
	ball and wire	5.2 7.1.7.4 7.4.2.3
	box	5.10
	edit labels	5.9
	hide	5.6
	hydrogens	5.7
	labels	5.8 7.1.7.4 7.4.2.3
	polyhedra	5.5.5
	space filling	5.5 7.4.2.3
	tube	5.3 7.4.2.3
	wire	5.1 7.1.7.4 7.4.2.3

MOL files

See SYBYL MOL files

MOL2 files

See SYBYL MOL2 files

Molecular complexes, forming from separate molecules

See File menu, merge as

Molecular mechanics	See mechanics methods
Molecular models
	ball and spoke	5.4
	ball and wire	5.2
	CPK	5.4
	editing labels	5.9
	hiding	5.6
	hiding hydrogens	5.6
	orthogonal projections	5.0
	perspective projections	5.0
	rotation of	2.4
	scaling	2.4
	showing labels	5.8
	simultaneous manipulations of two or more models	2.4
	space filling	5.5
	translation of	2.4
	tube	5.3
	tumbling	3.3
	wire	5.1

Molecule	See Help menu (spreadsheet), molecule
Molecule builders in SPARTAN
	add	7.1
	bond	7.1
	break	7.1
	build sequence	7.1.3 7.1.4
	clear	7.1
	delete	7.1
	entry	7.1.1
	expert	7.1.2
	going between builders	7.1.2
	groups	7.1
	ligands	7.1.2
	minimize	7.1
	move	7.1
	new	7.1
	nucleotide	7.1.4
	peptide	7.1.3
	rings	7.1
	terminate	7.1.3 7.1.4
Molecule centered rotation		3.3

Molecule menu (spreadsheet)
	align coordinates	11.2.2
	couple coordinates	11.2.2
	decouple coordinates	11.2.2
	delete	11.2.2
	delete to end	11.2.2
	extract as	11.2.2
	insert	11.2.2
Molecule selection		2.6
Molecule tumbling		3.3
Molecular Weight	See Properties menu, molecular weight; See Add menu (spreadsheet), molecular weight ;
Molecular weight dialog		9.2.6
Moment of inertia	See MOMENTS keyword;
Monitor		3.5
Monitor dialog		3.5.1
Monitor Overview	See Help menu (monitor), monitor overview;
Mouse, use of		2.4
Move	See Edit menu (builders), move;
Mulliken population analysis	See Population analyses, Mulliken;
MULTIMOL2	See SYBYL MULTIMOL2;

-- N --
NBO	See Population analyses, natural bond orbital;
New	See Edit menu (builders), new ; See File menu (builders), new ;
Normal modes of vibration	See Vibrational frequencies;
Nucleotides, building	See Molecule builders in SPARTAN, nucleotide;

-- O --
Open	See File menu, open
Open dialog		4.2
Organometallic molecules, building	See Molecule builders in SPARTAN, expert
Organic molecules, building	See Molecule builders in SPARTAN, entry
Orthogonal projections		3.3
Osawa conformational searching algorithm	See Conformer searching, Osawa method
Output	See Display menu, output
Output dialog		9.1
Overview	See Help menu (spreadsheet), overview

-- P --

Page layout dialog

3.4

Paste

See Column menu (spreadsheet), paste

PDB files

export, See file system, export PDB files; import, See file system, import PDB files;

Peptides, building

See Molecule builders in SPARTAN, peptide

Periodic Table	See Logo menu, Periodic Table
Periodic Table dialog		3.6

Perspective projections		3.3
Perspective projections		11.2.4
Plot	See Help menu (spreadsheet), plot

Plot dialog		11.2.4
Plot menu (spreadsheet)		11.2.4
	edit	11.2.4
	delete	11.2.4

PM3

See Semi-empirical methods, available models

PM3aq

See solvation models, available models

PM3hd

See solvation models, available models

PM3 (tm)

See Semi-empirical methods, available models

Point group	See symmetry point group
polyhedra	See Model menu, polyhedra
Population analyses
	Mulliken	8.7
	natural bond orbital	8.7

Preferences

See Logo menu, preferences See Logo menu (monitor), preferences

Preferences dialog

3.3

Print

See File menu, print See Sheet menu (spreadsheet), print

Printer parameters dialog

3.4

Printer setup dialog		3.4
Printing, of
	molecular orbitals	8.7
	on-screen graphics; SeeFile menu, print orbital energies
	spreadsheet; SeeSheet menu, (spreadsheet), print

SeePopulation analyses

Properties	See Display menu, properties See Setup menu, properties
Properties
	charges; SeeAtomic charges
	dipole moment; SeeDipole moments
	from 2D slices; SeeProperties menu, surfaces
	from surface displays; SeeProperties menu, surfaces
	hybrid orbital analyses	8.7
	population analyses

Properties dialog

8.7

Properties menu
	charges		9.2.7
	dipole		9.2.4
	E(HOMO/LUMO)		9.2.5
	energy in hartees		9.2.1
	energy in kcal/mol		9.2.2
	energy in kJ/mol		9.2.3
	molecular weight		9.2.6
	surfaces		9.2.8

Properties module	See SPARTAN, properties module
Properties Options	See Help menu, properties options

-- Q --
Quit	See File menu, quit See File menu (monitor) quit

-- R --
Redo	See Edit menu (builders), redo
Remove Pair	See Edit menu (transition search), remove pair
Report Symmetry	See Geometry menu, report symmetry
Report symmetry dialog		6.12
Rotation about single bonds	See Bond rotation

-- S --

Save

See File menu, save

Save As

See File menu, save as

Scaling, of molecular models or graphical displays		2.4
SCF
	changing convergence requirements; SeeConvergence difficulties
	increasing number of cycles; SeeMAXCYCLE keyword
	restart with potential	8.3
	restart using wavefunction	8.2 8.4

Screen centered rotation

3.3

Semi-Empirical

See Setup menu, semi-empirical

Semi-empirical methods
	available elements	8.4
	See also Logo menu, Periodic Table
	available mode