ICM Manual v.3.6 by Ruben Abagyan
Copyright © 2008, Molsoft LLC
Sep 1 2010

Contents


Introduction
Reference Guide
User's Guide
References
Glossary

Index

Index

&, 2.11.3	Cell, 2.28.24
2D labels, 2.27.53.1	Charge, 2.28.25
to 3D, 3.13.2.3	Chemical, 2.28.26
chemical builder, 1.4.2.8	Cluster, 2.28.27
font size, 2.27.23.12	Collada, 5.5.3
label, 2.27.23.12, 2.27.81.32	Collection, 2.28.27.1
labels, 2.27.53.1	Color, 2.28.28
mol file, 2.29.83	from gradient, 2.28.28.1
plots intro, 1.4.3.7	image, 2.28.28.2
smoothing, 2.28.134.2	Connolly surface, 5.9.7
superposition, 2.29.22	Consensus, 2.28.29
transformations, 2.27.94.2	Corr, 2.28.30
3dxml, 5.5.3	Cos, 2.28.31
=, 2.11.1	Cosh, 2.28.32
A, 5.1	Count, 2.28.33
Abs, 2.28.1	CubicRoot, 2.28.34
Acc, 2.28.2	D, 5.4
Acos, 2.28.3	DAE, 5.5.3
Acosh, 2.28.4	DE, 2.27.34.2
Adobe, 2.18.23	DNA Representation, 1.4.1.3
Align, 2.28.5	alignment, 2.27.3.3
sequence, 2.28.5.1	melting temperature, 2.28.150
Angle, 2.28.6	views, 1.4.1.3
Area, 2.28.7	Date, 2.28.35
residue contacts, 2.28.7.1	Deletion, 2.28.36
Asin, 2.28.8	Disgeo, 2.28.37
Asinh, 2.28.9	Distance, 2.28.38
Ask, 2.28.10	2 alignments, 2.28.38.11
Askg, 2.28.11	matrices, 2.28.38.7
Atan, 2.28.12	Dayhoff, 2.28.38.9
Atan2, 2.28.13	Tanimoto, 2.28.38.6
Atanh, 2.28.14	alignment, 2.28.38.10
Atom, 2.28.15	as_, 2.28.38.3
Augment, 2.28.16	rarray, 2.28.38.4
Axis, 2.28.17	atoms, 2.28.38.3
B, 5.2	chemical, 2.28.38.6, 2.28.38.13
BPMC, 5.2.5	dayhoff, 2.28.38.9
Bfactor, 2.28.18	iarray, 2.28.38.1
Boltzmann, 2.28.19	alignment, 2.28.38.10
Box, 2.28.20	matrix, 2.28.38.5, 2.28.38.7
Bracket, 2.28.21	multiple atomic, 2.28.38.4
C, 5.3	rarray, 2.28.38.2
CCP4, 5.7.6	tether, 2.28.38.8
CONSENSUS, 2.21.1	tree, 2.28.38.12
CONSENSUSCOLOR, 2.21.2	cluster, 2.28.38.12
CONSENSUS_strength, 2.16.9	H, 5.5
Cad, 2.28.22, 2.28.22.1, 2.28.22.2	EDS server, 2.29.42
Cad1, 2.28.22.1	EST-alignment, 2.27.3.3
Cadalign, 2.28.22.2	Eigen, 2.28.39
Ceil, 2.28.23	Energy, 2.28.40

soap, 2.28.42	hydrogenDisplay, 2.21.5.26
Exist, 2.28.43	light, 2.21.5.27
molcart, 2.28.43.1	lightPosition, 2.21.5.28
Existenv, 2.28.44	mapLineWidth, 2.21.5.29
Exp, 2.28.46	occupancyDisplay, 2.21.5.30
Extension, 2.28.45	occupancyRadiusRatio, 2.21.5.31
FILTER, 2.21.3	quality, 2.21.5.32, 2.28.80.1
Z, 2.21.3.1	rainbowBarStyle, 2.21.5.33
gz, 2.21.3.2	resLabelDrag, 2.21.5.34
uue, 2.21.3.3	resLabelShift, 2.21.5.35
FTP, 2.21.4	ribbonRatio, 2.21.5.36
createFile, 2.21.4.1	ribbonWidth, 2.21.5.37
keepFile, 2.21.4.2	ribbonWorm, 2.21.5.38
proxy, 2.21.4.3	rocking, 2.21.5.39
Field, 2.28.47, 2.28.47.1	rockingRange, 2.21.5.40
user, 2.28.47.1	rockingSpeed, 2.21.5.41
File, 2.28.48	selectionLevel, 2.21.5.42
Find, 2.28.49	selectionStyle, 2.21.5.43
chemical, 2.28.49.3	sketchAccents, 2.21.5.24
pattern, 2.28.49.3	stereoMode, 2.21.5.44
in array, 2.28.49.1	stickRadius, 2.21.5.25, 2.21.5.45
table, 2.28.49.2	surfaceDotDensity, 2.21.5.47
FlexLM license info, 2.28.173	surfaceDotSize, 2.21.5.46
Floor, 2.28.50	surfaceProbeRadius, 2.21.5.48
Formula, 2.28.51	transparency, 2.21.5.49
GRAPHICS, 2.21.5	wormRadius, 2.21.5.50
atomLabelShift, 2.21.5.1	GRID, 2.21.6
atomValueCircles, 2.21.5.2	gcghExteriorPenalty, 2.21.6.1
ballRadius, 2.21.5.3, 2.21.5.25	gpGaussianRadius, 2.21.6.6
ballStickRatio, 2.21.5.4	margin, 2.21.6.2
chainBreakLabelDisplay, 2.21.5.7	maxEl, 2.21.6.3
chainBreakStyle, 2.21.5.6	maxVw, 2.21.6.5
clashWidth, 2.21.5.5	minEl, 2.21.6.4
displayLineLabels, 2.21.5.8	GROB, 2.21.7
displayMapBox, 2.21.5.9	arrowRadius, 2.21.7.3
dnaBallRadius, 2.21.5.10	atomSphereRadius, 2.21.7.1
dnaRibbonRatio, 2.21.5.11	contourSigmaIncrement, 2.21.7.5
dnaRibbonWidth, 2.21.5.12	relArrowHead, 2.21.7.4
dnaRibbonWorm, 2.21.5.13	relArrowSize, 2.21.7.2
dnaStickRadius, 2.21.5.14	GUI, 2.21.8
formalChargeDisplay, 2.21.5.15	dialog customize programming, 2.26
grobLineWidth, 2.21.5.16	plot, 2.27.59.31
hbondAngleSharpness, 2.21.5.20	tableRowMarkColors, 2.21.8.4
hbondBallPeriod, 2.21.5.21	windowLayout, 2.21.8.5
hbondBallStyle, 2.21.5.22	workspaceFolderStyle, 2.21.8.8
hbondMinStrength, 2.21.5.19	workspaceStyle, 2.21.8.6
hbondRebuild, 2.21.5.18	workspaceTabStyle, 2.21.8.7
hbondStyle, 2.21.5.17	Getarg, 2.28.52
hbondWidth, 2.21.5.23	Getenv, 2.28.53
hetatmZoom, 2.21.5.25	Gradient, 2.28.54

Grob, 2.28.55	Index, 2.28.62
Group, 2.28.56	chemical, 2.28.62.1
HTTP.proxy, 2.21.4.4	element in array, 2.28.62.7
Hartree-Fock, 2.27.76.20, 2.27.102.17	regexp, 2.28.62.3
Header, 2.28.57	string, 2.28.62.2
Histogram, 2.28.58	table label, 2.28.62.5
N, 5.7	selection, 2.28.62.4
ICM desktop, 2.21.8.5	tree, 2.28.62.8
documents, 2.27.76.3	unique elements, 2.28.62.6
modules, 1.4.4	Indexx, 2.28.63
object, 2.29.13	Info, 2.28.65
residue library, 2.18.24	image, 2.28.66
ICM-shell, 3.1, 5.9.5	Insertion, 2.28.64
intro, 1.7.1	Integer, 2.28.67
script, 2.27.8	Integral, 2.28.68
ICMHOME, 3.1.2.1	Interrupt, 2.28.69
shell variable, 3.1.2.1	Introduction, 1
IMAGE, 2.21.9	LIBRARY, 2.21.10
bondLength2D, 2.21.9.15	men, 2.21.10.1
color, 2.21.9.8	res, 2.21.10.2
compress, 2.21.9.9	Label, 2.28.70
gammaCorrection, 2.21.9.7	Latent, 2.28.172.3
generateAlpha, 2.21.9.10	LatentVector, 2.28.172.3
lineWidth, 2.21.9.3	Length, 2.28.71
lineWidth2D, 2.21.9.14	LinearFit, 2.28.72
orientation, 2.21.9.16	LinearModel, 2.28.73
paperSize, 2.21.9.17	Log, 2.28.74
previewResolution, 2.21.9.13	LogP, 2.28.102
previewer, 2.21.9.12	LogS, 2.28.102
printerDPI, 2.21.9.2	M_out, 2.22.5
quality, 2.21.9.1	Map, 2.28.75
rgb2bw, 2.21.9.18	Markush structures, 2.27.50
scale, 2.21.9.4	Mass, 2.28.76
stereoAngle, 2.21.9.6	Match, 2.28.78
stereoBase, 2.21.9.5	Mathews, 2.28.124.2
stereoText, 2.21.9.11	Matrix, 2.28.79
writeScale, 2.21.9.19	alignment, 2.28.79.8
I_out, 2.22.4	boundary, 2.28.79.9
Iarray, 2.28.59, 2.28.59.4, 2.28.59.5	grob connectivity, 2.28.79.12
atom numbers, 2.28.59.4	histogram, 2.28.79.11
bits to integers, 2.28.59.3	new, 2.28.79.1
inverse, 2.28.59.2	residue areas, 2.28.79.7
residue numbers, 2.28.59.5	comparison, 2.28.79.4
reverse, 2.28.59.2	stack, 2.28.79.10
stack, 2.28.59.6	sub, 2.28.79.2
Icm Options, 2.1	symmetrical, 2.28.79.3
IcmSequence, 2.28.60	table, 2.28.79.5
Image, 2.28.61	tensor, 2.28.79.6
collection, 3.9.2.1	Max, 2.28.80
frame by frame, 3.9.2.2	image graphic, 2.28.80.1

Mean, 2.28.82	lineWidth, 2.21.12.3
Method, 2.19.12	logo, 2.21.12.6
Min, 2.28.83	markSize, 2.21.12.4
Mod, 2.28.85	numberOffset, 2.21.12.1
Mol, 2.28.86	orientation, 2.21.12.8
MolPSA, 5.8.12	rainbowStyle, 2.21.12.12
Moment, 2.28.77	seriesLabels, 2.21.12.9
of Inertia, 2.28.77	PLS, 2.28.90.6
Money, 2.28.84	error, 2.28.124.2
NOE averaging, 2.19.5	models, 2.28.124.2
Name, 2.28.87	Parray, 2.28.97
chemical, 2.28.87.6	Parray-object, 2.28.97
property, 2.28.87.1	Path, 2.28.96
close sequence, 2.28.87.3	Pattern, 2.28.98
image, 2.28.87.9	Pi, 2.28.99
molcart, 2.28.87.10	Polar Surface Area, 5.8.12
object parray, 2.28.87.8	Potential, 2.28.100
sequence, 2.28.87.7	Power, 2.28.101
soap, 2.28.87.2	Predict, 2.28.102
string, 2.28.87.4	Probability, 2.28.103
tree, 2.28.87.5	Profile, 2.28.104
Namex, 2.28.88	Property, 2.28.105
image, 2.28.88.2	Putarg, 2.28.106
sequence, 2.28.88.1	Putenv, 2.28.107
Newick tree format, 2.28.142.3	R-groups, 2.27.50
Next, 2.28.89, 2.28.89.1	REBEL, 3.7.2
covalent neighbors, 2.28.89.1	faq, 3.7.2
Nof, 2.28.90	file, 2.27.50
chemical, 2.28.90.2	R_2out, 2.22.7
distance, 2.28.90.3	R_out, 2.22.6
latent, 2.28.90.6	Radius, 2.28.108
library, 2.28.90.4	Random, 2.28.109
molcart, 2.28.90.5	string, 2.28.109.1
soap, 2.28.90.7	Rarray, 2.28.110
tree, 2.28.90.1	reverse, 2.28.110.2
Norm, 2.28.91	sequence projection, 2.28.110.1
Normalize, 2.28.92	alignment projection, 2.28.110.3
NotInList, 2.28.93	strength, 2.28.110.5
R, 5.8	property assignment, 2.28.110.4
OBJECT, 2.21.11	RarrayAlignment, 2.28.110.5
Obj, 2.28.94	Rarrayinverse, 2.28.110.2
Occupancy, 2.28.95	Real, 2.28.111
PBS, 3.13.3.6	array, 2.28.110
PLOT, 2.21.12	Reference, 2.28.113
Yratio, 2.21.12.5	Guide, 2
box, 2.21.12.13	Remainder, 2.28.112
color, 2.21.12.7	Replace, 2.28.114
font, 2.21.12.10	chemical, 2.28.114.4
fontSize, 2.21.12.2	exact, 2.28.114.1
labelFont, 2.21.12.11	regexp, 2.28.114.3

Res, 2.28.115, 2.28.116	array, 2.28.126.2
Resali, 2.28.116	Sequence(dna reverse), 2.28.126.1
Resolution, 2.28.117	Shuffle, 2.28.127
Rfactor, 2.28.119	Sign, 2.28.128
Rfree, 2.28.120	Simulations, 1.4.2
Ring, 2.28.118	Sin, 2.28.129
Rmsd, 2.28.121	Sinh, 2.28.130
of subset, 2.21.14	Site, 2.28.131
Rot, 2.28.122	Slide, 2.28.132
S, 5.9	Smiles, 2.28.133
SAR analysis, 2.27.59.27, 2.27.84.2	Smooth, 2.15.23, 2.28.134, 2.28.134.1, 2.28.134.2
SC, 2.27.34.2	Smoothrs, 2.28.134.2
SITE, 2.21.13	SoapMessage, 2.28.138
defSelect, 2.21.13.2	Sort, 2.28.139
labelOffset, 2.21.13.3	Sphere, 2.21.14.2, 2.28.137
labelStyle, 2.21.13.4	Split, 2.28.140
labelWrap, 2.21.13.5	chemical, 2.28.140.4
showSeqSkip, 2.21.13.6	multisep, 2.28.140.3
wrapComment, 2.21.13.7	regexp, 2.28.140.2
SLN notation, 2.28.142.9	tree, 2.28.140.1
SMARTS, 2.24, 2.27.10, 2.28.90.2	Sql, 2.28.135
SOAP, 2.28.87.2, 2.28.90.7, 2.28.167.1	Sqrt, 2.28.136
request message, 2.28.138	Srmsd, 2.28.141
SSSR, 2.28.118	Sstructure, 2.28.143
S_out, 2.22.8	String, 2.28.142, 2.28.142.7
Sarray, 2.28.123	alternative, 2.28.142.6
index, 2.28.123.1	mol, 2.28.142.2
Score, 2.28.124	selection, 2.28.142.7
alignment, 2.28.124.6	slide gui, 2.28.142.8
conservation, 2.28.124.5	substring, 2.28.142.1
model, 2.28.124.2	chemical formula, 2.28.142.9
overlap, 2.28.124.1	Sum, 2.28.144
predictions, 2.28.124.3	chemical, 2.28.144.1
sequence, 2.28.124.4	image, 2.28.144.2
Select, 2.28.125	Swissprot, 2.27.102.23
break, 2.28.125.1	Symgroup, 2.28.145
atom property, 2.28.125.7	T, 5.10
nmembers, 2.28.125.4	TOOLS, 2.21.14
string, 2.28.125.9	edsDir, 2.21.14.1
expand, 2.28.125.6	minSphereCubeSize, 2.21.14.2
fix, 2.28.125.2	pdbReadNmrModels, 2.21.14.3
graphical, 2.28.125.5	superimposeMaxDeviation, 2.21.14.6
neighbors, 2.28.125.3	superimposeMaxIterations, 2.21.14.4
Select_by atom numbers, 2.28.125.10	superimposeMinAtomFraction, 2.21.14.5
Select_by_sequence, 2.28.125.13	tsWeight, 2.21.14.7
Select_by_text, 2.28.125.9	Table, 2.28.146
Select_lists, 2.28.125.12	alignment numbers, 2.28.146.3
Select_patching, 2.28.125.11	distance, 2.28.146.9
Select_projection, 2.28.125.8	matrix, 2.28.146.4
Sequence, 2.28.126	model, 2.28.146.7

stack, 2.28.146.6	axes, 2.28.177.7
url_decoder, 2.28.146.1	chemical match, 2.28.177.5
Table(alignment), 2.28.146.2	fract, 2.28.177.3
Table(stack), 2.28.146.6	mesh, 2.28.177.2
Tan, 2.28.147	points, 2.28.177.1
Tanh, 2.28.148	transformed xyz, 2.28.177.4
Tanimoto, 2.28.59.3	vector2matrix, 2.28.177.6
distance, 2.27.59.35	ZEGA, 5.11.9
matrix, 2.28.38.6	intro, 1.4.3.6
Temperature, 2.28.150	_NAME, 2.27.81.40
Tensor, 2.28.149	_chemBatch, 3.1.2.5
Time, 2.28.151	_confGen, 3.13.2.3
Tointeger, 2.28.152	_dockScan, 3.13.2.7
Tolower, 2.28.153	_macro, 2.30.1
Toreal, 2.28.154	file, 2.30.1
Torsion, 2.28.155	_startup, 3.1.2.3
Tostring, 2.28.156	file, 2.30.2
Toupper, 2.28.157	icm, 2.30.2
Tr123, 2.28.158	a_, 2.8.1
Tr321, 2.28.159	abbr, 1.6
Trace, 2.28.160	abbreviations, 1.6
Trans, 2.28.161	absolute to cell x y z, 2.28.177.3
Transform, 2.28.162	accFunction, 2.22.2
Transpose, 2.28.163	acceptor, 3.6.1
Trim, 2.28.164	access large sdf file, 2.27.76.23
sequence, 2.28.165	accessMethod, 2.19.1
Turn, 2.28.166	accessible residues, 3.3.6
Type, 2.28.167	surface, 2.27.59.14, 5.9.15
molcart, 2.28.167.2	accessing sections, 2.27.102.23
soap, 2.28.167.1	accuracy, 2.28.124.2
Z, 5.11	activate fog, 2.27.23.24
Unique, 2.28.168	alignment, 2.27.81.33
Unix, 2.28.169	document, 2.27.81.33
Uppsala, 2.29.42	tab, 2.27.81.33
server, 2.29.43	table, 5.10.2.4
V_, 2.8.1	add, 2.27.1
Value, 2.28.170	column, 2.27.1.1
soap, 2.28.171	function, 2.27.1.1.1
Vector, 2.28.16, 2.28.172, 2.28.172.1, 2.28.172.3	matrix, 2.27.1.2
symmetry transformation, 2.28.172.2	slide, 2.27.1.3
Vectorproduct, 2.28.172.1	table, 2.27.1.4
Vectorsymmetrytransformation, 2.28.172.2	row, 2.27.1.4
Version, 2.28.173	addBfactor, 2.16.1
View, 2.28.175	adding atoms to non-ICM objects, 2.27.7.1
Volume, 2.28.174	columns to table, 2.27.1.1
WEBAUTOLINK, 2.21.16	hydrogens, 2.29.13
WEBLINK, 2.21.15	in place, 2.11.4
Warning, 2.28.176	to slideshow, 2.27.1.3
Wavefront format, 2.27.76.21	admet selection, 3.13.3.4
Xyz, 2.28.177	advanced chemical search, 3.6

ops, 2.11.6	alternative flag, 2.27.81.15
ali_seq_project, 2.28.142.4	amber, 5.1.4
alias, 2.27.2	amino acid, 2.18.24, 2.28.158, 2.28.159
align, 2.27.3	labels, 2.27.3.1
3D, 2.27.3.4	and, 2.11.3
faq, 3.3.2	angles, 2.28.90.3
heavy, 2.27.3.5	angular hbond dependence, 2.21.5.20
how to, 3.3.2	animated story, 5.9.14
chemical, 2.27.80.1	animation, 2.27.23.5, 2.27.23.6, 3.9
fragments, 2.27.3.3	annotation, 2.27.81.23
intro, 1.4.3.3	append, 5.1.5
number, 2.27.3.1	a tables, 2.27.1.4
res numbers, 2.27.3.1	column, 2.27.4.3
sequence, 2.27.3.2	command, 2.27.4
sequences, 2.27.3.2	sequence, 2.27.4.1
alignMethod, 2.19.2	to group, 2.27.4.1
alignMinCoverage, 2.16.2	stack, 2.27.4.2
alignMinMethod, 2.16.2	tables, 2.27.48
alignOldStatWeight, 2.16.3	by shared column, 2.27.4.3
alignSS, 2.29.1	appending, 2.27.1.1
alignTwoSequences, 2.29.2	an element, 2.11.4
aligned residues, 2.28.116	menu items, 2.21.10.1
alignment, 5.1.1	representations to a slide, 2.27.23.21
as table, 2.28.146.2	rows to matrix, 2.27.1.2
block length, 2.15.21	area under curve, 2.29.21
secondary structure, 2.29.1	arguments, 2.27.58
cleaning, 2.28.134.3	arithmetic operations, 2.11.2
color by property, 2.27.81.29	arithmetics, 2.11
coloring, 2.18.1	array, 2.27.65.4, 5.8.3.1
distance, 2.28.125.13	assignment, 2.11.1
editor, 2.4	derivative, 2.28.134.1
extraction, 2.28.5	overlap, 2.28.124.1
gap format, 5.1.1.1	parray, 2.27.22.29
intro, 1.4.3.4	size, 2.28.90
projection, 2.28.142, 2.28.142.4, 2.28.142.5	subset, 2.6
score, 2.28.124.5	arrow from selection, 2.29.36
sequence reordering, 2.28.5	length, 2.27.81.23
strength, 2.28.110.5	as2_out, 2.22.13
structural, 2.27.3.4, 2.28.5	as_, 2.8.8
to sequence transfer, 2.28.110.1	as_graph, 2.21.5.42, 2.21.5.43, 2.28.125.5
text conversion, 2.28.142.3	as_out, 2.22.12
weighted, 2.28.5	assign, 2.27.5
gapExtension, 2.16.15	ring conformation to template, 2.27.60.4
gapOpen, 2.16.16	sstructure, 2.27.5.1
alignment_as_text, 2.28.142.3	segment, 2.15.19, 2.27.5.2
aliphatic amines, 2.27.63.2	assignment, 2.11.1
all, 5.1.2	structure, 2.27.5.1
torsions table, 3.3.11	atom, 2.27.13.1, 5.1.6
alpha, 2.21.5.49, 2.27.81.35, 5.1.3	code file, 2.30.4
channel, 2.21.9.10	coordinates, 2.28.177.1

name, 2.28.70	box, 2.28.20
pairs, 2.27.81.58, 2.28.146.9	break, 2.27.6
proximity to surface, 2.27.82.8	brightness, 2.21.5.27
selection by number, 2.28.59.4	build, 2.27.7
type, 2.28.167	atom, 2.27.7.1
user field, 2.28.47.1	column, 2.27.7.2
atomLabelStyle, 2.19.3	faq, 3.8.1
atomSingleStyle, 2.19.4	from string, 2.27.7.7
atomic coordinate transfer, 2.27.81.2	helix, 3.10.5
solvation contributions, 2.28.7	how to, 3.8.1
alternative position, 2.27.81.15	hydrogen, 2.27.7.8
selecting, 2.8.8	loop, 2.27.7.5
translate, 2.27.81.2	model, 2.27.7.4, 2.27.102.9
attenuation by occupancy, 2.27.59.25	molcart, 2.27.7.9
auc enrichment, 2.29.21	sequence, 2.27.7.3
auto saving log, 2.19.10	smiles, 2.27.7.6
autoSavePeriod, 2.15.1	string, 2.27.7.7
avi, 2.27.102.30	built-in functions, 5.5.5
axis, 5.1.7	atoms, 2.27.14
axisLength, 2.16.4	contact surface, 2.27.14
background, 2.28.28.2	molecule, 2.27.13.1
ball, 5.2.2	number of bonds, 2.28.125.3
base, 5.2.1	variables, 2.27.14
basis set, 2.27.76.20, 2.27.102.17	calcArea, 2.29.3
batch chemical processing, 3.1.2.5	calcBindingEnergy, 2.29.4
docking, 3.13.2.7	calcDihedralAngle, 2.29.5
beta, 5.2.3	calcEnergyStrain, 2.29.20
bfactor circles, 2.21.5.2	calcEnsembleAver, 2.29.6
binary file table of contents, 2.27.76.2	calcMaps, 2.29.7
files, 2.27.102.2	calcPairSeqIdsFromAli, 2.29.8
key, 2.27.81.36	calcPepHelicity, 2.29.9
binding energy, 3.7.4	calcProtUnfoldingEnergy, 2.29.10
pocket finding, 3.4.2	calcRmsd, 2.29.11
pockets, 2.27.84.1	calcSeqContent, 2.29.12
site analysis, 3.4.2	calc_nosauc, 2.29.21
biological symmetry, 2.27.81.8	calculate phases, 3.11.2
vector, 2.28.59.3	call, 2.27.8
to integers compression, 2.28.59.3	carboxylic acid, 2.27.63.2
blast files, 2.27.102.24	cartesian cooridnates, 2.28.177
blast-formatted database, 2.27.34.3, 2.27.102.24	cartridge, 3.5
blending, 2.27.102.30	cavities, 2.27.84.1
images, 2.28.144.2	cavity, 5.3.1
bold, 2.27.81.31.1	analysis, 3.3.13
bond angle bending, 2.30.5	ccp4 maps, 2.27.76.26
stretching, 2.30.6	cd, 2.27.81.18
to protein, 2.27.65.3	cell axis vectors, 2.28.177.7
bonded atoms, 2.28.89.1	specific icm commands, 5.10.2.4
born radii, 2.27.82.8	center, 2.10.1, 2.27.9
boundary element, 5.2.4	chain breaks, 2.21.5.6, 2.21.5.7, 2.28.125.1
matrix, 2.28.79.9	symbol, 2.27.81.8

sequence position in multiple alignment, 2.27.65.6	screen, 2.27.10
unix directory, 2.27.81.18	click and lock, 5.10.2.4
changing local stick radii, 2.27.81.74	clipping plane, 5.3.3
surface dot size, 2.21.5.46	closer than threshold, 2.28.38.7
charge, 5.3.2	closest sequence, 2.28.87.3
compounds, 2.27.63.2	value, 2.28.49.1
change, 2.27.81.9	cluster, 2.28.140.1
chem formula, 2.28.142.9	center, 2.28.62.8
chemSuper3D, 2.29.22	centers, 2.10.1
chemical, 2.23, 2.27.34.9	selection, 2.28.62.8
2D drawings, 2.27.59.9	tree, 2.28.87.5
SMARTS search, 2.27.34.5	size, 2.28.90.1
database, 3.5	clustering, 2.10, 2.27.59.35, 2.27.84.6
decomposition, 2.27.59.27, 2.27.84.2	clusters, 2.10, 2.10.1
descriptors, 5.8.12	cnMethodAverage, 2.19.5
diversity, 3.14.6.3	cnWeight, 2.16.6
drawing, 2.21.9.14	coil, 5.3.4
quality, 2.21.9.15	collection, 2.21
formula, 2.28.142.9	color, 2.21.5.27, 2.27.11
fragment counting, 2.28.90.2	accessibility, 2.27.13
keys, 2.27.59.21	background, 2.27.13.2
match coordinates, 2.28.177.5	example, 3.2.7
matching, 2.27.34.4, 2.27.76.45, 2.27.76.46, 2.28.121, 2.28.141	accessibility, 3.2.11
models, 2.28.87.1	alignment, 2.27.13.3
modification, 2.27.62, 2.27.63, 2.29.37	atom contributions, 2.27.12
name, 2.28.87.6	bfactor, 3.2.9
normalization, 2.27.63	charge, 3.2.12
rules, 2.27.63.4	electrostatic potential, 2.15.5
pattern, 2.24, 2.27.80.1	hydrophobicity, 3.2.10
search, 2.28.49.3	pharmacophore, 2.27.12
reaction product generation, 2.27.59.32	potential, 2.29.25
search, 2.27.34.10, 2.27.80.1, 2.28.90.2	shape depth, 2.27.13
similarity, 3.5	chemical, 2.27.12, 2.27.80.1
spreadsheet, 2.27.12, 2.27.76.44, 2.27.76.45, 2.27.76.46, 2.27.81.40, 2.27.102.11	file, 2.30.15
structure from smiles, 2.27.81.6	grob, 2.27.13.4
substructure, 2.27.34.4	by atom selection, 2.27.13.4.3
mask, 2.27.59.21	atoms, 2.21.7.1
superposition, 2.19.6, 2.28.121	map, 2.27.13.4.4
table, 2.23	matrix, 2.27.13.4.2
view, 2.27.81.45	potential, 2.27.13.4.5
chemistry, 2.23, 2.28.26	unique, 2.27.13.4.1
chiral isomer generation, 2.27.29	label, 2.27.13.5
chirality, 2.17.16, 2.27.29	map, 2.27.13.6
choosing ligands, 3.13.1.2	by value, 2.27.23.16
cif, 2.27.76.44	molecule, 2.27.13.1
clamp values to range, 2.28.164	names, 2.28.28
clashThreshold, 2.16.5	object, 2.27.11.2
labels, 2.28.152	specification, 2.27.11.1
clear, 2.27.10	surface by conservation, 2.27.13.3
graphical selection, 2.27.10	volume, 2.27.13.7

function, 2.27.7.2	stack, 2.27.102.40, 5.3.11, 5.9.9
selection, 2.28.87	compression, 2.27.15.2
combinatorial compounds, 2.28.26	file, 2.30.7
libraries, 2.27.59.32, 2.28.90.4	transition, 2.29.38
PDB, 2.29.89	conformer storage, 2.27.57.5, 2.27.86.2
transformations, 3.10.4	conformers, 3.13.2.3
combining plots, 2.27.59.31	connect, 2.27.16
receptor and ligand stacks, 2.27.4.2	chains with alignments, 2.27.52
command, 2.28.87.4, 5.3.9	molcart, 2.27.16.1
line editing, 2.2	consensus, 2.16.7
help, 2.27.43	coloring, 2.16.9, 2.21.2
options, 2.1	definitions, 2.21.1
word list, 3.1.5	consensusStrength, 2.16.7
commands, 2.19.10	conservation, 2.28.110.5, 2.28.124.5
communication protocols, 2.25	constant, 2.5
comp, 2.28.93	constants, 2.5
comp_matrix, 2.27.81.17, 2.27.82.14, 5.3.10	contact areas, 2.28.79
compare, 2.15.11, 2.15.14, 2.27.14	continue, 2.27.17
angles, 2.27.14.2	contour surfaces, 2.21.7.5
atom, 2.27.14.1	contouring density, 2.27.59.14
by rmsd without superposition, 2.27.14.1	contrast, 2.21.5.27
chemical tables, 2.27.34.10	conversion to real array, 2.28.154
patch only, 2.27.14.3	convert, 2.27.18, 2.27.18.2, 3.13.2
rmsd, 2.27.14.1	3D to chemical, 2.28.26
surface, 2.27.14.3	3D/0D to 2D, 2.27.59.9
variables, 2.27.14.2	ICM object to PDB, 2.27.88
compareMethod, 2.19.6	and reroot, 2.27.18.4
comparing two sarrays, 2.28.93	chemical 3D, 2.29.80
comparison operations, 2.11.5	and optmimize geometry, 2.29.81
complete view, 2.28.132	comp, 2.27.18.1
compound accessibilities, 3.14.4.1	comparison, 2.27.18.1
array, 2.23	fragments, 2.27.18.2
compress, 2.27.15	mol, 2.27.18.3
binary, 2.27.15.3	object 3D and optmimize geometry, 2.29.82
conf, 2.27.15.2	macro, 2.29.13
grob, 2.27.15.1	pdb, 3.8.2
in place, 2.27.15.3	to 3D, 2.27.81.7
objects, 2.27.15	ICM object, 2.29.83
stack, 2.27.15.2	iarray, 2.28.152
compressed table view, 2.27.81.21	icm-object, 2.27.18
conditional buttons, 5.5.5	integer, 2.28.152
string, 2.28.142.6	convert2Dto3D, 2.29.82
conf, 2.27.81.51, 2.27.102.40, 2.28.146.6, 5.3.11, 5.9.9	convert3Dto3D, 2.29.83
data, 2.28.146.6	convertObject, 2.29.13
confgen, 3.13.2.3	converting a chemical, 2.27.18.3
configuration, 2.30.14	pdb-chemical, 3.13.2
memory usage, 2.15.6	alignment to table, 2.28.146.2
conformation comparison, 2.19.6	chemicals, 3.13.2.4
conformational generator, 2.27.60.1, 3.13.2.3	table columns into matrix, 2.28.79.5
interpolation, 2.27.23.6	to, 2.28.111

pictures, 2.21.5.24	defining space box, 2.28.20
cooling schedule, 2.16.43	dehtml, 2.28.114.3
coordinate frame, 2.16.4, 2.27.23.4	delete, 2.27.22
copy, 2.27.19	3D graphics panel, 2.27.97
chemical image, 2.21.9.15	alias, 2.27.22.2
file, 2.18.26	array element, 2.27.22.6
site, 2.27.81.24	index, 2.27.22.6
correlation matrix, 2.28.149	selection, 2.27.22.1
covalent bound count, 2.28.125.3	atom, 2.27.22.7
neighbors, 2.28.89.1	bond, 2.27.22.14
covalently attached molecule, 2.28.89.1	boundary, 2.27.22.15
cpk, 5.3.12	chemical, 2.27.22.34
create a covalent bond, 2.27.59.2	fragment, 2.27.22.34
pharmacophore, 2.29.84	selection, 2.27.22.34
creating a local patch object, 2.27.18.2	class, 2.27.22
credits, 4.5	conf, 2.27.22.16
crypt, 2.27.20	directory, 2.27.22.8
crystal axis vectors, 2.28.16	disulfide bond, 2.27.22.25
symmetry transformation, 3.10.2	drestraint, 2.27.22.17
transformations, 2.28.162	element, 2.27.22.29
crystallographic occupancy, 2.28.95	file, 2.27.22.9
symmetry intro, 1.4.2.4	from array, 2.27.22.6
crystallography, 2.28.117	hydrogen, 2.27.22.11
csv format, 2.27.76.41	label, 2.27.22.18, 2.27.22.19
csym, 1.4.2.4	chemical, 2.27.22.19
current, 5.3.8	link, 2.27.22.20
icm-process number, 2.15.4	map, 2.27.22.21
map, 5.3.6	molcart, 2.27.22.3
object, 5.3.7	molecule, 2.27.22.13
working directory, 2.28.96	object, 2.27.22.12
cursor action, 5.10.2.4	parray, 2.27.22.33
customization, 3.1.2	element, 2.27.22.33
and paste chemicals, 2.21.9.14, 2.21.9.15	peptide bond, 2.27.22.26
cyclic temperature protocol, 2.16.43	plot, 2.27.22.4
cz32, 4.5	salts, 2.27.63.3
database, 5.4.1	selection, 2.27.22.5
browser, 2.27.57.3	sequence, 2.27.22.22
connection, 2.27.16.1	session, 2.27.22.10
file, 3.5.1	shell object, 2.27.22.1
import, 2.27.59.26	site, 2.27.22.23
date, 2.27.21	sstructure, 2.27.22.24
array, 2.27.21	stack, 2.27.22.27
dcMethod, 2.19.7	object, 2.27.22.28
dcWeight, 2.16.8	system, 2.27.22.9
decomposition, 2.27.59.27, 2.27.84.2	table, 2.27.22.30
defCell, 2.22.1	rows, 2.27.22.30
defSymGroup, 2.15.2	term, 2.27.22.31
default atom colors, 2.27.81.13	tether, 2.27.22.32
value, 5.9.2	tree, 2.27.22.33
define axis, 3.10.3	variable, 2.27.22.6

backbone, 2.28.125.1	surface, 2.27.23.20
restraint, 2.27.22.17	area, 2.21.5.2
deleting sites by number, 2.27.22.23	tethers, 2.27.23.23
delphi, 2.29.25	trajectory, 2.27.23.17
density correlation, 2.16.8, 3.11.3	volume, 2.27.23.24
fitting, 2.19.7	window, 2.3, 2.27.23.25
in unit cell, 2.27.59.23	distance, 2.21.5.18, 5.4.3
densityCutoff, 2.16.10	averaging, 2.19.5
dependent columns, 2.27.1.1.1	contact-based, 2.28.22, 2.28.22.1
depth cueing, 2.27.13.7, 5.4.2	geometry, 5.4.4
depth-cueing, 2.16.14	matrix, 2.28.146.5, 2.29.8
desolvation, 2.19.24	between stack conformations, 2.28.79.10
detecting proximity, 2.28.38.7	restraint, 5.4.6
dialog generation, 2.28.11	file, 2.30.9
in html documents, 2.27.42	type file, 2.30.8
tables, 2.27.42	restraints, 2.27.81.19
scripting, 2.28.11	distances, 2.28.90.3
dielConst, 2.16.11	distribution, 1.3
dielConstExtern, 2.16.12	comparison, 2.28.124
dielectric constant, 2.16.11	disulfide bond, 5.4.5
diff, 2.28.93	diverse subset, 3.14.6.3
dihedral angle, 2.27.59.19	dividing chemical into individual molecules, 2.28.140.4
calculation, 3.3.10	dna to protein sequence translation, 2.28.161.1
directory, 2.27.22.8, 2.27.59.5, 2.28.123	translate, 2.28.161.1
display, 2.27.23	dockScan, 3.13.2.7
GUI window, 2.27.23.26	docking, 2.29.86
box, 2.27.23.7	intro, 3.13.2.1
clash, 2.16.5, 2.27.23.8	result viewing, 2.29.28
drestraint, 2.27.23.9	simple models, 3.14.3
field, 2.21.5.2	timing, 3.13.1.3
from script, 2.27.23.3	with template, 3.13.2.8
gradient, 2.27.23.10	documents, 5.6.2
grob, 2.27.23.11	dominant color, 2.28.28.2
label, 2.27.23.12	donor, 3.6.1
gui, 2.27.23.26	plot intro, 1.4.3.2
hbond, 2.27.23.13	dots, 2.27.70
label, 2.27.23.15	dotted surface, 2.21.5.48
map, 2.21.5.9, 2.27.23.16	double click action, 5.10.2.4
model, 2.27.23.1	drestraint, 2.27.82.16, 5.4.6
new, 2.27.23.2	generate from structure, 2.27.59.7
off-screen, 2.27.23.3	global weight, 2.16.6
offscreen, 2.27.23.3	set, 2.27.81.19
origin, 2.27.23.4	type, 5.4.7
ribbon, 2.27.23.18	drop, 2.16.13
rotate, 2.27.23.5	ds3D, 2.29.31
site, 2.27.23.19	dsCellBox, 2.29.15
skin, 2.27.23.20	dsChem, 2.29.17
slide, 2.27.23.21	dsCustom, 2.29.18
stack, 2.27.23.6	dsPocket, 2.29.28
string, 2.27.23.22	dsPropertySkin, 2.29.19

dsRebel, 2.15.5, 2.29.25	exact, 2.27.34.9, 2.27.34.10
dsSeqPdbOutput, 2.29.26	match, 2.28.114.1
dsSkinLabel, 2.29.27	example scripts, 3.14
dsStackConf, 2.29.29	exit, 2.27.33
dsVarLabels, 2.29.30	exitSeslogStyle, 2.19.10
dsXyz, 2.29.32	expanding substructure match, 2.27.81.59
dump database, 2.27.102.7	export, 2.27.102.7
dynamic gui, 5.5.5	animation, 2.27.102.30
ecepp, 5.5.1	exporting sdf, 2.27.102.11
edit, 2.27.24	expression shortcuts, 2.9.1.2
files, 2.21.14.1	comparison, 2.11.5
electro intro, 1.4.2.9	arithmetics, 2.11.2
electroMethod, 2.19.8	assignment, 2.11.1
density, 2.21.7.5, 2.29.42, 2.29.43	comparison, 2.11.5
around selection, 2.16.22	logical, 2.11.3
map generation, 2.16.1	extending to bonded hydrogens, 2.28.125.6
maps, 2.21.14.1	terminal atoms, 2.28.125.6
electrostatic boundary matrix, 2.28.79.9	external process, 2.27.59.1
isopotential surfaces, 2.27.59.13	extracting from Markush, 2.27.50
potential, 2.27.13.4.5	icm script arguments, 2.28.52
solvation, 3.7.2	stack from object, 2.27.57.5
surface, 2.29.25	ez25, 3.7
troubleshooting, 5.8.13	factor, 5.9.13
intro, 1.4.2.9	false negatives, 2.28.124.2
ellipsoid, 2.28.149	family, 2.27.81.31.1
elseif, 2.27.25	faq, 1.3
endfor, 2.27.26	cheminformatics, 3.14.6
endif, 2.27.27	chemsuper, 3.14.5
endmacro, 2.27.28	molcart dump, 3.14.6.2
endwhile, 2.27.32	query, 3.14.6.1
energetics, 3.7	multiple chem overlay, 3.14.5.1
function, 2.21.14.2	residue table, 3.14.4.1
terms, 2.14	fast Fourier transform, 2.27.59.24
ensemble average, 3.7.5	sequence search, 2.27.34.3
entropy of alignment, 2.28.124.5	fasta, 5.5.2
atom, 2.27.18.4	feature table, 2.28.146.8
enumerate, 2.27.29, 2.27.30, 2.27.31	in sequences, 2.27.81.23
chiral, 2.27.29	ffMethod, 2.19.11
library, 2.27.31	field name, 2.28.87.2
tautomer, 2.27.30	file, 2.27.102.23
enumeration, 2.28.26	exists, 2.28.43
eps files, 2.18.23	list, 2.28.52
error SOAP services, 2.28.42	length, 2.28.48
ignoring, 2.18.25	object origin, 2.28.48
error/warning bits cleanup, 2.27.10	permissions, 2.28.48
errorAction, 2.19.9	time modified, 2.28.48
vrestraint vs_var, 2.27.81.70	type, 2.28.48
evalSidechainFlex, 2.29.87	files, 2.30
evol tree intro, 1.4.3.5	filter, 2.27.34.10, 2.27.57.3
evolutionary tree intro, 1.4.3.5	functions, 5.5.4

find, 2.27.34	expansion, 2.28.134.3
alignment, 2.27.34.1	gapExtension, 2.16.15
and replace a chemical pattern, 2.27.63.1	gapFunction, 2.22.3
chemical fragment, 2.27.63	gapOpen, 2.16.16
chemical, 2.27.34.5	gcMethod, 2.19.12
pattern, 2.27.63	generate intermediate conformers, 2.29.38
substructure, 2.28.62.1	generating movie images, 3.9.2.1
database, 2.16.2, 2.27.34.2	genomics, 1.4.3.1
fast, 2.27.34.3	clustering, 2.27.41.2
family of commands, 2.27.34	intro, 1.4.3.1
in sarray, 2.28.62.7	geometry optimization, 2.27.60.1
molcart, 2.27.34.9, 3.5	started, 1.7
molecule, 2.27.34.4	getting data from outside, 2.25
pattern, 2.27.34.8	started, 1.7
pdb, 2.27.34.6	global, 2.27.39
pharmacophore, 2.27.34.11	glossary, 5
prosite, 2.27.34.7	goto, 2.27.40
table, 2.27.34.10	term, 2.16.17, 2.27.81.61
findFuncMin, 2.29.33, 2.29.34	gpWeights, 2.16.17
findFuncZero, 2.29.35	graph matching, 2.28.121
findSymNeighbors, 2.29.16	graphical box, 2.27.23.7
find_related_sequences, 2.29.33	row selection, 2.28.62.4
finding long covalent bonds, 2.28.125.1	selection, 2.28.125.5
to density, 2.19.7	graphics, 2.27.81.3, 2.28.173, 3.2, 5.3.3
fix, 2.27.35	card, 2.21.5.44
fixed branches, 2.28.125.2	controls, 2.3, 2.30.15, 5.4.2
flattening 3D molecule, 2.29.17	exists, 2.28.43
flow control, 2.12	intro, 1.4.1, 1.4.1.4
fog, 2.16.14, 2.27.13.7, 2.27.23.24, 5.4.2	learning, 3.2.1
color, 2.16.14	attributes, 2.16.4
fogStart, 2.16.14	fogStart, 2.16.14
fold search, 5.9.4	view vector, 2.27.81.68
foldbank.db, 2.30.3	greedy matching, 2.9.1.4
folding procedure, 3.14.1	grid potentials, 2.27.59.25
font, 2.27.53.1	grob, 5.5.3
size, 2.27.81.31.1, 2.30.14	coloring, 2.27.13
specification, 2.27.81.31.1	files, 2.30.10
for, 2.27.36	inside-out flip, 2.27.81.35
fork, 2.27.37	normal directions, 2.27.81.35
formal charge, 2.21.5.15, 5.3.2	translate, 2.27.95
formatdb, 2.27.102.24	group, 2.27.41
fprintf, 2.27.38	by column, 2.27.41.4
fractional coordinates, 2.28.177.3	column, 2.27.41.4
to abs coordinates, 2.28.16	replacement, 2.27.62
fragmented molecule, 2.27.18.2	sequence, 2.27.41.1
frame, 2.27.86, 2.27.102.30	unique, 2.27.41.2
fullscreen, 2.27.81.73	table, 2.27.41.3
function, 2.27.58	grouping table by a column, 2.27.81.21
selecting in objects, 2.8.10	gui, 2.27.42, 5.10.2.4
gamess, 5.6	exists, 2.28.43

panels, 2.27.97	hydration, 2.28.7
programming, 2.26, 2.27.42, 2.27.81.21	parameters, 2.30.13
gzip files, 2.27.15.3	hydrogen bond, 2.21.5.19, 2.21.5.20, 2.27.59.17, 5.6.1
hash table, 2.21	bonding parameters, 2.30.12
haze, 2.16.14	cutoff, 2.16.18
hb, 2.16.18	bonds, 2.28.90.3
hbCutoff, 2.16.18	display, 2.21.5.26
hbond, 2.21.5.19, 2.21.5.20, 2.27.22.6, 5.6.1	placement, 2.27.81.22
color, 2.27.23.14	hydrophobicity profile, 3.3.12
display, 2.21.5.21, 2.21.5.22	iProc, 2.15.4
energy, 2.27.23.14	iSee, 5.9.14
list, 2.28.146.9	i_out, 2.15.3
show, 2.27.82.20	iarray, 2.27.22.6, 2.28.49.1, 2.28.59.2, 2.28.62.7, 5.7.1
hbondMinStrength, 2.21.5.19	making, 2.28.59.1
faq, 3.3.4	icb files, 5.9.14
how to, 3.3.4	algorithms, 4.3
header, 2.27.1.1	application refs, 4.4
helical axis, 2.29.36	literature, 4.3
helicity, 3.7.6	archive, 2.27.76.2
content calculation, 3.7.6	arguments, 2.28.52
help, 2.27.43, 2.27.43.1, 2.27.43.2	binary, 2.28.96
browser, 2.27.43.1	branching, 2.12.2
commands, 2.27.43.3	commands, 2.27
functions, 2.27.43.4	controls, 2.12
getting, 3.1.1	flags, 2.1
word, 2.27.43.2	functions, 2.28
getting, 3.1.1	graphics, 3.2
hidden blocks, 5.1.1.1	history, 1.2
display, 2.27.23.3	jumps, 2.12.3
hydrogens, 2.21.5.26	learning, 3.1.4
stack in object, 2.27.86.2	loops, 2.12.1
hierarchical, 2.10	macros, 2.29
highEnergyAction, 2.19.13	main refs, 4.2
his-tags, 2.28.165	menus, 2.21.10.1
histogram, 2.27.59.31	method literature, 4.4
2D, 2.28.79	molecules, 2.13
history, 2.27.44, 2.27.102.39	object file, 2.30.18
delete, 2.27.22.10	session, 2.19.10
of ICM, 1.2	shell, 3.1
homodel, 2.29.41	support, 1.3
homology modeling, 1.4.2.2, 2.27.7.4, 2.27.81.58, 2.29.1, 3.14.4	table, 2.20
faq, 3.14.4	ali, 2.30.31
intro, 1.4.2.2	all, 2.30.32
output, 2.27.7.4.3	bbt, 2.30.5
steps, 2.27.7.4.1	bst, 2.30.6
to export a molcart table, 3.14.6.2	cfg, 2.30.14
html, 2.27.42, 2.28.87.4, 5.6.2	clr, 2.30.15
document order, 2.27.81.33	cmp, 2.30.33
tag removal, 2.28.114.3	cn, 2.30.9
html-formatted text, 5.6.2	cnf, 2.30.7

cod, 2.30.4	entry, 2.28.123.1
col, 2.30.24	sdf-file path, 2.28.96
gro, 2.30.10	indices of labeled table rows, 2.28.62.5
hbt, 2.30.12	selected table rows, 2.28.62.4
hdt, 2.30.13	infinity, 2.28.154
htm, 2.30.11	info, 2.27.46
iar, 2.30.35	molcart, 2.27.46.1
map, 2.30.16	inner join, 2.27.48
mat, 2.30.37	insert rows, 2.27.1.4
ob, 2.30.18	integer, 5.7.2
pdb, 2.30.28	array, 2.28.59, 5.7.1
prf, 2.30.34	shell variables, 2.15
rar, 2.30.38	interaction cutoff, 2.17.27
res, 2.30.20	lists, 2.17.27, 2.21.14.2
rs, 2.30.23	interactive docking, 1.4.2.8
rst, 2.30.22	interface comparison, 2.27.14.3
sar, 2.30.36	residues, 3.3.5
se, 2.30.30	torsions, 3.3.7
seq, 2.30.29	view, 2.29.28
tab, 2.30.25	intermolecular bond, 2.27.65.3
tot, 2.30.26	internal coordinate file, 2.30.21
trj, 2.30.17	coordinates, 2.8.9
var, 2.30.21	interpolate, 2.28.28.1
vwt, 2.30.27	interpolation, 2.28.28.1
icmCavityFinder, 2.29.14	interruptAction, 2.19.14
icmMacroShape, 2.29.85	inverting array order, 2.28.59.2, 2.28.110.2
icmPmfProfile, 2.29.23	italic, 2.27.81.31.1
icmPocketFinder, 2.29.86	iterative overlay, 2.27.89
icmscript, 2.27.76.3	superposition, 2.21.14, 2.27.90
arguments, 2.28.52	join, 2.27.48
if, 2.27.45	tables, 2.27.48
ignoring swiss secondary structure, 2.22.9	keep, 2.27.47
image, 3.2.6	kernel models quality, 2.28.124.2
annotation, 3.2.5	mapping, 2.30.15
center, 3.2.8	kmz, 5.5.3
format, 5.10.3	l_antiAlias, 2.17.1
high quality, 3.2.2	l_autoLink, 2.17.2
parray, 5.8.3.3	l_bpmc, 2.17.3
resolution, 3.2.2	l_breakRibbon, 2.17.4
rotation, 3.2.3	l_bufferedOutput, 2.17.5
imposing tether, 2.27.81.58	l_bug, 2.17.6
place, 2.11.4	l_caseSensitivity, 2.17.7
ops, 2.11.4	l_commands, 2.17.8
incidence, 2.28.79.12	l_confirm, 2.17.9
increasing the number of shell variables, 2.30.14	l_easyRotate, 2.17.10
increment charge, 2.27.81.9	l_info, 2.17.11
index expressions, 2.6	l_minRedraw, 2.17.12
in array, 2.28.62.3	l_neutralAcids, 2.17.13
substring, 2.28.62.2	l_out, 2.17.14
table, 2.27.102.23	l_print, 2.17.15

l_readMolArom, 2.17.17	database, 2.27.55
l_showAccessibility, 2.17.18	font, 2.27.53.1
l_showMC, 2.17.19	html documents, 2.28.87
l_showMinSteps, 2.17.20	molcart, 2.27.56
l_showResCodeInSelection, 2.17.21	database, 2.27.56
l_showSites, 2.17.23	of files, 2.28.123
l_showSpecialChar, 2.17.22	updates, 2.27.60
l_showSstructure, 2.17.24	listUpdateThreshold, 2.16.20
l_showTerms, 2.17.26	literature, 4.1
l_showWater, 2.17.25	load, 2.27.57
l_updateLists, 2.17.27	conf, 2.27.57.1
l_warn, 2.17.28	frame, 2.27.57.2
l_wrapLine, 2.17.29	molcart, 2.27.57.3
l_writeStartObjMC, 2.17.30	object, 2.27.57.6
l_xrUseHydrogen, 2.17.31	solution, 2.27.57.4
label, 2.27.23.22, 5.7.3	stack object, 2.27.57.5
fonts, 2.30.15	loadEDS, 2.29.42
latent, 2.28.90.6	loadEDSweb, 2.29.43
learn, 2.27.49	local, 3.5.1
atom, 2.27.49.1	logarithm, 2.28.74
left join, 2.27.48	logical, 5.7.4
triangle of a matrix, 2.28.79.3	operations, 2.11.3
library to replacement groups, 2.27.59.27, 2.27.84.2	variables, 2.17
ligand binding, 2.29.28	logical_ops, 2.11.3
dock faq, 3.13.2	logicals, 2.17
docking, 3.13, 3.13.1, 3.13.2	long axes, 2.28.149
intro, 1.4.2.6	loop database rebuilding, 2.27.102.27
editing, 1.4.2.8	interrupt, 2.16.44
editor, 2.29.37	modeling, 1.4.2.3
fit, 3.13	intro, 1.4.2.3
setting, 3.13.2	search, 2.27.7.4.2
view, 2.21.5.25	resolution shape, 2.29.85
light, 2.21.5.28	ma29, 3.11
limits, 2.30.14	macro, 2.27.58, 5.7.5
line thickness in 2D chemicals, 2.21.9.14	macro_def, 5.7.5
lineWidth, 2.16.19	main ICM references, 4.2
linear chemical notation, 2.24	concepts, 3.10.1
regression, 2.28.73	make, 2.27.59
group, 2.27.50	3d label, 2.27.59.15
internal variables of molecular object, 2.27.51	angle, 2.27.59.18
ms2ali, 2.27.52	background, 2.27.59.1
sequences to 3D objects, 2.27.52	bond, 2.27.59.2
to alignment, 2.27.52	chain, 2.27.59.3
variable, 2.27.51	multi, 2.27.59.3
variables, 2.27.51	boundary, 2.27.59.4
linked alignment, 2.28.87	directory, 2.27.59.5
sequence, 2.28.87	distance, 2.27.59.16
linux shell, 2.27.91, 5.11.2	disulfide bond, 2.27.59.6
list, 2.27.53	drestraint, 2.27.59.7
binary, 2.27.54	factor, 2.27.59.8

chem_array, 2.27.59.9	transformations, 2.28.134.4
grob, 2.29.36	trimming, 2.28.21
from image, 2.27.59.11	value sigma, 2.28.121
matrix, 2.27.59.12	contouring, 2.27.59.14
image, 2.27.59.11	mapAtomMargin, 2.16.22
map, 2.27.59.10	mapSigmaLevel, 2.16.21
matrix, 2.27.59.12	mapping properties to sequence, 2.28.110.4
potential, 2.27.59.13	and factors, 3.11
skin, 2.27.59.14	mass-spectrometry functions, 2.27.29, 2.27.30, 2.27.31
hbond, 2.27.59.17	matching chemicals, 2.28.62.1
image, 2.27.59.20	hydrogens, 2.27.81.59
key, 2.27.59.21	matrix, 5.7.7
map, 2.27.59.22	new, 2.28.79.1
cell, 2.27.59.23	map value, 2.28.80
factor, 2.27.59.24	maxColorPotential, 2.15.5
potential, 2.27.59.25	maxMemory, 2.15.6
xray, 2.27.59.30	movie, 3.9.2
molcart, 2.27.59.26	mcBell, 2.16.23
molsar, 2.27.59.27	mcJump, 2.16.24
pca, 2.27.59.28	mcShake, 2.16.25
peptide bond, 2.27.59.29	mcStep, 2.16.26
plot, 2.27.59.31	memorizing positions, 3.2.4
reaction, 2.27.59.32	menu, 2.27.61
sequence, 2.27.59.34	script, 3.1.3
alignment, 2.27.59.33	merge PDB, 2.29.89
from alignment, 2.27.59.33	arrays to table, 2.27.41.3
torsion, 2.27.59.19	continuation lines, 2.27.76.37
tree, 2.27.59.35	objects, 2.27.65.2
unique, 2.27.59.36	parts of molecule, 2.27.65.3
makeAxisArrow, 2.29.36	pdb, 3.4.4
makeIndexChemDb, 2.29.44	sarray into string, 2.28.144
makeIndexSwiss, 2.29.45	stacks, 3.7.7
makePdbFromStereo, 2.29.46	tables, 2.27.4.3, 2.27.48
makePharma, 2.29.84	merge2, 3.8.7
makeSimpleDockObj, 2.29.47	mergePdb, 2.29.89
makeSimpleModel, 2.29.48	several chemical, 2.28.144.1
making predictive models, 2.27.49	merging into one molecule, 2.27.65.3
manual style, 1.5	mesh, 2.28.174
map, 2.16.22, 2.21.5.9, 5.7.6	score, 3.13.3.3
aa property to sequence, 2.28.110.1	mfMethod, 2.19.15
averaging, 2.28.134.4	mfWeight, 2.16.27
calculation, 2.27.59.24	mimel, 5.7.8
conversion, 2.27.59.30	mimelDepth, 2.16.28
file, 2.30.16	mimelMolDensity, 2.16.29
fitting, 2.19.7	minNumGrad, 2.27.60
format, 5.7.6	minTetherWindow, 2.15.7
mean value, 2.28.82	minimization exit criteria, 2.27.60
min value, 2.28.83	minimize, 2.15.9, 2.27.60
name, 2.28.75	cartesian, 2.27.60.1
operations, 5.7.6	loop, 2.27.60.2

tether, 2.15.7, 2.27.60.4	properties, 2.27.81.29
drop, 2.16.13	rotation, 3.2.3
minimizeMethod, 2.19.16	translation, 3.2.3, 3.2.4
missing bonds, 2.27.65.3	create, 1.7.2
loop, 2.21.5.6, 2.21.5.7	intro, 1.7.2, 2.7
residues, 2.28.47.1	sort/reorder, 2.27.83.4
triangles, 2.28.174	selecting, 2.8.6
mkUniqPdbSequences, 2.29.49	montecarlo, 2.15.10, 2.15.12, 2.15.13, 2.15.14, 2.15.18, 2.19.6, 2.27.64
mm26, 3.8	command, 2.27.64
mmcif, 5.7.10	local, 2.15.15
mmff, 5.7.9	trajectory, 2.27.23.17
type, 2.28.167	moprphing, 2.29.38
show atom types, 2.27.82.10	more, 5.7.13
mnSolutions, 2.15.8	morph, 2.27.23.6
mncalls, 2.15.9	to tether target, 2.29.38
mncallsMC, 2.15.10	morph2tz, 2.29.38
mnconf, 2.15.11	morphing, 2.27.23.6, 2.27.81.58, 2.27.86.3
mnhighEnergy, 2.15.12	mouse controls, 2.3
mnreject, 2.15.13	file, 2.27.102.30
mnvisits, 2.15.14	move, 2.27.65
model reliability, 2.29.23	alignment sequence, 2.27.65.6
modify, 2.27.62	atoms, 2.27.81.2
and reroot, 2.27.18.4	bonding, 2.27.65.3
chem, 2.27.63	column, 2.27.65.5
charge, 2.27.63.2	element, 2.27.65.4
delete salt, 2.27.63.3	file, 2.18.28, 2.27.77.3
normalize, 2.27.63.4	fragments together, 2.27.65.3
chemical find replace, 2.27.63.1	molecule, 2.27.65.1
molcart, 2.27.63.5	ms_molecule, 2.27.65.1
modifyGroupSmiles, 2.29.37	multiple molecules, 2.27.65.2
modules, 1.4.4	object, 2.27.65.2
mol, 2.27.76.45, 2.27.76.46, 2.27.102.11, 2.27.102.23, 5.7.11	sequence, 2.27.65.6
file, 2.28.142.2	table column, 2.27.65.5
to icm, 2.27.18.3	movie, 2.27.86.3
translation, 3.2.4	images by frame, 3.9.2.2
mol-file to chem-table element, 2.28.97	molecular simulation, 3.9.2
mol2, 5.7.12	rotate view, 3.9.1
molcart, 2.27.16.1, 3.5	zooming, 3.9.1
connection options, 3.5.2	moving selection to another object, 2.28.125.8
molecular, 2.28.51, 5.8.3.1	mpeg, 2.27.102.30
arrays, 5.8.3	ms_, 2.8.6
manipulations, 3.8	multi center drestraint, 2.19.5
modifications, 3.8.5	multi-part molecule, 2.27.18.2
object, 5.8.1	multiple NMR models, 2.21.14.3
objects, 2.13	alignment, 2.27.3.2
surface, 2.27.82.8, 5.9.7	to pairwise similarities, 2.29.8
views, 1.4.1.1	conformation storage, 5.9.9
volume, 2.28.102	mol as text, 2.28.142.2
molecule, 2.7	object file, 2.27.76.2
create, 3.8.4	sequence alignment intro, 1.4.3.4

mutate residue, 2.27.62	openGL window, 2.27.97
mutating residue, 3.8.5	operating system, 2.27.91, 2.28.173, 5.11.2
mute, 5.7.15	optimal chemical superposition, 3.14.5.1
mysql, 2.27.16.1	optimize Hbond, 2.29.88
nLocalDeformVar, 2.15.15	hydrogen bond, 2.29.88
nProc, 2.15.17	optimizeHbonds, 2.29.88
nSsearchStep, 2.15.16	or, 2.11.3
name, 2.28.70	order, 2.27.65.6
atom fields, 2.27.81.29	os_, 2.8.5
naming compounds, 2.27.81.40	other variables, 2.22
nearest sequence, 2.28.83	output, 2.15.3
nested script, 5.9.2	overlay by atom pairs, 2.27.89
nice, 2.29.39	chemical substructure, 2.29.22
image, 3.2.2	overview, 1.4
non-redundant, 3.4.3	pK shift, 3.7.3
normal distribution, 2.28.109	packing density, 3.3.8
normalize chemicals, 2.27.63.4	pair-distances, 2.27.22.6
defined, 2.28.154	pairdistance parray, 2.21.5.18
nota, 1.5	panel layout, 2.21.8.5
notational conventions, 1.5	paragraphs, 2.27.102.23
nucleotides, 2.18.24	parallelization, 2.15.4, 2.15.17
number of dots, 2.21.5.47	parray, 2.27.22.6, 5.8.3
elements, 2.28.90	parrayTo3D, 2.29.81
hydrogen bonds, 2.27.82.20	parrayToMol, 2.29.80
molecules in objects, 2.28.125.4	parse SOAP message, 2.28.171
occurrences, 2.28.90	parsing, 2.28.78
residues in molecules, 2.28.125.4	web pages, 2.27.76.43
van der Waals contacts, 2.27.82.11	partial least squares, 2.27.49
transfer from sequence, 2.27.3.1	slide display, 2.27.23.21
nvis, 2.28.59.6	sum, 2.28.68
object, 2.27.13.1, 5.8.1	passing arguments, 5.9.2
parray, 5.8.3.1	by reference, 2.27.58
properties, 2.27.81.29	pattern, 5.8.4
stack, 5.9.9	search, 2.27.34.2
to chemarray, 2.28.26	pause, 2.27.66
user fields, 2.28.47.1	pdb, 5.7.10, 5.8.6
assign comment, 2.27.81.14	file creation time, 2.28.35
source file, 2.28.48	files, 2.30.28
translate, 2.27.95	format, 2.27.76.44
merge, 3.8.6	merge, 3.4.4
selecting, 2.8.5	sequence generation, 3.4.3
obsolete, 2.16.51	pdbDirStyle, 2.19.17
occlusion shading, 2.27.13	peptide, 5.8.7
octanol transfer, 2.28.102	docking, 3.12.5
off, 2.27.76.21	folding, 1.4.2.1
format, 5.5.3	intro, 1.4.2.1
oligonucleotide melting, 2.28.150	personal gui controls, 3.1.2
on-line help, 2.27.43.1, 2.27.43.2	setup, 3.1.2
third, 2.28.34	ph30, 3.12
only, 5.8.2	ph4, 5.8.8

pharmacophore, 2.27.12, 3.5, 5.8.8	prediction model, 2.28.73
faq, 3.6	quality, 2.28.124
grid type definitions, 2.27.81.61	score, 2.28.124
object, 3.6.1	preference, 2.19
objects, 3.6	preferences, 3.1.2.3
pharmacophores, 3.6	prepSwiss, 2.29.61
psi plot, 2.29.57	previous atom, 2.28.89.1
pipe, 2.27.76.40	principal axes, 2.28.149
planar angle, 2.27.59.18	component analysis, 3.3.9
plot, 2.27.67	inertia moments, 2.28.77
3D 2Dfunction, 3.12.3	print, 2.27.69
shape, 3.12.4	bar, 2.27.70
area, 2.27.68	image, 2.27.72
histogram, 3.12.2	to string, 2.27.85
how to, 3.12	printMatrix, 2.29.62
simple, 3.12.1	printPostScript, 2.29.63
plot2DSeq, 2.29.50	printTorsions, 2.29.64
plotBestEnergies, 2.29.53	printf, 2.27.71
plotCluster, 2.29.55	profile, 5.8.9
plotFlexibility, 2.29.54	program overview, 1.4
plotMatrix, 2.29.56	progress bar, 2.27.70
plotRama, 2.29.57	progression, 2.27.70
plotRose, 2.29.58	project setup, 3.13.2.2
plotSeqDotMatrix, 2.29.51	projected alignment, 2.28.87.3
plotSeqDotMatrix2, 2.29.52	projecting surface charge, 3.7.2
plotSeqProperty, 2.29.59	property, 2.27.81.44, 2.27.81.45
3d, 1.4.3.7	grids, 2.16.17
plotting van der Waals, 3.7.1	map, 2.27.81.61
faq, 3.7.1	superposition, 2.27.81.61
pls, 2.27.49	prosite, 5.8.10
column contributions, 2.28.146.7	pattern, 5.8.4
model, 2.28.146.7	protein docking, 2.28.177.2
weights, 2.28.146.7	intro, 1.4.2.5
pmf, 2.19.15	grid docking, 3.14.2
residue profile, 2.29.23	health, 2.29.57
pmf-file, 2.30.19	psa, 5.8.12
pmffile, 2.30.19	purple box, 2.28.20
png, 2.27.102.35, 5.8.5	quantum mechanics, 2.27.76.20, 2.27.102.17
pocket, 2.29.28, 2.29.86, 3.13.1.1	query, 3.14.6.1
point coordinates, 2.28.177.1	molcart, 2.27.73
pointer array, 5.8.3	question mark operator, 2.28.142.6
polar hydrogens, 2.21.5.26	quit, 2.27.74
surface area, 2.28.102	property transfer via alignment, 2.28.110.3
polarization charge, 3.7.2, 5.8.13	r_2out, 2.16.31
postscript, 2.18.23	r_out, 2.16.30
potential surface coloring, 5.8.13	radii.electrostatic, 2.28.108
pov-ray, 2.27.102.37	van der Waals, 2.28.108
pow, 2.28.34	rainbow, 2.28.28.1
precision, 2.28.124.2	ramachandran faq, 3.3.3
predictSeq, 2.29.60	how to, 3.3.3

order, 2.28.127	profile, 2.27.76.34
randomSeed, 2.15.18	prosite, 2.27.76.35
randomize, 2.15.18, 2.27.75	rarray, 2.27.76.36
angles, 2.27.75.1	sarray, 2.27.76.37
coordinates, 2.27.75	sequence, 2.27.76.7, 2.27.76.38
torsions, 2.27.75	database, 2.27.76.38.1
rarray, 2.27.22.6, 2.28.49.1, 2.28.110.2, 5.8.11	smiles, 2.27.76.42
properties, 2.28.110.4	stack, 2.27.76.39
rdBlastOutput, 2.29.67	string, 2.27.76.40
rdSeqTab, 2.29.68	table, 2.27.76.41
reaction, 2.27.59.32	csv, 2.27.76.41
group file, 2.27.50	html, 2.27.76.43
read, 2.27.76	mmcif, 2.27.76.44
FILTER, 2.27.76.5	mol, 2.27.76.46
alignment, 2.27.76.11	mol2, 2.27.76.45
all, 2.27.76.6	trajectory, 2.27.76.30
binary, 2.27.76.2	and save a fragment, 2.27.76.30.1
color, 2.27.76.12	write, 2.27.76.30.1
column, 2.27.76.47	unix, 2.27.76.9
comp_matrix, 2.27.76.13	cat, 2.27.76.10
conf, 2.27.76.14	variable, 2.27.76.48
csd, 2.27.76.15	view, 2.27.76.49
csv, 2.27.76.41	vrestraint, 2.27.76.50
database, 2.27.76.16	type, 2.27.76.51
drestraint, 2.27.76.17	with filter, 2.27.76.5
type, 2.27.76.18	readMolNames, 2.22.10
entries from database, 2.27.76.7	readcomp_matrix, 2.27.76.13
factor, 2.27.76.19	reading external tool output, 2.27.59.1
from file, 2.27.76.1	from standard input, 2.27.76.40
string, 2.27.76.4	pdb from ftp, 2.18.18
fromstring, 2.27.76.4	web, 2.18.19
ftp http, 2.27.76.8	restraint, 2.27.76.50
gamess, 2.27.76.20	real, 5.8.14
grob, 2.27.76.21	array, 5.8.11
html, 2.27.76.3	shell variables, 2.16
file, 2.27.76.3	space refinement, 2.27.59.30
iarray, 2.27.76.22	reals, 2.16
index, 2.27.76.23	rebel, 2.15.5, 5.8.13
table, 2.27.76.7	rebuild molcart index, 2.27.7.9
library, 2.27.76.24	recalculate dependent values, 2.27.7.2
mmff, 2.27.76.25	values, 2.27.1.1.1
librarymmff, 2.27.76.25	receptor, 3.13.1.1
map, 2.27.76.26	preparation, 3.13.1.1
matrix, 2.27.76.27	redefine hydrogen coordinates, 2.27.81.22
mol, 2.17.13, 2.27.76.7, 2.27.76.28	references, 4
mol2, 2.27.76.7, 2.27.76.29	refineModel, 2.29.65
object, 2.27.76.31	reflections, 2.21.5.27
parray, 2.27.76.31.1	refresh view, 2.27.23.2
pdb, 2.21.14.3, 2.27.76.32	refs, 4.1
sequence, 2.27.76.33	regexp, 2.9, 2.28.78

syntax, 2.9.1	number, 2.28.59.5
regression, 2.27.49	table, 2.28.146.3
regul, 2.29.66	property averaging, 2.28.134.2
regular expression, 2.9, 2.28.62.3, 2.28.78	calculation, 2.28.56
filter, 2.27.76.1	proximity, 2.28.79.7
expression, 2.28.114.3	ranges, 2.8.11
regularization, 2.15.7, 2.27.60.4, 5.8.15	selection, 2.17.21
procedure, 3.8.3	as string, 2.28.142.7
rejectAction, 2.19.18	function, 2.28.115
relational database, 2.28.135	table, 3.14.4.1
relative accessible area of atoms, 2.19.1	tethering, 2.27.81.58
release notes, 1.1	user field, 2.28.47.1
remarkObj, 2.29.69	residue_selections, 2.8.11
remove expression tags, 2.28.165	selecting, 2.8.7
file, 2.27.22.9	resizing, 2.28.61
trailing blanks, 2.28.164	restraints, 2.14, 2.27.81.58
removing html tags, 2.27.76.43	torsion, 2.27.81.69
outliers, 2.28.164	return, 2.27.78
rename, 2.27.77	reverse complement, 2.28.126.1
chemicals, 2.27.81.40	lighting, 2.27.81.35
file, 2.27.77.3	normals, 2.27.81.35
molcart, 2.27.77.2	reversing order, 2.28.59.2
object, 2.27.77.1	rgb, 5.8.17
system, 2.27.77.3	matrix, 2.28.28
atom, 2.27.77.1	ribbon, 5.8.18
molecule, 2.27.77.1	bullets, 2.21.5.6
residue, 2.27.77.1	ribbonColorStyle, 2.19.20
reorder, 2.27.65.6	ribbonStyle, 2.19.21
alignment sequences, 2.27.102.1	right join, 2.27.48
array, 2.28.127	rigid chemical superposition, 2.27.89
objects, 2.27.83.3	ring, 2.28.118
replace matching array element, 2.28.114.1	sampling, 3.13.2.3
without interpretation, 2.28.114.2	templates, 2.27.81.7
replacing scaffold in a library, 2.27.63.1	rocking, 2.27.23.5
reproducible randomness, 2.15.18	root mean square deviation, 2.28.124.2
reroot, 2.27.18.4	rotate, 2.27.79
selections, 3.3.6	grob, 2.27.79.2
resLabelShift, 2.16.32	object, 2.27.79.1
resLabelStyle, 2.19.19	view, 2.27.79.3
reserved names, 2.22	rotation, 2.27.23.5
residue, 2.27.13.1, 5.8.16	angle, 2.28.17
alignment, 2.27.81.58	rounding a real, 2.28.142
conservation, 2.28.110.5	output, 2.27.82.41
contact area matrix, 2.28.79.7	rsWeight, 2.16.33
areas, 2.28.7.1	rs_, 2.8.7
field, 2.27.81.29	run script, 2.27.8
gap, 2.21.5.6, 2.21.5.7	running a docking job, 3.13.2.7
label, 2.27.3.1	dock job, 3.13.2.5
library file, 2.30.20	script, 3.13.2.6
name, 2.28.70	script from html, 5.9.2

s_alignment_rainbow, 2.18.1	inside ICM, 5.9.2
s_blastdbDir, 2.18.2	name, 5.9.2
s_editor, 2.18.3	image generation, 2.27.23.3
s_entryDelimiter, 2.18.4	scripting molecular movements, 3.2.4
s_errorFormat, 2.18.5	sdf, 2.27.102.23
s_fieldDelimiter, 2.18.6	file, 2.27.76.45, 2.27.76.46, 2.27.81.40, 2.27.102.11, 2.28.142.2, 5.8.3
s_helpEngine, 2.18.7	to chem-table, 2.28.97
s_icmPrompt, 2.18.10	search for chemical pattern, 2.28.49.3
s_icmhome, 2.18.8, 3.1.2.1	pdb headers, 3.4.5
s_imageViewer, 2.18.11	prosite, 3.4.1
s_inxDir, 2.18.9	sequence pattern, 2.27.34.8
s_javaCodeBase, 2.18.12	searchObjSegment, 2.29.72
s_labelHeader, 2.18.13	searchPatternDb, 2.29.70
s_lib, 2.18.14	searchPatternPdb, 2.29.71
s_logDir, 2.18.15	searchSeqDb, 2.29.73
s_out, 2.18.16	searchSeqFullPdb, 2.29.75
s_pdbDir, 2.18.17	searchSeqPdb, 2.29.74
s_pdbDirFtp, 2.18.18	searchSeqProsite, 2.29.76
s_pdbDirWeb, 2.18.19	searchSeqSwiss, 2.29.77
s_printCommand, 2.18.21	searches and alignments, 3.4
s_projectDir, 2.18.20	second moments, 2.28.149
s_prositeDat, 2.18.22	secondary structure derivation from 3D, 2.27.5.1
s_psViewer, 2.18.23	segMinLength, 2.15.19
s_reslib, 2.18.24	segment, 5.9.4
s_skipMessages, 2.18.25	select, 2.27.80
s_sysCp, 2.18.26	atoms by number of bonded atoms, 2.28.125.3
s_sysLs, 2.18.27	of the fixed torsions, 2.28.125.2
s_sysMv, 2.18.28	by bfactor, 2.28.125.7
s_sysRm, 2.18.29	center of mass, 2.28.125.14
s_tempDir, 2.18.30	coordinates, 2.28.125.7
s_translateString, 2.18.31	iarray, 2.28.125
s_userDir, 2.18.32	length, 2.28.125.13
s_usrlib, 2.18.33	occupancy, 2.28.125.7
s_webEntrezLink, 2.18.34	user field, 2.28.125.7
s_webViewer, 2.18.35	chemical, 2.27.80.1
s_xpdbDir, 2.18.36	lines, 2.27.76.1
sa23, 3.3	tether partners, 2.28.125.12
sampling grid, 2.28.177.2	vw partners, 2.28.125.12
sarray, 2.27.22.6, 5.9.1	selectMinGrad, 2.16.34
transformation in place, 2.27.94.1	selectSphereRadius, 2.16.35
save print, 3.2.6	selected stack conformations, 2.27.22.16
sdf file, 2.27.102.11	selecting by b-factor, 2.28.125
saving graphics to album, 2.27.59.20	y z, 2.28.125
image, 2.27.102.35	columns, 5.10.1
scaffolds, 2.27.50	from clusters, 3.14.6.3
scoring, 3.13.1.4	neighboring elements, 2.28.89
screen X, 2.28.175	residues, 3.3.6
coordinates, 2.28.175	saving, 2.28.59.4
script, 2.28.87.4, 5.9.2	selection, 2.8, 2.28.125, 2.28.125.6
file name, 2.28.48	elements, 2.8.4

functions, 2.8.10	sequenceLine, 2.15.21
gap patching, 2.28.125, 2.28.125.11	sequences, 3.4
level, 2.8, 2.28.167	not in alignments, 2.27.22.22
levels, 2.8.2	set, 2.27.81
simplification, 2.28.125.11	alternative atom, 2.27.81.15
transfer, 2.28.125, 2.28.142.7	area, 2.27.81.1
type, 2.8	atom, 2.27.81.2
types, 2.8.1	background image, 2.27.81.3
variable, 2.22.11	bfactor, 2.27.81.4
atoms, 2.8.8	biological symmetry, 2.27.81.54
functions, 2.8.10	bond topology, 2.27.81.6
molecules, 2.8.6	type, 2.27.81.5
objects, 2.8.5	and formal charges, 2.27.81.6
output, 2.22.14	cartesian, 2.27.81.7
residues, 2.8.7	chain, 2.27.81.8
torsions, 2.8.9	charge, 2.27.81.9
variables, 2.8.9	formal, 2.27.81.10
selections, 2.27.81.29	mmff, 2.27.81.11
in molecular objects, 2.8	chargemmff, 2.27.81.11
seq_ali_project, 2.28.142.5	chiral, 2.27.81.12
sequence, 2.28.158, 2.28.159, 5.9.3	color, 2.27.81.13
alignment, 2.28.5.1, 2.29.2	comment, 2.27.81.14, 2.27.81.15
intro, 1.4.3.3	sequence, 2.27.81.16
analysis intro, 1.4.3	comp_matrix, 2.27.81.17
assembly, 2.27.41.2	current map, 2.27.81.38
belongs to alignment, 2.28.62	object, 2.27.81.41
conservation, 2.28.124.5	directory, 2.27.81.18
distance, 2.28.125	drestraint, 2.27.81.19
matrix from alignment, 2.28.79.8	type, 2.27.81.20
dotplot, 1.4.3.2	electrostatic radii, 2.27.81.67
from pdb, 2.27.59.34	error, 2.27.81.28
identity, 2.29.8	field, 2.27.81.29
intro, 1.4.3	name, 2.27.81.30
modification, 2.28.165	font, 2.27.81.31
neighbor, 2.28.87.3	grob, 2.27.81.32
parray, 5.8.3.2	foreground, 2.27.81.33
pattern, 5.8.4	format, 2.27.81.34
position correspondence, 2.28.146.3	grob, 2.27.81.35
positional weights, 2.27.81.1	coordinates, 2.27.81.35
redundancy removal, 2.27.41.2	label, 2.27.81.35
search, 2.27.34.2	group, 2.27.81.53
selection, 2.27.22.22	column, 2.27.81.21
structure alignment, 2.29.1	hydrogen, 2.27.81.22
to alignment transfer, 2.28.110.3	key, 2.27.81.36
type, 5.9.3	label, 2.27.81.37
sequence-alignment mapping, 2.28.142.4, 2.28.142.5	3d label, 2.27.81.37.4
sequence-structure alignment, 2.28.5.1	chemical, 2.27.81.37.3
output format, 2.15.20, 2.15.21	distance, 2.27.81.37.1
sequenceBlock, 2.15.20	table, 2.27.81.37.2
sequenceColorScheme, 2.19.22	map, 2.27.81.38

molecular variables, 2.27.81.71	setResLabel, 2.29.78
name, 2.27.81.40	setcomp_matrix, 2.27.81.17
sequence, 2.27.81.40.1	setting conf properties, 2.27.81.51
object, 2.27.81.41	setvs_var, 2.27.81.71
occupancy, 2.27.81.42	sfWeight, 2.16.36
plane, 2.27.81.43	sh24, 3.4
property, 2.27.81.44, 2.27.81.45	shadows, 2.21.5.28
chemical view, 2.27.81.45	shell, 3.1, 5.9.5
radii graphical, 2.27.81.74	intro, 1.7.1
randomSeed, 2.27.81.46	progression, 2.27.70
randomize, 2.27.81.46	warning message, 2.28.176
resolution, 2.27.81.47	shineStyle, 2.19.23
site, 2.27.81.23	shininess, 2.16.37
residue, 2.27.81.25	show, 2.27.82, 2.27.82.35
slide, 2.27.81.26	alias, 2.27.82.6
sstructure backbone, 2.27.81.49	aliases, 2.27.82.6
sequence, 2.27.81.50	alignment, 2.27.82.7
to sequence, 2.27.81.50	area, 2.27.82.8
stack, 2.27.81.51	atom, 2.27.82.9
energy, 2.27.81.51, 2.27.86.1	type, 2.27.82.10
stereo, 2.27.81.48	atoms, 2.27.82.9
swiss, 2.27.81.52	clash, 2.27.82.11
name, 2.27.81.52	color, 2.27.82.12
symmetry, 2.27.81.55	column, 2.27.82.13
bio, 2.27.81.54	comp_matrix, 2.27.82.14
crystal, 2.27.81.53	database, 2.27.82.15
group, 2.27.81.53	drestraint, 2.27.82.16
to a torsion, 2.27.81.55	type, 2.27.82.17
table, 2.27.81.56	energy, 2.27.82.18
terms, 2.27.81.57	gradient, 2.27.82.19
tether, 2.27.81.58	hbond, 2.27.82.20
append, 2.27.81.59	exact, 2.27.82.21
texture, 2.27.81.27	hbondexact, 2.27.82.21
type, 2.27.81.60	html, 2.27.82.22
mmff, 2.27.81.65	iarray, 2.27.82.23
molecule, 2.27.81.63	integer, 2.27.82.24
object, 2.27.81.62	key, 2.27.82.3
property, 2.27.81.61	label, 2.27.82.25
sequence, 2.27.81.64	library, 2.27.82.26
variable grid, 2.27.81.72	link, 2.27.82.27
variablegrid, 2.27.81.72	logical, 2.27.82.28
view, 2.27.81.68	map, 2.27.82.4
vrestraint, 2.27.81.69	mol, 2.27.82.29
vrestraintvs_var, 2.27.81.70	mol2, 2.27.82.30
radii, 2.27.81.66	molecule, 2.27.82.31
vwelradii, 2.27.81.67	molecules, 2.27.82.5
vwradii, 2.27.81.66	object, 2.27.82.32
window, 2.27.81.73	pdb, 2.27.82.33
xstick, 2.27.81.74	pharmacophore type, 2.27.82.49
radii, 2.27.81.74	preferences, 2.27.82.34

residue, 2.27.82.36	to chem-table element, 2.28.97
type, 2.27.82.37	smooth alignment, 2.28.134.3
residuetype, 2.27.82.37	interpolation, 2.27.86.3
segment, 2.27.82.38	map, 2.28.134.4
sequence, 2.27.82.39	rarray, 2.28.134.1
shell variable, 2.27.82.2	surface, 2.29.85
site, 2.27.82.1	soap, 2.25
stack, 2.27.82.40	soft trim, 2.28.164
svariable, 2.27.82.2	solubility, 2.28.102
table, 2.27.82.41	solvation, 2.19.24
as database, 2.27.82.15	energy, 2.16.36, 2.19.24
term, 2.27.82.42	solvent accessible area, 2.15.22
tethers, 2.27.82.43	surface, 2.21.5.47, 2.21.5.48, 2.27.82.8
version, 2.27.82.44	sort, 2.27.83, 2.27.83.3
volume, 2.27.82.47	array, 2.27.83.1
map, 2.27.82.48	arrays, 2.27.83.1
volumemap, 2.27.82.48	molecules, 2.27.83.4
vrestraint, 2.27.82.45	object, 2.27.83.3
type, 2.27.82.46	stack, 2.27.83.5
vrestraints, 2.27.82.45	table, 2.27.83.2
showcomp_matrix, 2.27.82.14	sortSeqByLength, 2.29.79
showing weak hydrogen bonds, 2.21.5.19	space transformations, 2.28.162
side chain, 2.29.87	sparse atoms, 2.21.14.2
flexibility, 2.29.87	spawn background job, 2.27.59.1
sigma level, 2.21.7.5	special values, 2.28.154
signal recognition measure, 2.29.21	specificity, 2.28.124.2
similar chains, 2.28.125.13	split, 2.27.84
similarity, 2.27.34.9, 2.27.34.10	column values, 2.27.84.4
simple expressions, 2.9.1.1	grob, 2.27.84.1
string substitution, 2.28.114.2	group, 2.27.84.2
simplify mesh structure, 2.27.15.1	object, 2.27.84.5
simulation duration, 2.16.44	to molecules, 2.27.84.5
temperature, 2.16.43	table, 2.27.84.3
intro, 1.4.2	cell, 2.27.84.4
site, 2.27.11.2, 5.9.6	to columns, 2.27.84.3
arrows, 2.27.81.23	tree, 2.27.84.6
table, 2.28.146.8	splitting selection, 2.8.11
by residue selection, 2.27.22.23	sprintf, 2.27.85
sequences, 2.28.146.8	sql, 2.27.73, 2.27.81.39, 2.28.43.1, 2.28.87.10, 2.28.90.5, 2.28.167.2
sixthe power, 2.19.5	sqlite, 3.5.1
skin, 5.9.7	sqrt, 2.28.34
intro, 1.4.1.2	square matrix to element pairs, 2.28.146.5
slide, 2.27.1.3, 2.28.132, 5.9.14	ssThreshold, 2.16.38
transition time, 2.27.23.21	ssWeight, 2.16.39
slides, 2.28.175	ssbond, 5.4.5
slideshow, 2.27.1.3, 2.27.23.21, 2.28.132	ssearch, 2.15.16, 2.27.87
sln, 5.9.8	ssearchStep, 2.16.40
smallest set of smallest rings, 2.28.118	ssign sstructure segment, 2.27.5.2
smarts, 2.28.62.1	stack, 2.15.11, 2.15.12, 2.15.14, 2.19.6, 2.27.81.51, 2.27.86, 2.27.86.1, 2.28.59.6, 2.28.146.6, 5.3.11, 5.9.9
smiles, 2.24	bin size, 2.27.14

extension, 2.27.4.2	minimize, 2.27.90
multiplication, 2.27.4.2	support, 1.3
merge, 3.7.7	suppressing view changes, 2.27.23.21
standard chemical form, 2.27.63.4	surface, 5.9.15
deviation, 2.28.121	accessibility, 2.27.82.8
standardize chemical, 2.27.63	area, 2.29.3, 5.9.15
startup, 3.1.2.3	charge, 5.8.13
static RMSD, 2.28.141	color, 2.27.81.13
and dynamic hbonds, 2.21.5.18	dot density, 2.21.5.47
stereo, 2.21.5.44, 2.27.29, 2.27.81.48	energy, 2.19.24
reconstruction, 3.8.9	mesh, 2.28.177.2
stereoisomer, 2.27.29	point selection, 2.28.177
stereoisomers, 2.17.16	term, 2.16.36
stick, 5.9.10	surfaceAccuracy, 2.15.22
store, 2.27.86	surfaceMethod, 2.19.24
conf, 2.27.86, 2.27.86.1	surfaceTension, 2.16.41
frame, 2.27.86.3	svariable, 5.9.12
image, 2.27.59.20	swapping protein fragments, 3.8.7
stack object, 2.27.86.2	swiss, 2.27.81.52
torsion type, 2.27.86	swissFields, 2.22.9
strength of hydrogen bond, 2.27.23.14	swissprot, 2.27.81.23
string, 5.9.11	symmetrization of a matrix, 2.28.79.3
array, 2.28.123, 5.9.1	symmetry, 2.28.162
filtering, 2.28.164	faq, 3.10
inversion, 2.28.142.1	group, 2.15.2
label, 2.27.23.12	sys, 2.27.91
matching, 2.9, 2.28.78	system, 5.11.2
variables, 2.18	command, 2.27.91
strings, 2.18	copy, 2.18.26
strip, 2.27.88	file move, 2.18.28
struct, 2.28.87.2	list file, 2.18.27
structural alignment, 2.27.3.4, 2.28.5.2	remove, 2.18.29
optimization, 2.27.34.1	table, 2.27.22.4, 2.27.81.44, 2.27.81.45, 5.10.1
superposition, 2.27.3.4	actions, 5.10.2.4
analysis, 3.3	column, 2.28.87
comparison, 2.28.22.2	format, 2.27.81.34
factors, 3.11.1	plot, 2.27.59.31
structure, 3.11.1	transformations, 2.28.92
sub-alignment to selection, 2.28.116	creation, 2.27.41.3
sub-matrix, 2.28.79.2	display style, 5.10.1
subalignment, 2.28.5.3	expression, 5.10.2
submap, 2.28.75	from matrix, 2.28.146.4
subroutine, 2.27.58	grid view, 5.10.1
subset, 2.6	of atoms and distances, 2.28.146.9
substring, 2.28.78, 2.28.142, 2.28.142.1	operations, 5.10.2.1
substructure, 2.27.34.9, 2.27.34.10	plot, 5.10.2.3
search, 2.27.34.4	principal component analysis, 2.27.59.28
superimpose, 2.21.14, 2.27.89	print, 2.27.82.41
faq, 3.3.1	row, 2.27.65.4
how to, 3.3.1	label mark, 2.27.81.37.2

selected row numbers, 2.28.62	transforming points, 2.28.177.4
subset, 5.10.2.2	translate, 2.27.95
show html, 2.27.100.1	transparency, 2.27.81.35, 5.5.3
targa, 5.10.3	background, 2.27.102.35
tautomer, 2.27.30	grob, 2.27.23.11
tempCycle, 2.16.43	grobs, 2.21.5.49
tempLocal, 2.16.42	tree, 2.27.59.35, 2.28.87.5
temperature, 2.16.43	cluster, 2.10
variations in optimizer, 2.16.43	delete, 2.27.22.33
template docking, 3.13.2.8	label format, 2.28.87.5
tensor product of two vectors, 2.28.79	representatives, 2.10.1
terminal font, 2.30.14	trim string array, 2.27.94.1
window, 2.27.42	trimming grid map values, 2.28.164
terms, 2.14	true positives, 2.28.124.2
hydrogen bonding, 2.16.18	truncate alignment, 2.27.59.33
test, 2.27.92	values, 2.28.164
binary, 2.27.92.1	tsv table format, 2.27.76.41
testing if argument exists, 2.28.52	two alignments, 2.28.38.11
tether, 2.27.102.9, 5.10.4	txdoc browser, 2.27.76.3
text, 2.28.78	type, 2.28.167.1
search in tables, 2.28.49.2	tzMethod, 2.19.25
to script, 5.9.2	tzWeight, 2.16.47
texture, 5.5.3	uncharge functional groups, 2.27.63.2
tga, 5.10.3	unclip, 2.27.23.2
then, 2.27.93	underline, 2.27.81.31.1
thread to template, 2.27.60.4	undisplay, 2.27.96
threading, 2.28.5.1	graphics, 2.27.97
letter code, 2.28.158, 2.28.159	window, 2.27.97
thumbnails, 2.28.61	unfix, 2.27.98
tif, 5.10.5	unique, 2.27.13.1, 5.11.1
time, 2.28.35	atomic order, 2.27.59.36
timeLimit, 2.16.44	column values, 2.27.41.4
tolFunc, 2.16.46	names, 2.28.87
tolGrad, 2.16.45	new object name, 2.28.87
topological psa, 5.8.12	smiles, 2.27.59.36
torsion rmsd comparison, 2.27.14.2	unix, 2.27.91, 5.11.2
torsions, 2.28.90.3	grep, 2.27.76.1
tpsa, 5.8.12	unlink alignments, 2.27.22.20
trajectory, 2.27.57.2, 2.27.86, 2.27.86.3, 5.7.14	sequences, 2.27.22.20
file, 2.30.17	variables, 2.27.22.20
frame writing, 2.27.23.17	update database, 2.27.63.5
smoothing, 2.27.23.17	updates, 1.1
transform, 2.27.94, 2.27.94.2	updating atom pairs, 2.17.27
general, 2.27.94	url string parsing, 2.28.146
grob coordinates, 2.27.94.2	user atom display, 2.21.5.2
molecules, 2.27.94.2	environment, 3.1.2.2
sarray, 2.27.94.1	menu, 2.21.10.1
transformation, 5.10.6	user-defined properties, 2.27.81.29
vector, 5.10.6	solvation parameters, 2.28.7
and symmetry, 3.10	user_startup, 3.1.2.4

guide, 3	vwMethod, 2.19.28
v_, 2.8.1	vwSoftMaxEnergy, 2.16.52
van der Waals surface, 2.21.5.48	wait, 2.27.99
varLabelStyle, 2.19.26	warning, 2.21.14.2
variable restraint, 2.27.81.69	message, 2.28.176
selection, 2.8.9	suppression, 2.17.28
vector, 2.28.90.6	water.dielectric constant, 2.16.12
dot product, 2.28.172.1	waterRadius, 2.16.53
length, 2.28.91	wavefront format, 2.27.59.11
product, 2.28.172.1	web, 2.27.100
transformation, 2.28.92	table, 2.27.100.1
vertex, 2.27.13.4.2	webEntrezOption, 2.19.29
connectivity, 2.28.79.12	weighted rmsd, 2.21.14
vertexes, 2.27.13.4.2	while, 2.27.101
vertical alignment block, 2.27.59.33	whole string, 2.28.114.1
workspace, 2.21.8.5	window averaging, 2.28.134.1
vertices, 2.27.13.4.2	layout, 2.28.142.8
vicinity, 2.16.48	width and height, 2.28.175
video, 2.27.102.30	windowSize, 2.15.23
view point, 2.28.175	movie, 2.27.102.30
restoration, 2.28.65	wire, 5.11.7
transition, 2.27.81.68	wireBondSeparation, 2.16.54
views, 5.9.14	wireStyle, 2.19.30
virtual, 5.11.3	workspace, 2.27.97
chemistry, 2.27.63, 2.28.90.4	write, 2.27.102
field, 2.27.7.2	album, 2.27.102.21
ligand screening, 3.13, 3.13.1, 3.13.2, 3.13.3	alignment, 2.27.102.1
intro, 1.4.2.7	array, 2.27.102.8
visitsAction, 2.19.27	table, 2.27.102.8
vls, 3.13, 3.13.1, 3.13.2, 3.13.3	binary, 2.27.102.2
cluster, 3.13.3.6	blast, 2.27.102.24
faq, 3.13.3	column, 2.27.102.12
intro, 1.4.2.7	database, 2.27.102.13
job queueing, 3.13.3.6	drestraint, 2.27.102.14
overview, 3.13.1	type, 2.27.102.15
parallelization, 3.13.3.5	factor, 2.27.102.16
results, 3.13.3.8	gamess, 2.27.102.17
scores storage, 3.13.3.7	grob, 2.27.102.18
threshold, 3.13.3.2	html, 2.27.102.19
vls_intro, 3.13.3.1	iarray, 2.27.102.3
volume, 5.11.4	image, 2.27.102.20
vrestraint, 5.11.5	chemical, 2.27.102.22
file, 2.30.23	parray, 2.27.102.21
type, 5.11.6	index, 2.27.102.23
file, 2.30.22	blast, 2.27.102.24
vs_, 2.8.9	library, 2.27.102.25
vs_out, 2.22.14	map, 2.27.102.26
vwCutoff, 2.16.49	matrix, 2.27.102.6
vwExpand, 2.16.50	model, 2.27.102.27
vwExpandDisplay, 2.16.51	mol, 2.27.102.28

molcart, 2.27.102.7
movie, 2.27.102.30
object, 2.27.102.31
parray, 2.27.102.33
simple, 2.27.102.32
pdb, 2.27.102.34
png, 2.27.102.35
postscript, 2.27.102.36
pov, 2.27.102.37
povray, 2.27.102.37
project, 2.27.102.2
rarray, 2.27.102.4
sarray, 2.27.102.5
sequence, 2.27.102.38
session, 2.27.102.39
several array, 2.27.102.8
simple object, 2.27.102.32
stack, 2.27.102.40
table, 2.27.102.10
mol, 2.27.102.11
with links, 2.27.102.19
tether, 2.27.102.9
tethers, 2.27.102.9
trajectory, 2.27.23.17
vs_var, 2.27.102.41
writevs_var, 2.27.102.41
xml, 2.28.78
xplor format, 2.27.76.26
xrMethod, 2.19.31
xrWeight, 2.16.55
xray density to rectangular energy map, 2.27.59.30
xstick, 5.11.8
xyz morphing, 3.8.8
zega, 5.11.9
intro, 1.4.3.6
\|, 2.11.3

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