Index

&, 2.11.3	Color, 2.27.28
2D labels, 2.26.51.1	from gradient, 2.27.28.1
3D font size, 2.26.21.12	image, 2.27.28.2
label, 2.26.21.12, 2.26.79.31	Connolly surface, 5.8.7
labels, 2.26.51.1	Consensus, 2.27.29
mol file, 2.28.91	Corr, 2.27.30
plots intro, 1.4.3.7	Cos, 2.27.31
smoothing, 2.27.134.2	Cosh, 2.27.32
superposition, 2.28.25	Count, 2.27.33
transformations, 2.26.92.2	D, 5.4
=, 2.11.1	DE, 2.26.32.2
A, 5.1	DNA Representation, 1.4.1.3
Abs, 2.27.1	alignment, 2.26.3.3
Acc, 2.27.2	melting temperature, 2.27.150
Acos, 2.27.3	views, 1.4.1.3
Acosh, 2.27.4	Date, 2.27.34
Align, 2.27.5	Deletion, 2.27.35
sequence, 2.27.5.1	Det, 2.27.36
Angle, 2.27.6	Disgeo, 2.27.37
Area, 2.27.7	Distance, 2.27.38
residue contacts, 2.27.7.1	2 alignments, 2.27.38.11
Asin, 2.27.8	matrixes, 2.27.38.7
Asinh, 2.27.9	Dayhoff, 2.27.38.9
Ask, 2.27.10	Tanimoto, 2.27.38.6
Askg, 2.27.11	alignment, 2.27.38.10
Atan, 2.27.12	as_, 2.27.38.3
Atan2, 2.27.13	rarray, 2.27.38.4
Atanh, 2.27.14	atoms, 2.27.38.3
Atom, 2.27.15	chemical, 2.27.38.6, 2.27.38.13
Augment, 2.27.16	dayhoff, 2.27.38.9
Axis, 2.27.17	iarray, 2.27.38.1
B, 5.2	alignment, 2.27.38.10
BPMC, 5.2.5	matrix, 2.27.38.5, 2.27.38.7
Bfactor, 2.27.18	multiple atomic, 2.27.38.4
Boltzmann, 2.27.19	rarray, 2.27.38.2
Box, 2.27.20	tether, 2.27.38.8
Bracket, 2.27.21	tree, 2.27.38.12
C, 5.3	cluster, 2.27.38.12
CCP4, 5.6.6	H, 5.5
CONSENSUS, 2.20.1	EDS server, 2.28.46
CONSENSUSCOLOR, 2.20.2	EST-alignment, 2.26.3.3
CONSENSUS_strength, 2.16.9	Eigen, 2.27.39
Cad, 2.27.22, 2.27.22.1, 2.27.22.2	Energy, 2.27.40
Cad1, 2.27.22.1	Error, 2.27.41
Cadalign, 2.27.22.2	soap, 2.27.42
Ceil, 2.27.23	Exist, 2.27.43
Cell, 2.27.24	molcart, 2.27.43.1
Charge, 2.27.25	Existenv, 2.27.44
Chemical, 2.27.26	Exp, 2.27.46
Cluster, 2.27.27	Extension, 2.27.45

Z, 2.20.3.1	ribbonWidth, 2.20.5.32
gz, 2.20.3.2	ribbonWorm, 2.20.5.33
uue, 2.20.3.3	rocking, 2.20.5.34
FTP, 2.20.4	rockingRange, 2.20.5.35
createFile, 2.20.4.1	rockingSpeed, 2.20.5.36
keepFile, 2.20.4.2	selectionLevel, 2.20.5.37
proxy, 2.20.4.3	selectionStyle, 2.20.5.38
Field, 2.27.47, 2.27.47.1	stereoMode, 2.20.5.39
user, 2.27.47.1	stickRadius, 2.20.5.20, 2.20.5.40
File, 2.27.48	surfaceDotDensity, 2.20.5.42
Find, 2.27.49	surfaceDotSize, 2.20.5.41
chemical, 2.27.49.3	surfaceProbeRadius, 2.20.5.43
pattern, 2.27.49.3	transparency, 2.20.5.44
in array, 2.27.49.1	wormRadius, 2.20.5.45
table, 2.27.49.2	GRID, 2.20.6
FlexLM license info, 2.27.173	gcghExteriorPenalty, 2.20.6.1
Floor, 2.27.50	gpGaussianRadius, 2.20.6.6
Formula, 2.27.51	margin, 2.20.6.2
GRAPHICS, 2.20.5	maxEl, 2.20.6.3
atomLabelShift, 2.20.5.1	maxVw, 2.20.6.5
ballRadius, 2.20.5.2, 2.20.5.20	minEl, 2.20.6.4
ballStickRatio, 2.20.5.3	GROB, 2.20.7
chainBreakLabelDisplay, 2.20.5.6	arrowRadius, 2.20.7.3
chainBreakStyle, 2.20.5.5	atomSphereRadius, 2.20.7.1
clashWidth, 2.20.5.4	contourSigmaIncrement, 2.20.7.5
displayLineLabels, 2.20.5.7	relArrowHead, 2.20.7.4
displayMapBox, 2.20.5.8	relArrowSize, 2.20.7.2
dnaBallRadius, 2.20.5.9	GUI, 2.20.8
dnaRibbonRatio, 2.20.5.10	dialog customize programming, 2.25
dnaRibbonWidth, 2.20.5.11	plot, 2.26.57.31
dnaRibbonWorm, 2.20.5.12	tableRowMarkColors, 2.20.8.1
dnaStickRadius, 2.20.5.13	workspaceFolderStyle, 2.20.8.4
formalChargeDisplay, 2.20.5.14	workspaceStyle, 2.20.8.2
grobLineWidth, 2.20.5.15	workspaceTabStyle, 2.20.8.3
hbondAngleSharpness, 2.20.5.18	Getarg, 2.27.52
hbondMinStrength, 2.20.5.17	Getenv, 2.27.53
hbondStyle, 2.20.5.16	Gradient, 2.27.54
hbondWidth, 2.20.5.19	Graphics, 1.4.1
hetatmZoom, 2.20.5.20	Grob, 2.27.55
hydrogenDisplay, 2.20.5.21	Group, 2.27.56
light, 2.20.5.22	Header, 2.27.57
lightPosition, 2.20.5.23	Histogram, 2.27.58
mapLineWidth, 2.20.5.24	N, 5.6
occupancyDisplay, 2.20.5.25	ICM documents, 2.26.74.3
occupancyRadiusRatio, 2.20.5.26	modules, 1.4.4
quality, 2.20.5.27, 2.27.81.1	object, 2.28.14
rainbowBarStyle, 2.20.5.28	ICM-shell, 3.1, 5.8.5
resLabelDrag, 2.20.5.29	intro, 1.7.1
resLabelShift, 2.20.5.30	script, 2.26.8
ribbonRatio, 2.20.5.31	ICMHOME, 3.1.2.1

IMAGE, 2.20.9	LD_ASSUME_KERNEL, 1.3.1.1
bondLength2D, 2.20.9.15	LIBRARY, 2.20.10
color, 2.20.9.8	res, 2.20.10.1
compress, 2.20.9.9	Label, 2.27.70
gammaCorrection, 2.20.9.7	Length, 2.27.71
generateAlpha, 2.20.9.10	LinearFit, 2.27.72
lineWidth, 2.20.9.3	LinearModel, 2.27.73
lineWidth2D, 2.20.9.14	Link, 2.27.74
orientation, 2.20.9.16	Log, 2.27.75
paperSize, 2.20.9.17	LogP, 2.27.103
previewResolution, 2.20.9.13	LogS, 2.27.103
previewer, 2.20.9.12	M_out, 2.21.5
printerDPI, 2.20.9.2	Map, 2.27.76
quality, 2.20.9.1	Markush structures, 2.26.48
rgb2bw, 2.20.9.18	Mass, 2.27.77
scale, 2.20.9.4	Match, 2.27.79
stereoAngle, 2.20.9.6	Mathews, 2.27.124.2
stereoBase, 2.20.9.5	Matrix, 2.27.80
stereoText, 2.20.9.11	alignment, 2.27.80.7
writeScale, 2.20.9.19	boundary, 2.27.80.8
I_out, 2.21.4	histogram, 2.27.80.10
Iarray, 2.27.59, 2.27.59.4, 2.27.59.5	new, 2.27.80.1
atom numbers, 2.27.59.4	residue areas, 2.27.80.6
bits to integers, 2.27.59.3	comparison, 2.27.80.4
inverse, 2.27.59.2	stack, 2.27.80.9
residue numbers, 2.27.59.5	sub, 2.27.80.2
reverse, 2.27.59.2	symmetrical, 2.27.80.3
stack, 2.27.59.6	tensor, 2.27.80.5
Icm Options, 2.1	Max, 2.27.81
IcmSequence, 2.27.60	image graphic, 2.27.81.1
Image, 2.27.61	MaxHKL, 2.27.82
collection, 3.9.2.1	Mean, 2.27.83
frame by frame, 3.9.2.2	Method, 2.19.12
Index, 2.27.62	Min, 2.27.84
chemical, 2.27.62.1	Mod, 2.27.86
element in array, 2.27.62.7	Mol, 2.27.87
regexp, 2.27.62.3	Moment, 2.27.78
string, 2.27.62.2	of Inertia, 2.27.78
table label, 2.27.62.5	Money, 2.27.85
selection, 2.27.62.4	NOE averaging, 2.19.5
tree, 2.27.62.8	Name, 2.27.88
unique elements, 2.27.62.6	chemical, 2.27.88.5
Indexx, 2.27.63	property, 2.27.88.1
Info, 2.27.65	close sequence, 2.27.88.2
image, 2.27.66	image, 2.27.88.8
Insertion, 2.27.64	molcart, 2.27.88.9
Integer, 2.27.67	object parray, 2.27.88.7
Integral, 2.27.68	sequence, 2.27.88.6
Interrupt, 2.27.69	string, 2.27.88.3
Introduction, 1	tree, 2.27.88.4

image, 2.27.89.2	faq, 3.7.2
sequence, 2.27.89.1	file, 2.26.48
Newick tree format, 2.27.142.3	R_2out, 2.21.7
Next, 2.27.90, 2.27.90.1	R_out, 2.21.6
covalent neighbors, 2.27.90.1	Radius, 2.27.109
Nof, 2.27.91	Random, 2.27.110
chemical, 2.27.91.2	string, 2.27.110.1
library, 2.27.91.3	Rarray, 2.27.111
molcart, 2.27.91.4	reverse, 2.27.111.2
soap, 2.27.91.5	sequence projection, 2.27.111.1
tree, 2.27.91.1	alignment projection, 2.27.111.3
Norm, 2.27.92	strength, 2.27.111.5
Normalize, 2.27.93	property assignment, 2.27.111.4
NotInList, 2.27.94	RarrayAlignment, 2.27.111.5
R, 5.7	Rarrayinverse, 2.27.111.2
OBJECT, 2.20.11	Real, 2.27.112
Obj, 2.27.95	array, 2.27.111
Occupancy, 2.27.96	Reference, 2.27.114
PBS, 3.13.3.6	Guide, 2
PLOT, 2.20.12	Remainder, 2.27.113
Yratio, 2.20.12.5	Replace, 2.27.115
box, 2.20.12.13	chemical, 2.27.115.4
color, 2.20.12.7	exact, 2.27.115.1
font, 2.20.12.10	regexp, 2.27.115.3
fontSize, 2.20.12.2	simple, 2.27.115.2
labelFont, 2.20.12.11	Res, 2.27.116, 2.27.117
lineWidth, 2.20.12.3	Resali, 2.27.117
logo, 2.20.12.6	Resolution, 2.27.118
markSize, 2.20.12.4	Rfactor, 2.27.119
numberOffset, 2.20.12.1	Rfree, 2.27.120
orientation, 2.20.12.8	Rmsd, 2.27.121
rainbowStyle, 2.20.12.12	of subset, 2.20.14
seriesLabels, 2.20.12.9	Rot, 2.27.122
error, 2.27.124.2	S, 5.8
models, 2.27.124.2	SAR analysis, 2.26.57.27, 2.26.82.2
Parray, 2.27.98	SC, 2.26.32.2
Parray-object, 2.27.98	SITE, 2.20.13
Path, 2.27.97	defSelect, 2.20.13.1
Pattern, 2.27.99	labelOffset, 2.20.13.2
Pi, 2.27.100	labelStyle, 2.20.13.3
Potential, 2.27.101	labelWrap, 2.20.13.4
Power, 2.27.102	showSeqSkip, 2.20.13.5
Predict, 2.27.103	wrapComment, 2.20.13.6
Probability, 2.27.104	SLN notation, 2.27.142.9
Profile, 2.27.105	SMARTS, 2.23, 2.27.91.2
Property, 2.27.106	SOAP, 2.27.91.5
Putarg, 2.27.107	request message, 2.27.138
Putenv, 2.27.108	SVM models quality, 2.27.124.2
R-groups, 2.26.48	S_out, 2.21.8
REBEL, 3.7.2	Sarray, 2.27.123

Score, 2.27.124	substring, 2.27.142.1
alignment, 2.27.124.6	chemical formula, 2.27.142.9
conservation, 2.27.124.5	Sum, 2.27.144
model, 2.27.124.2	chemical, 2.27.144.1
overlap, 2.27.124.1	image, 2.27.144.2
predictions, 2.27.124.3	Swissprot, 2.26.100.22
sequence, 2.27.124.4	Symgroup, 2.27.145
Select, 2.27.125	T, 5.9
break, 2.27.125.1	TOOLS, 2.20.14
atom property, 2.27.125.7	edsDir, 2.20.14.1
nmembers, 2.27.125.4	pdbReadNmrModels, 2.20.14.2
string, 2.27.125.9	superimposeMaxDeviation, 2.20.14.5
expand, 2.27.125.6	superimposeMaxIterations, 2.20.14.3
fix, 2.27.125.2	superimposeMinAtomFraction, 2.20.14.4
graphical, 2.27.125.5	tsWeight, 2.20.14.6
neighbors, 2.27.125.3	Table, 2.27.146
Select_by atom numbers, 2.27.125.10	alignment numbers, 2.27.146.3
Select_by_text, 2.27.125.9	matrix, 2.27.146.4
Select_lists, 2.27.125.12	model, 2.27.146.6
Select_patching, 2.27.125.11	stack, 2.27.146.5
Select_projection, 2.27.125.8	url_decoder, 2.27.146.1
Sequence, 2.27.126	Table(alignment), 2.27.146.2
array, 2.27.126.2	Table(stack), 2.27.146.5
Sequence(dna reverse), 2.27.126.1	Tan, 2.27.147
Shuffle, 2.27.127	Tanh, 2.27.148
Sign, 2.27.128	Tanimoto, 2.27.59.3
Simulations, 1.4.2	distance, 2.26.57.35
Sin, 2.27.129	matrix, 2.27.38.6
Sinh, 2.27.130	Temperature, 2.27.150
Site, 2.27.131	Tensor, 2.27.149
Slide, 2.27.132	Time, 2.27.151
Smiles, 2.27.133	Tointeger, 2.27.152
Smooth, 2.15.23, 2.27.134, 2.27.134.1, 2.27.134.2	Tolower, 2.27.153
Smoothrs, 2.27.134.2	Toreal, 2.27.154
SoapMessage, 2.27.138	Torsion, 2.27.155
Sort, 2.27.139	Tostring, 2.27.156
Sphere, 2.27.137	Toupper, 2.27.157
Split, 2.27.140	Tr123, 2.27.158
chemical, 2.27.140.3	Tr321, 2.27.159
regexp, 2.27.140.2	Trace, 2.27.160
tree, 2.27.140.1	Trans, 2.27.161
Sql, 2.27.135	Transform, 2.27.162
Sqrt, 2.27.136	Transpose, 2.27.163
Srmsd, 2.27.141	Trim, 2.27.164
Sstructure, 2.27.143	sequence, 2.27.165
String, 2.27.142, 2.27.142.7	Turn, 2.27.166
alternative, 2.27.142.6	Type, 2.27.167
mol, 2.27.142.2	molcart, 2.27.167.1
selection, 2.27.142.7	Z, 5.10
slide gui, 2.27.142.8	Unique, 2.27.168

Uppsala, 2.28.46	column, 2.26.1.1
server, 2.28.47	function, 2.26.1.1.1
V_, 2.8.1	matrix, 2.26.1.2
Value, 2.27.170	rows to a table, 2.26.1.4
soap, 2.27.171	slide, 2.26.1.3
Vector, 2.27.16, 2.27.172, 2.27.172.1	table, 2.26.1.4
symmetry transformation, 2.27.172.2	addBfactor, 2.16.1
Vectorproduct, 2.27.172.1	adding atoms to non-ICM objects, 2.26.7.1
Vectorsymmetrytransformation, 2.27.172.2	columns to table, 2.26.1.1
Version, 2.27.173	hydrogens, 2.28.14
View, 2.27.175	in place, 2.11.4
Volume, 2.27.174	to slideshow, 2.26.1.3
WEBAUTOLINK, 2.20.16	admet selection, 3.13.3.4
WEBLINK, 2.20.15	advanced chemical search, 3.6
Warning, 2.27.176	operations, 2.11.6
Wavefront format, 2.26.74.20	ops, 2.11.6
Xyz, 2.27.177	ali_seq_project, 2.27.142.4
axes, 2.27.177.7	alias, 2.26.2
chemical match, 2.27.177.5	align, 2.26.3
fract, 2.27.177.3	3D, 2.26.3.4
mesh, 2.27.177.2	faq, 3.3.2
points, 2.27.177.1	heavy, 2.26.3.5
transformed xyz, 2.27.177.4	how to, 3.3.2
vector2matrix, 2.27.177.6	chemical, 2.26.78.1
ZEGA, 5.10.8	fragments, 2.26.3.3
intro, 1.4.3.6	intro, 1.4.3.3
_chemBatch, 3.1.2.5	number, 2.26.3.1
_dockScan, 3.13.2.6	res numbers, 2.26.3.1
_macro, 2.29.1	sequence, 2.26.3.2
file, 2.29.1	sequences, 2.26.3.2
_startup, 3.1.2.3	alignMethod, 2.19.2
file, 2.29.2	alignMinCoverage, 2.16.2
icm, 2.29.2	alignMinMethod, 2.16.2
a_, 2.8.1	alignOldStatWeight, 2.16.3
abbr, 1.6	alignSS, 2.28.1
abbreviations, 1.6	alignTwoSequences, 2.28.2
absolute to fractionals, 2.27.177.3	aligned residues, 2.27.117
accFunction, 2.21.2	alignment, 5.1.1
acceptor, 3.6.1	as table, 2.27.146.2
access large sdf file, 2.26.74.22	block length, 2.15.21
accessMethod, 2.19.1	secondary structure, 2.28.1
accessible residues, 3.3.6	cleaning, 2.27.134.3
surface, 2.26.57.14, 5.8.15	coloring, 2.18.1
accessing sections, 2.26.100.22	editor, 2.4
accuracy, 2.27.124.2	extraction, 2.27.5
activate fog, 2.26.21.24	gap format, 5.1.1.1
alignment, 2.26.79.32	intro, 1.4.3.4
document, 2.26.79.32	projection, 2.27.142, 2.27.142.4, 2.27.142.5
tab, 2.26.79.32	score, 2.27.124.5
add, 2.26.1	sequence reordering, 2.27.5

structural, 2.26.3.4, 2.27.5	segment, 2.15.19, 2.26.5.2
to sequence transfer, 2.27.111.1	assignment, 2.11.1
text conversion, 2.27.142.3	structure, 2.26.5.1
weighted, 2.27.5	atom, 2.26.12.1, 5.1.6
gapExtension, 2.16.15	code file, 2.29.5
gapOpen, 2.16.16	coordinates, 2.27.177.1
alignment_as_text, 2.27.142.3	label font, 2.29.16
aliphatic amines, 2.26.61.2	name, 2.27.70
all, 5.1.2	proximity to surface, 2.26.80.8
torsions table, 3.3.11	selection by number, 2.27.59.4
alpha, 2.20.5.44, 2.26.79.34, 5.1.3	type, 2.27.167
channel, 2.20.9.10	user field, 2.27.47.1
alternative flag, 2.26.79.15	atomLabelStyle, 2.19.3
amber, 5.1.4	atomSingleStyle, 2.19.4
amino acid, 2.27.158, 2.27.159	atomic solvation contributions, 2.27.7
and, 2.11.3	alternative position, 2.26.79.15
angular hbond dependence, 2.20.5.18	selecting, 2.8.8
animated story, 5.8.14	translate, 2.26.79.2
animation, 2.26.21.5, 2.26.21.6, 3.9	attenuation by occupancy, 2.26.57.25
append, 5.1.5	auc enrichment, 2.28.24
a tables, 2.26.1.4	auto saving log, 2.19.10
column, 2.26.4.3	autoSavePeriod, 2.15.1
command, 2.26.4	average hydrophobicity around a pocket, 1.3.1.3
sequence, 2.26.4.1	avi, 2.26.100.29
to group, 2.26.4.1	axis, 5.1.7
stack, 2.26.4.2	axisLength, 2.16.4
tables, 2.26.46	background, 2.27.28.2
by shared column, 2.26.4.3	ball, 5.2.2
appending, 2.26.1.1	base, 5.2.1
an element, 2.11.4	batch chemical processing, 3.1.2.5
representations to a slide, 2.26.21.21	docking, 3.13.2.6
rows to matrix, 2.26.1.2	beta, 5.2.3
area under curve, 2.28.24	binary file table of contents, 2.26.74.2
arithmetic operations, 2.11.2	files, 2.26.100.2
arithmetics, 2.11	key, 2.26.79.35
array, 2.26.63.4, 5.7.3.1	binding energy, 3.7.4
assignment, 2.11.1	pocket finding, 3.4.3
derivative, 2.27.134.1	pockets, 2.26.82.1
overlap, 2.27.124.1	site analysis, 3.4.3
parray, 2.26.20.28	biological symmetry, 2.26.79.8
size, 2.27.91	vector, 2.27.59.3
subset, 2.6	to integers compression, 2.27.59.3
arrow from selection, 2.28.40	blast files, 2.26.100.23
as2_out, 2.21.13	blast-formatted database, 2.26.32.3, 2.26.100.23
as_, 2.8.8	blending, 2.26.100.29
as_graph, 2.20.5.37, 2.20.5.38, 2.27.125.5	images, 2.27.144.2
as_out, 2.21.12	bold, 2.26.79.30.1
assign, 2.26.5	bond angle bending, 2.29.6
ring conformation to template, 2.26.58.4	stretching, 2.29.7
sstructure, 2.26.5.1	to protein, 2.26.63.3

born radii, 2.26.80.8	center, 2.10.1, 2.26.9
boundary element, 5.2.4	chain breaks, 2.20.5.5, 2.20.5.6, 2.27.125.1
matrix, 2.27.80.8	symbol, 2.26.79.8
box, 2.27.20	change atom position, 2.26.79.2
break, 2.26.6	unix directory, 2.26.79.18
brightness, 2.20.5.22	changing local stick radii, 2.26.79.73
build, 2.26.7	surface dot size, 2.20.5.41
atom, 2.26.7.1	charge, 5.3.2
column, 2.26.7.2	compounds, 2.26.61.2
faq, 3.8.1	change, 2.26.79.9
from string, 2.26.7.7	chem formula, 2.27.142.9
helix, 3.10.5	chemSuper3D, 2.28.25
how to, 3.8.1	chemical, 2.22, 2.26.32.9
hydrogen, 2.26.7.8	2D drawings, 2.26.57.9
loop, 2.26.7.5	SMARTS search, 2.26.32.5
model, 2.26.7.4, 2.26.100.9	database, 3.5
molcart, 2.26.7.9	decomposition, 2.26.57.27, 2.26.82.2
sequence, 2.26.7.3	diversity, 3.14.6.3
smiles, 2.26.7.6	drawing, 2.20.9.14
string, 2.26.7.7	quality, 2.20.9.15
buildpep, 2.28.3	formula, 2.27.142.9
built-in functions, 5.5.5	fragment counting, 2.27.91.2
atoms, 2.26.13	keys, 2.26.57.21
contact surface, 2.26.13	match coordinates, 2.27.177.5
molecule, 2.26.12.1	matching, 2.26.32.4, 2.26.74.45, 2.26.74.46, 2.27.121, 2.27.141
number of bonds, 2.27.125.3	models, 2.27.88.1
variables, 2.26.13	modification, 2.26.60, 2.26.61, 2.28.41
calcArea, 2.28.4	name, 2.27.88.5
calcBindingEnergy, 2.28.5	normalization, 2.26.61
calcDihedral4atoms, 2.28.6	rules, 2.26.61.4
calcDihedralAngle, 2.28.7	pattern, 2.23, 2.26.78.1
calcEnergyStrain, 2.28.23	search, 2.27.49.3
calcEnsembleAver, 2.28.8	reaction product generation, 2.26.57.32
calcMaps, 2.28.9	search, 2.26.32.10, 2.26.78.1, 2.27.91.2
calcPepHelicity, 2.28.10	similarity, 3.5
calcProtUnfoldingEnergy, 2.28.11	spreadsheet, 2.26.74.44, 2.26.74.45, 2.26.74.46, 2.26.100.11
calcRmsd, 2.28.12	substructure, 2.26.32.4, 2.27.62.2
calcSeqContent, 2.28.13	mask, 2.26.57.21
calc_nosauc, 2.28.24	superposition, 2.19.6, 2.27.121
calculate phases, 3.11.2	table, 2.22
call, 2.26.8	view, 2.26.79.45
carboxylic acid, 2.26.61.2	chemistry, 2.22, 2.27.26
cartesian cooridnates, 2.27.177	chiral isomer generation, 2.26.27
cartridge, 3.5	chirality, 2.17.16, 2.26.27
cavities, 2.26.82.1	choosing ligands, 3.13.1.2
cavity, 5.3.1	cif, 2.26.74.44
analysis, 3.3.13	clashThreshold, 2.16.5
ccp4 maps, 2.26.74.25	labels, 2.27.152
cd, 2.26.79.18	clear, 2.26.10
cell axis vectors, 2.27.177.7	graphical selection, 2.26.10

click and lock, 5.9.2.4	receptor and ligand stacks, 2.26.4.2
clipping plane, 5.3.3	command, 2.27.88.3, 5.3.9
closest sequence, 2.27.88.2	line editing, 2.2
value, 2.27.49.1	help, 2.26.41
cluster, 2.27.140.1	options, 2.1
center, 2.27.62.8	word list, 3.1.5
centers, 2.10.1	commands, 2.19.10
selection, 2.27.62.8	communication protocols, 2.24
tree, 2.27.88.4	comp, 2.27.94
size, 2.27.91.1	comp_matrix, 2.26.79.17, 2.26.80.14, 5.3.10
clustering, 2.10, 2.26.57.35, 2.26.82.6	compare, 2.15.11, 2.15.14, 2.26.13
clusters, 2.10, 2.10.1	angles, 2.26.13.2
cnMethodAverage, 2.19.5	atom, 2.26.13.1
cnWeight, 2.16.6	by rmsd without superposition, 2.26.13.1
coil, 5.3.4	chemical tables, 2.26.32.10
color, 2.20.5.22, 2.26.11	patch only, 2.26.13.3
accessibility, 2.26.12	rmsd, 2.26.13.1
background, 2.26.12.2	surface, 2.26.13.3
example, 3.2.7	variables, 2.26.13.2
accessibility, 3.2.11	compareMethod, 2.19.6
alignment, 2.26.12.3	comparing two sarrays, 2.27.94
bfactor, 3.2.9	comparison operations, 2.11.5
charge, 3.2.12	complete view, 2.27.132
electrostatic potential, 2.15.5	compound accessibilities, 3.14.4.1
hydrophobicity, 3.2.10	array, 2.22
shape depth, 2.26.12	compress, 2.26.14
chemical, 2.26.78.1	binary, 2.26.14.3
file, 2.29.16	conf, 2.26.14.2
grob, 2.26.12.4	grob, 2.26.14.1
by atom selection, 2.26.12.4.3	in place, 2.26.14.3
atoms, 2.20.7.1	objects, 2.26.14
map, 2.26.12.4.4	stack, 2.26.14.2
matrix, 2.26.12.4.2	compressed table view, 2.26.79.21
potential, 2.26.12.4.5	conditional buttons, 5.5.5
unique, 2.26.12.4.1	string, 2.27.142.6
label, 2.26.12.5	conf, 2.26.79.50, 2.26.100.39, 2.27.146.5, 5.3.11, 5.8.9
map, 2.26.12.6	data, 2.27.146.5
by value, 2.26.21.16	configuration, 2.29.15
molecule, 2.26.12.1	memory usage, 2.15.6
names, 2.27.28	conformation comparison, 2.19.6
object, 2.26.11.2	conformational generator, 2.26.58.1
specification, 2.26.11.1	interpolation, 2.26.21.6
surface by conservation, 2.26.12.3	stack, 2.26.100.39, 5.3.11, 5.8.9
volume, 2.26.12.7	compression, 2.26.14.2
column, 5.3.5	file, 2.29.8
function, 2.26.7.2	transition, 2.28.42
combinatorial compounds, 2.27.26	conformer storage, 2.26.55.5, 2.26.84.2
libraries, 2.26.57.32, 2.27.91.3	connect, 2.26.15
transformations, 3.10.4	molcart, 2.26.15.1
combining plots, 2.26.57.31	consensus, 2.16.7

definitions, 2.20.1	create a covalent bond, 2.26.57.2
consensusStrength, 2.16.7	pharmacophore, 2.28.92
conservation, 2.27.111.5, 2.27.124.5	creating a local patch object, 2.26.17.2
constant, 2.5	credits, 4.5
constants, 2.5	crypt, 2.26.19
contact areas, 2.27.80	crystal axis vectors, 2.27.16
continue, 2.26.16	symmetry transformation, 3.10.2
contour surfaces, 2.20.7.5	transformations, 2.27.162
contouring density, 2.26.57.14	crystallographic occupancy, 2.27.96
contrast, 2.20.5.22	symmetry intro, 1.4.2.4
convert, 2.26.17, 2.26.17.2, 3.13.2	crystallography, 2.27.118
3D to chemical, 2.27.26	csv format, 2.26.74.41
3D/0D to 2D, 2.26.57.9	csym, 1.4.2.4
ICM object to PDB, 2.26.86	current, 5.3.8
and reroot, 2.26.17.4	icm-process number, 2.15.4
chemical 3D, 2.28.88	map, 5.3.6
and optmimize geometry, 2.28.89	object, 5.3.7
comp, 2.26.17.1	working directory, 2.27.97
comparison, 2.26.17.1	cursor action, 5.9.2.4
fragments, 2.26.17.2	customization, 3.1.2
mol, 2.26.17.3	and paste chemicals, 2.20.9.14, 2.20.9.15
object 3D and optmimize geometry, 2.28.90	cyclic temperature protocol, 2.16.43
macro, 2.28.14	cz32, 4.5
pdb, 3.8.2	database, 5.4.1
to 3D, 2.26.79.7	browser, 2.26.55.3
ICM object, 2.28.91	file, 3.5.1
iarray, 2.27.152	import, 2.26.57.26
icm-object, 2.26.17	dcMethod, 2.19.7
integer, 2.27.152	dcWeight, 2.16.8
convert2Dto3D, 2.28.90	decomposition, 2.26.57.27, 2.26.82.2
convert3Dto3D, 2.28.91	defCell, 2.21.1
convertObject, 2.28.14	defSymGroup, 2.15.2
converting a chemical, 2.26.17.3	default atom colors, 2.26.79.13
pdb-chemical, 3.13.2	value, 5.8.2
alignment to table, 2.27.146.2	define axis, 3.10.3
chemicals, 3.13.2.3	defining space box, 2.27.20
table columns into matrix, 2.27.146.4	delete, 2.26.20
to, 2.27.112	alias, 2.26.20.2
cool, 2.28.44	array element, 2.26.20.6
cooling schedule, 2.16.43	index, 2.26.20.6
coordinate frame, 2.16.4, 2.26.21.4	selection, 2.26.20.1
copy, 2.26.18	atom, 2.26.20.7
chemical image, 2.20.9.15	bond, 2.26.20.14
file, 2.18.26	boundary, 2.26.20.15
site, 2.26.79.24	chemical, 2.26.20.33
correlation matrix, 2.27.149	fragment, 2.26.20.33
covalent bound count, 2.27.125.3	selection, 2.26.20.33
neighbors, 2.27.90.1	class, 2.26.20
covalently attached molecule, 2.27.90.1	conf, 2.26.20.16
cpk, 5.3.12	directory, 2.26.20.8

drestraint, 2.26.20.17	diff, 2.27.94
element, 2.26.20.28	dihedral angle, 2.26.57.19
file, 2.26.20.9	calculation, 3.3.10
from array, 2.26.20.6	directory, 2.26.20.8, 2.26.57.5
hydrogen, 2.26.20.11	display, 2.26.21
label, 2.26.20.18	GUI window, 2.26.21.26
link, 2.26.20.19	box, 2.26.21.7
map, 2.26.20.20	clash, 2.16.5, 2.26.21.8
molcart, 2.26.20.3	drestraint, 2.26.21.9
molecule, 2.26.20.13	from script, 2.26.21.3
object, 2.26.20.12	gradient, 2.26.21.10
parray, 2.26.20.32	grob, 2.26.21.11
element, 2.26.20.32	label, 2.26.21.12
peptide bond, 2.26.20.25	gui, 2.26.21.26
plot, 2.26.20.4	hbond, 2.26.21.13
salts, 2.26.61.3	label, 2.26.21.15
selection, 2.26.20.5	map, 2.20.5.8, 2.26.21.16
sequence, 2.26.20.21	model, 2.26.21.1
session, 2.26.20.10	new, 2.26.21.2
shell object, 2.26.20.1	off-screen, 2.26.21.3
site, 2.26.20.22	offscreen, 2.26.21.3
sstructure, 2.26.20.23	origin, 2.26.21.4
stack, 2.26.20.26	ribbon, 2.26.21.18
object, 2.26.20.27	rotate, 2.26.21.5
system, 2.26.20.9	site, 2.26.21.19
table, 2.26.20.29	skin, 2.26.21.20
rows, 2.26.20.29	slide, 2.26.21.21
term, 2.26.20.30	stack, 2.26.21.6
tether, 2.26.20.31	string, 2.26.21.22
tree, 2.26.20.32	surface, 2.26.21.20
variable, 2.26.20.6	tethers, 2.26.21.23
views, 2.26.20	trajectory, 2.26.21.17
backbone, 2.27.125.1	volume, 2.26.21.24
restraint, 2.26.20.17	window, 2.3, 2.26.21.25
deleting sites by number, 2.26.20.22	distance, 5.4.3
density correlation, 2.16.8, 3.11.3	averaging, 2.19.5
fitting, 2.19.7	contact-based, 2.27.22, 2.27.22.1
in unit cell, 2.26.57.23	geometry, 5.4.4
densityCutoff, 2.16.10	matrix between stack conformations, 2.27.80.9
depenedent columns, 2.26.1.1.1	restraint, 5.4.6
depth cueing, 2.26.12.7, 5.4.2	file, 2.29.10
depth-cueing, 2.16.14	type file, 2.29.9
desolvation, 2.19.24	restraints, 2.26.79.19
dialog generation, 2.27.11	distribution, 1.3
in html documents, 2.26.40	comparison, 2.27.124
tables, 2.26.40	disulfide bond, 5.4.5
scripting, 2.27.11	diverse subset, 3.14.6.3