ICM Manual v.3.9 by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2025, Molsoft LLC
Jun 30 2025

Contents


Introduction
Reference Guide
Command Line User's Guide
References
Glossary

Index

Index

&, 2.14.3	Box, 2.35.21
2D chemicals, 2.23.9.16	Bracket, 2.35.22
labels, 2.34.58.1	C, 5.3
to 3D, 3.17	CCP4, 5.6.6
trees, 2.34.65.38	CGI, 2.11
smooth, 2.35.146.2	COLOR.bg, 2.19.9
3D chemical builder, 1.4.2.8	distanceAtom, 2.19.10
font size, 2.34.23.12	label, 2.19.11
label, 2.34.23.12, 2.34.89.39	CONSENSUS, 2.23.1
labels, 2.34.58.1	CONSENSUSCOLOR, 2.23.2
mol file, 2.37.86	CONSENSUS_strength, 2.19.12
plots intro, 1.4.3.7	Cad, 2.35.23, 2.35.23.1, 2.35.23.2
smoothing, 2.35.146.3	Cad1, 2.35.23.1
superposition, 2.37.22	Cadalign, 2.35.23.2
transformations, 2.34.102.2	Ceil, 2.35.24
tree, 2.34.65.38	Cell, 2.35.25
chemical similarity, 2.35.136	Charge, 2.35.26
pharmacophore comparison, 2.35.136.4	Chemical, 2.35.27
3dxml, 5.5.3	Functions, 2.28
=, 2.14.1	Synthetic Accessibility, 2.31
A, 5.1	Cluster, 2.35.28
ANN, 2.34.53	Collada, 5.5.3
APF distance, 2.35.136	Collection, 2.35.28.1
Abs, 2.35.1	Color, 2.35.29
Acc, 2.35.2	from gradient, 2.35.29.1
Acos, 2.35.3	image, 2.35.29.2
Acosh, 2.35.4	protein, 2.35.29.3
Adobe, 2.21.23	CombiRIDGE, 3.13.1.22
Align, 2.35.5	Compare, 2.35.30
sequence, 2.35.5.1	Connolly surface, 5.8.7
AlignSS, 2.36.1	Consensus, 2.35.31
Angle, 2.35.6	Contour, 2.35.32
Apple, 3.14.6.2	Corr, 2.35.33
Area, 2.35.7	Cos, 2.35.34
residue contacts, 2.35.7.1	Cosh, 2.35.35
Asin, 2.35.8	Count, 2.35.36
Asinh, 2.35.9	CubicRoot, 2.35.37
Ask, 2.35.10	D, 5.4
Askg, 2.35.11	DAE, 5.5.3
Atan, 2.35.12	DE, 2.34.35.2
Atan2, 2.35.13	DNA Representation, 1.4.1.3
Atanh, 2.35.14	alignment, 2.34.3.4
Atom, 2.35.15	melting temperature, 2.35.164
Augment, 2.35.16	to RNA conversion, 2.35.138.1
Axis, 2.35.17	views, 1.4.1.3
B, 5.2	Date, 2.35.38
BPMC, 5.2.6	Deletion, 2.35.39
Bfactor, 2.35.19	Descriptor, 2.35.40, 2.35.41
Blob, 2.35.18	numeric, 2.35.40
Boltzmann, 2.35.20	Det, 2.35.42

Distance, 2.35.44, 2.35.44.6	chemical, 2.35.56.3
2 alignments, 2.35.44.13	pattern, 2.35.56.3
matrices, 2.35.44.9	in array, 2.35.56.1
Dayhoff, 2.35.44.11	table, 2.35.56.2
Tanimoto, 2.35.44.7	FlexLM license info, 2.35.188
alignment, 2.35.44.12	Floor, 2.35.57
as_, 2.35.44.3	Formula, 2.35.58
rarray, 2.35.44.4	GCNN, 3.13.1.25
atoms, 2.35.44.3	GINGER, 3.13.1.20
chemical, 2.35.44.7, 2.35.44.15	GPU, 3.13.1.20, 3.18
chemset, 2.35.44.8	GRAPHICS, 2.23.5
dayhoff, 2.35.44.11	alignmentRainbow, 2.23.5.1
hierarchical, 2.35.44.6	atomLabelShift, 2.23.5.2
iarray, 2.35.44.1	atomValueCircles, 2.23.5.3
alignment, 2.35.44.12	ballRadius, 2.23.5.4, 2.23.5.31
matrix, 2.35.44.5, 2.35.44.9	ballStickRatio, 2.23.5.5
multiple atomic, 2.35.44.4	chainBreakLabelDisplay, 2.23.5.8
rarray, 2.35.44.2	chainBreakStyle, 2.23.5.7
tether, 2.35.44.10	clashWidth, 2.23.5.6
tree, 2.35.44.14	clipStatic, 2.23.5.10
cluster, 2.35.44.14	clippingPlane, 2.23.5.9
Docking, 3.18	cpkClipCaps, 2.23.5.11
H, 5.5	displayLineLabels, 2.23.5.12
Ligase protacModel.icm, 3.16	displayMapBox, 2.23.5.13
number, 2.35.44.6	dnaBallRadius, 2.23.5.14
EDS server, 2.37.42	dnaRibbonRatio, 2.23.5.15
EST-alignment, 2.34.3.4	dnaRibbonStyle, 2.23.5.16
Eigen, 2.35.45	dnaRibbonWidth, 2.23.5.17
Enamine, 3.13.1.24	dnaRibbonWorm, 2.23.5.18
Energy, 2.35.46	dnaStickRadius, 2.23.5.19
Entropy, 2.35.47	formalChargeDisplay, 2.23.5.20
Error, 2.35.48	grobDotSize, 2.23.5.21
soap, 2.35.49	grobLineWidth, 2.23.5.22
Exist, 2.35.50	hbondAngleSharpness, 2.23.5.26
molcart, 2.35.50.1	hbondBallPeriod, 2.23.5.27
Existenv, 2.35.51	hbondBallStyle, 2.23.5.28
Exp, 2.35.53	hbondMinStrength, 2.23.5.25
Extension, 2.35.52	hbondRebuild, 2.23.5.24
FILTER, 2.23.3	hbondStyle, 2.23.5.23
Z, 2.23.3.1	hbondWidth, 2.23.5.29
gz, 2.23.3.2	hetatmZoom, 2.23.5.31
uue, 2.23.3.3	hydrogenDisplay, 2.23.5.32
FTP, 2.23.4	light, 2.23.5.33
createFile, 2.23.4.1	lightPosition, 2.23.5.34
keepFile, 2.23.4.2	mapLineWidth, 2.23.5.35
proxy, 2.23.4.3	occupancyDisplay, 2.23.5.36
Field, 2.35.54, 2.35.54.1	occupancyRadiusRatio, 2.23.5.37
user, 2.35.54.1	quality, 2.23.5.38, 2.35.91.1
File, 2.35.55	rainbowBarStyle, 2.23.5.39
Find, 2.35.56	resLabelDrag, 2.23.5.40

ribbonCylinderRadius, 2.23.5.42	proxy, 2.23.4.4
ribbonGapDistance, 2.23.5.43	Hartree-Fock, 2.34.84.21, 2.34.110.17
ribbonRatio, 2.23.5.44	Header, 2.35.64
ribbonWidth, 2.23.5.45	Histogram, 2.35.65
ribbonWorm, 2.23.5.46	N, 5.6
rocking, 2.23.5.47	ICM desktop, 2.23.8.6
rockingRange, 2.23.5.48	documents, 2.34.84.4
rockingSpeed, 2.23.5.49	modules, 1.4.4
selectionLevel, 2.23.5.50	object, 2.37.13
selectionStyle, 2.23.5.51	residue library, 2.21.24
sketchAccents, 2.23.5.30	ICM-shell, 3.1, 5.8.5
stereoMode, 2.23.5.52	intro, 1.7.1
stickRadius, 2.23.5.31, 2.23.5.53	script, 2.34.8
surfaceDotDensity, 2.23.5.55	ICMFF force field, 2.37.79
surfaceDotSize, 2.23.5.54	ICMHOME, 3.1.2.1
surfaceProbeRadius, 2.23.5.56	shell variable, 3.1.2.1
transparency, 2.23.5.57	IMAGE, 2.23.9
wormRadius, 2.23.5.58	bondLength2D, 2.23.9.15
GRID, 2.23.6	color, 2.23.9.8
gcghExteriorPenalty, 2.23.6.1	compress, 2.23.9.9
gpGaussianRadius, 2.23.6.6	font, 2.23.9.16
margin, 2.23.6.2	gammaCorrection, 2.23.9.7
maxEl, 2.23.6.3	generateAlpha, 2.23.9.10
maxVw, 2.23.6.5	lineWidth, 2.23.9.3
minEl, 2.23.6.4	lineWidth2D, 2.23.9.14
GROB, 2.23.7	orientation, 2.23.9.17
arrowRadius, 2.23.7.3	paperSize, 2.23.9.18
atomSphereRadius, 2.23.7.1	previewResolution, 2.23.9.13
contourSigmaIncrement, 2.23.7.5	previewer, 2.23.9.12
relArrowHead, 2.23.7.4	printerDPI, 2.23.9.2
relArrowSize, 2.23.7.2	quality, 2.23.9.1
GUI, 2.23.8	rgb2bw, 2.23.9.19
defaults, 3.14.6.2	scale, 2.23.9.4
dialog, 2.33	stereoAngle, 2.23.9.6
plot, 2.34.65.32	stereoBase, 2.23.9.5
preferences, 2.34.85.4	stereoText, 2.23.9.11
tableRowMarkColors, 2.23.8.5	writeScale, 2.23.9.20
windowLayout, 2.23.8.6	I_out, 2.24.4
workspaceFolderStyle, 2.23.8.9	Iarray, 2.35.66, 2.35.66.4, 2.35.66.5
workspaceStyle, 2.23.8.7	atom numbers, 2.35.66.4
workspaceTabStyle, 2.23.8.8	bits to integers, 2.35.66.3
GaussFit, 2.35.82	inverse, 2.35.66.2
Getarg, 2.35.59	residue numbers, 2.35.66.5
Getenv, 2.35.60	reverse, 2.35.66.2
GigaScreen, 3.13.1.25	stack, 2.35.66.6
Gradient, 2.35.61	Icm Options, 2.1
Graphics, 1.4.1	IcmSequence, 2.35.67
Grob, 2.35.62	Image, 2.35.68
Group, 2.35.63	collection, 3.9.2.1
HTTP.ignoreProxyDomains, 2.23.4.5	frame by frame, 3.9.2.2

InChi, 2.35.69	new, 2.35.90.1
InList, 2.35.105	residue areas, 2.35.90.8
Index, 2.35.70	comparison, 2.35.90.5
chemical, 2.35.70.2	stack, 2.35.90.11
compare, 2.35.70.10	sub, 2.35.90.2
element in array, 2.35.70.8	symmetric, 2.35.90.3
fork, 2.35.70.1	table, 2.35.90.6
regexp, 2.35.70.4	tensor, 2.35.90.7
string, 2.35.70.3	Max, 2.35.91
table label, 2.35.70.6	image graphic, 2.35.91.1
selection, 2.35.70.5	MaxHKL, 2.35.92
tree, 2.35.70.9	Mean, 2.35.94
unique elements, 2.35.70.7	Median, 2.35.93
Indexx, 2.35.71	Method, 2.22.13
Info, 2.35.73	Min, 2.35.95
image, 2.35.74	Mod, 2.35.97
model, 2.35.75	Mol, 2.35.98
Insertion, 2.35.72	MolLogP, 2.29
Integer, 2.35.76	MolLogS, 2.30
Integral, 2.35.77	MolPSA, 5.7.12
Interrupt, 2.35.78	MolSynth, 2.31
Introduction, 1	Moment, 2.35.88
JSON, 2.34.84.57	of Inertia, 2.35.88
LIBRARY, 2.23.10	Money, 2.35.96
men, 2.23.10.1	N-terminus, 2.23.14.4
res, 2.23.10.2	NMR, 2.34.63.1
Label, 2.35.79	NOE averaging, 2.22.6
Laplacian, 2.35.80	Name, 2.35.99
Latent, 2.35.187.3	chemical, 2.35.99.6
LatentVector, 2.35.187.3	property, 2.35.99.1
Length, 2.35.81	close sequence, 2.35.99.3
LinearFit, 2.35.83	conf, 2.35.99.7
LinearModel, 2.35.84	image, 2.35.99.11
Log, 2.35.85	molcart, 2.35.99.12
LogP, 2.29, 2.35.114	object parray, 2.35.99.10
LogS, 2.30, 2.35.114	sequence, 2.35.99.8
MD, 3.20	soap, 2.35.99.2
M_out, 2.24.5	string, 2.35.99.4
Mac, 3.14.6.2	tree, 2.35.99.5
Map, 2.35.86	Namex, 2.35.100
Markush structures, 2.34.55	image, 2.35.100.2
Mass, 2.35.87	sequence, 2.35.100.1
Match, 2.35.89	Newick tree format, 2.35.156.4
Mathews, 2.35.136.5	Next, 2.35.101, 2.35.101.1
Matrix, 2.35.90	covalent neighbors, 2.35.101.1
alignment, 2.35.90.9	Nof, 2.35.102
boundary, 2.35.90.10	chemical, 2.35.102.2
color, 2.35.90.4	distance, 2.35.102.3
grob connectivity, 2.35.90.13	latent, 2.35.102.6
histogram, 2.35.90.12	library, 2.35.102.4

soap, 2.35.102.7	faq, 3.7.2
tree, 2.35.102.1	file, 2.34.55
Norm, 2.35.103	RIDE, 3.19
Normalize, 2.35.104	RIDGE, 3.13.1.21, 3.13.1.25, 3.18
NotInList, 2.35.105	RNA topology, 2.23.5.16
R, 5.7	RTCNN, 3.13.1.25
OBJECT, 2.23.11	R_2out, 2.24.7
Obj, 2.35.106	R_out, 2.24.6
Occupancy, 2.35.107	Radius, 2.35.120
PBS, 3.13.1.15, 3.13.1.19	Random, 2.35.121
PCA, 3.3.9	string, 2.35.121.1
PLOT, 2.23.12	Rarray, 2.35.122
Yratio, 2.23.12.9	reverse, 2.35.122.2
box, 2.23.12.1	sequence projection, 2.35.122.1
color, 2.23.12.2	alignment projection, 2.35.122.3
font, 2.23.12.3	strength, 2.35.122.5
fontSize, 2.23.12.4	property assignment, 2.35.122.4
gridLineWidth, 2.23.12.5	RarrayAlignment, 2.35.122.5
labelFont, 2.23.12.13	Rarrayinverse, 2.35.122.2
lineWidth, 2.23.12.6	Real, 2.35.123
logo, 2.23.12.10	Reference, 2.35.125
markSize, 2.23.12.7	Guide, 2
numberOffset, 2.23.12.8	Remainder, 2.35.124
orientation, 2.23.12.11	Replace, 2.35.126
rainbowStyle, 2.23.12.14	chemical, 2.35.126.4
seriesLabels, 2.23.12.12	exact, 2.35.126.1
PLS, 2.35.102.6	regexp, 2.35.126.3
error, 2.35.136.5	simple, 2.35.126.2
models, 2.35.136.5	Res, 2.35.127, 2.35.128
PROTAC, 3.16	Resali, 2.35.128
Parray, 2.35.109	Resolution, 2.35.129
Parray-object, 2.35.109	Rfactor, 2.35.131
Path, 2.35.108	Rfree, 2.35.132
Pattern, 2.35.110	Ride, 3.19
Pi, 2.35.111	Ring, 2.35.130
Polar Surface Area, 5.7.12	Rmsd, 2.35.133
Potential, 2.35.112	of subset, 2.23.14
Power, 2.35.113	Rot, 2.35.134
Predict, 2.35.114	S, 5.8
Probability, 2.35.115	SAR analysis, 2.34.65.27, 2.34.65.28, 2.34.92.2, 2.34.92.3
Profile, 2.35.116	SC, 2.34.35.2
Property, 2.35.117	SEQUENCE.restoreOrigNames, 2.23.12.15
Protac, 3.16	SGE, 3.13.1.19
Protonation state, 2.35.160.11	SITE, 2.23.13
Putarg, 2.35.118	defSelect, 2.23.13.2
Putenv, 2.35.119	labelOffset, 2.23.13.3
QSAR, 2.34.53	labelStyle, 2.23.13.4
R-groups, 2.34.55	labelWrap, 2.23.13.5
REAL, 3.13.1.24	showSeqSkip, 2.23.13.6
REBEL, 3.7.2	wrapComment, 2.23.13.7

SLURM, 3.13.1.19	Smooth, 2.18.24, 2.35.146, 2.35.146.1, 2.35.146.3
SMARTS, 2.26, 2.34.10, 2.35.102.2	matrix, 2.35.146.2
SMILES, 2.27	Smoothrs, 2.35.146.3
SOAP, 2.35.99.2, 2.35.102.7, 2.35.182.1	SoapMessage, 2.35.152
request message, 2.35.152	SolveQuadratic, 2.35.147
SSSR, 2.35.130	SolveQubic, 2.35.148
S_out, 2.24.8	Sort, 2.35.153
S_proteinTags, 2.24.9	Sphere, 2.23.14.3, 2.35.151
Sarray, 2.35.135	Split, 2.35.154
index, 2.35.135.1	chemical, 2.35.154.4
Score, 2.35.136	multisep, 2.35.154.3
alignment, 2.35.136.9	regexp, 2.35.154.2
apf, 2.35.136.4	tree, 2.35.154.1
chemset, 2.35.136.2	Sql, 2.35.149
conservation, 2.35.136.8	Sqrt, 2.35.150
model, 2.35.136.5	Srmsd, 2.35.155
overlap, 2.35.136.1	Sstructure, 2.35.157
predictions, 2.35.136.6	String, 2.35.156, 2.35.156.8
sequence, 2.35.136.7	alternative, 2.35.156.7
torsion, 2.35.136.3	date, 2.35.156.2
Scripting Tutorials, 1.8	mol, 2.35.156.3
Select, 2.35.137	selection, 2.35.156.8
break, 2.35.137.1	slide gui, 2.35.156.9
alignment, 2.35.137.14	substring, 2.35.156.1
atom property, 2.35.137.7	chemical formula, 2.35.156.10
nmembers, 2.35.137.4	Sum, 2.35.158
string, 2.35.137.9	chemical, 2.35.158.1
expand, 2.35.137.6	image, 2.35.158.2
fix, 2.35.137.2	Swissprot, 2.34.110.24
graphical, 2.35.137.5	Symgroup, 2.35.159
neighbors, 2.35.137.3	T, 5.9
Select_by atom numbers, 2.35.137.10	TOOLS, 2.23.14
Select_by_sequence, 2.35.137.13	edsDir, 2.23.14.1
Select_by_text, 2.35.137.9	membrane, 2.23.14.2
Select_lists, 2.35.137.12	minSphereCubeSize, 2.23.14.3
Select_patching, 2.35.137.11	pdbChargeNterm, 2.23.14.4
Select_projection, 2.35.137.8	pdbReadNmrModels, 2.23.14.5
Sequence, 2.35.138	rebelPatchSize, 2.18.5, 2.23.14.6
array, 2.35.138.3	smilesXyzSeparator, 2.23.14.7
Sequence(dna_or_rna nucleotide), 2.35.138.1	superimposeMaxDeviation, 2.23.14.10
reverse), 2.35.138.2	superimposeMaxIterations, 2.23.14.8
Shannon, 2.35.47	superimposeMinAtomFraction, 2.23.14.9
Shuffle, 2.35.139	tsShape, 2.23.14.12
Sign, 2.35.140	tsWeight, 2.23.14.13
Simulations, 1.4.2	writePdbRenameRes, 2.23.14.14
Sin, 2.35.141	Table, 2.35.160
Sinh, 2.35.142	alignment numbers, 2.35.160.3
Site, 2.35.143	distance, 2.35.160.10
Slide, 2.35.144	matrix, 2.35.160.4
Smiles, 2.35.145	model, 2.35.160.8

pairs, 2.35.160.5	Volume, 2.35.189
plot, 2.35.160.7	WEBAUTOLINK, 2.23.16
stack, 2.35.160.6	WEBLINK, 2.23.15
url_decoder, 2.35.160.1	Warning, 2.35.191
Table(alignment), 2.35.160.2	Wavefront format, 2.34.84.22
Table(stack), 2.35.160.6	XML, 2.12
Tan, 2.35.161	Xyz, 2.35.192
Tanh, 2.35.162	axes, 2.35.192.8
Tanimoto, 2.35.66.3	chemical match, 2.35.192.6
distance, 2.34.65.37	fract, 2.35.192.4
matrix, 2.35.44.7	mesh, 2.35.192.3
Temperature, 2.35.164	points, 2.35.192.1
Tensor, 2.35.163	rings, 2.35.192.2
Time, 2.35.165	transformed xyz, 2.35.192.5
Tointeger, 2.35.166	vector2matrix, 2.35.192.7
Tolower, 2.35.167	Z-shift, 2.19.35
Toreal, 2.35.168	ZEGA, 5.10.9
Torsion, 2.35.169	intro, 1.4.3.6
Tostring, 2.35.170	_NAME, 2.34.89.47
Toupper, 2.35.171	_chemBatch, 3.1.2.5
ToxScore, 2.36.2	_chemSuper, 3.15
Tr123, 2.35.172	_confGen, 3.17
Tr321, 2.35.173	_dockBatch, 3.13.1.7
Trace, 2.35.174	_dockScan, 3.13.1.18
Trans, 2.35.175	_macro, 2.38.1
Transform, 2.35.176	file, 2.38.1
Transpose, 2.35.177	_startup, 3.1.2.3
Trim, 2.35.178	file, 2.38.2
chemical, 2.35.179	icm, 2.38.2
sequence, 2.35.180	a_, 2.8.1
Turn, 2.35.181	abbr, 1.6
Type, 2.35.182	abbreviations, 1.6
molcart, 2.35.182.2	absolute to cell x y z, 2.35.192.4
soap, 2.35.182.1	accFunction, 2.24.2
Z, 5.10	acceptor, 3.6.1
Unique, 2.35.183	access large sdf file, 2.34.84.24
Unix, 2.35.184	accessMethod, 2.22.2
Uppsala, 2.37.42	accessible residues, 3.3.6
server, 2.37.43	surface, 2.34.65.14, 5.8.15
SYNTHES, 3.13.1.24	accessing sections, 2.34.110.24
VLS, 3.18	accuracy, 2.35.136.5
V_, 2.8.1	acidity constant, 2.34.89.11, 2.34.89.12
Value, 2.35.185	activate fog, 2.34.23.24
soap, 2.35.186	alignment, 2.34.89.40
Vector, 2.35.16, 2.35.187, 2.35.187.1, 2.35.187.3	document, 2.34.89.40
symmetry transformation, 2.35.187.2	tab, 2.34.89.40
Vectorproduct, 2.35.187.1	table, 5.9.2.4
Vectorsymmetrytransformation, 2.35.187.2	add, 2.34.1
Version, 2.35.188	column, 2.34.1.1
View, 2.35.190	function, 2.34.1.1.1

slide, 2.34.1.3	sequence reordering, 2.35.5
table, 2.34.1.4	strength, 2.35.122.5
row, 2.34.1.4	structural, 2.34.3.5, 2.35.5
addBfactor, 2.19.1	to sequence transfer, 2.35.122.1
adding atoms to non-ICM objects, 2.34.7.1	text conversion, 2.35.156.4
columns to table, 2.34.1.1	weighted, 2.35.5
hydrogens, 2.37.13	gapExtension, 2.19.18
in place, 2.14.4	gapOpen, 2.19.19
to slideshow, 2.34.1.3	alignment_as_text, 2.35.156.4
admet selection, 3.13.1.13	aliphatic amines, 2.34.70.2
advanced chemical search, 3.6	all, 5.1.2
operations, 2.14.6	torsions table, 3.3.11
ops, 2.14.6	alpha, 2.23.5.57, 2.34.89.42, 5.1.3
ahfs, 2.35.44.6	channel, 2.23.9.10
ali_seq_project, 2.35.156.5	alternative flag, 2.34.89.18
alias, 2.34.2	amber, 5.1.4
align, 2.34.3	amino acid, 2.21.24, 2.35.172, 2.35.173
3D, 2.34.3.5	colors, 2.35.29.3
faq, 3.3.2	labels, 2.34.3.2
heavy, 2.34.3.6	anchor, 3.13.1.22
how to, 3.3.2	and, 2.14.3
chemical, 2.34.88.1	angle rotation, 2.37.84
fragments, 2.34.3.4	angles, 2.35.102.3
intro, 1.4.3.3	angular hbond dependence, 2.23.5.26
number, 2.34.3.2	animated story, 5.8.14
chemical, 2.34.3.1	animation, 2.34.23.5, 2.34.23.6, 3.9
res numbers, 2.34.3.2	annotation, 2.34.22.26, 2.34.89.26, 2.34.89.27
sequence, 2.34.3.3	apf, 3.15, 3.19
sequences, 2.34.3.3	append, 5.1.5
alignMethod, 2.22.3	a tables, 2.34.1.4
alignMinCoverage, 2.19.2	column, 2.34.4.3
alignMinMethod, 2.19.2	command, 2.34.4
alignOldStatWeight, 2.19.3	sequence, 2.34.4.1
alignTwoSequences, 2.37.1	to group, 2.34.4.1
aligned residues, 2.35.128	stack, 2.34.4.2
alignment, 2.34.22.26, 2.34.89.27, 2.34.89.35, 2.34.89.55, 5.1.1	tables, 2.34.50
as table, 2.35.160.2	by shared column, 2.34.4.3
block length, 2.18.22	appending, 2.34.1.1
secondary structure, 2.36.1	an element, 2.14.4
cleaning, 2.35.146.4	menu items, 2.23.10.1
color by property, 2.34.89.34	representations to a slide, 2.34.23.21
coloring, 2.21.1	rows to matrix, 2.34.1.2
conservation, 2.37.8	area under curve, 2.37.21
distance, 2.35.137.13	arguments, 2.34.64
editor, 2.4	arithmetic operations, 2.14.2
extraction, 2.35.5	arithmetics, 2.14
gap format, 5.1.1.1	aromatic planes, 2.37.4
intro, 1.4.3.4	array, 2.34.72.4, 5.1.6, 5.7.3.1
projection, 2.35.156, 2.35.156.5, 2.35.156.6	assignment, 2.14.1
score, 2.35.136.8	derivative, 2.35.146.1

parray, 2.34.22.31	ball, 2.34.89.2, 5.2.2
size, 2.35.102	base, 5.2.1
subset, 2.6	pair diagram, 2.23.5.16
arrow from selection, 2.37.36	basis set, 2.34.84.21, 2.34.110.17
length, 2.34.89.26	batch chemical processing, 3.1.2.5
as2_out, 2.24.14	docking, 3.13.1.18
as_, 2.8.8	beta, 5.2.3
as_graph, 2.23.5.50, 2.23.5.51, 2.35.137.5	bfactor circles, 2.23.5.3
as_out, 2.24.13	biased probability monte carlo, 2.34.71
assign, 2.34.5	binary file table of contents, 2.34.84.2
residue, 2.34.6.1	files, 2.34.110.2
ring conformation to template, 2.34.66.4	string, 5.2.4
sstructure, 2.34.5.1	key, 2.34.89.43
segment, 2.18.20, 2.34.5.2	binding energy, 3.7.4
assignment, 2.14.1	pocket finding, 3.4.2
atc code, 2.35.44.6	pockets, 2.34.92.1
atom, 2.34.13.1, 5.1.7	side comparison, 2.37.8
centers within, 2.35.151	site analysis, 3.4.2
code file, 2.38.4	biological symmetry, 2.34.89.9
coordinates, 2.35.192.1	vector, 2.35.66.3
flickering, 2.34.89.3	to integers compression, 2.35.66.3
label font, 2.38.15	blast, 2.34.110.25
labels, 2.34.89.2	files, 2.34.110.25
name, 2.34.3.1, 2.35.79	blast-formatted database, 2.34.35.3, 2.34.110.25
pairs, 2.34.89.68, 2.34.89.69, 2.35.160.10	blending, 2.34.110.31
proximity to surface, 2.34.90.9	images, 2.35.158.2
selection by number, 2.35.66.4	blob, 5.2.4
type, 2.35.182	bold, 2.34.89.38.1
user field, 2.35.54.1	bond angle bending, 2.38.5
atomLabelStyle, 2.22.4	errors, 2.34.90.12
atomSingleStyle, 2.22.5	stretching, 2.38.6
atomic contributions, 2.34.90.20, 2.34.90.21	to protein, 2.34.72.3
coordinate transfer, 2.34.89.3	width, 2.23.9.14
property fieds, 3.19	bonded atoms, 2.35.101.1
fields, 3.15	born radii, 2.34.90.9
solvation contributions, 2.35.7	boundary element, 5.2.5
in residue, 2.35.63	matrix, 2.35.90.10
alternative position, 2.34.89.18	box, 2.35.21
selecting, 2.8.8	break, 2.34.6
translate, 2.34.89.3	brightness, 2.23.5.33
attenuation by occupancy, 2.34.65.25	build, 2.34.7
auc enrichment, 2.37.21	atom, 2.34.7.1
auto saving log, 2.22.11	column, 2.34.7.2
autoSavePeriod, 2.18.1	conf, 2.34.7.3
automated setup, 3.13.1.7	faq, 3.8.1
avi, 2.34.110.31	from string, 2.34.7.9
axis, 5.1.8	helix, 3.10.5
axisLength, 2.19.4	how to, 3.8.1
background, 2.35.29.2	hydrogen, 2.34.7.10
color, 2.19.9	loop, 2.34.7.7

molcart, 2.34.7.11	compounds, 2.34.70.2
sequence, 2.34.7.4	prediction, 2.34.89.11, 2.34.89.12
smiles, 2.34.7.8	state, 2.34.29
string, 2.34.7.9	change, 2.34.89.10
tautomer, 2.34.7.5	chem formula, 2.35.156.10
built-in functions, 5.5.5	chemSuper3D, 2.37.22
plot, 2.34.89.53	chemical, 2.23.14.7, 2.25, 2.34.35.9, 2.35.69, 2.35.136.3
atoms, 2.34.14	2D drawings, 2.34.65.9
contact surface, 2.34.14	SMARTS search, 2.34.35.5
molecule, 2.34.13.1	atom annotation, 2.34.22.20
number of bonds, 2.35.137.3	database, 3.5
variables, 2.34.14	decomposition, 2.34.65.27, 2.34.92.2, 2.34.92.3
cage, 2.37.4	descriptors, 2.35.41, 5.7.12
calcArea, 2.37.2	distance, 2.35.44.8, 2.35.136.2, 2.35.136.4
calcBindingEnergy, 2.37.3	diversity, 3.14.6.4
calcDihedralAngle, 2.37.4	drawing, 2.23.9.14, 2.23.9.16
calcEnergyStrain, 2.37.20	quality, 2.23.9.15
calcEnsembleAver, 2.37.5	fingerprints, 2.9
calcMaps, 2.37.6	formula, 2.35.156.10
calcPairSeqIdsFromAli, 2.37.7	fragment counting, 2.35.102.2
calcPepHelicity, 2.37.9	functions, 2.28
calcProtUnfoldingEnergy, 2.37.10	keys, 2.34.65.21
calcRmsd, 2.37.11	match coordinates, 2.35.192.6
calcRoc, 2.37.21	matching, 2.34.35.4, 2.34.84.49, 2.34.84.50, 2.35.133, 2.35.155
calcSeqContent, 2.37.12	models, 2.35.99.1
calcSeqSimilarity, 2.37.8	modification, 2.34.68, 2.34.70, 2.37.37
calculate phases, 3.11.2	name, 2.35.99.6
call, 2.34.8	normalization, 2.34.70
canonical form, 2.35.45	rules, 2.34.70.4
carboxylic acid, 2.34.70.2	pattern, 2.26, 2.34.88.1
cartesian cooridnates, 2.35.192	search, 2.35.56.3
cartridge, 3.5	reaction product generation, 2.34.65.33
cavities, 2.34.92.1	search, 2.34.35.10, 2.34.88.1, 2.35.102.2
cavity, 5.3.1	similarity, 3.5
analysis, 3.3.13	simplification, 2.35.178
ccp4 maps, 2.34.84.27	spreadsheet, 2.34.12, 2.34.84.48, 2.34.84.49, 2.34.84.50, 2.34.89.47, 2.34.110.11
cd, 2.34.89.21	structure, 2.34.110.22
cell axis vectors, 2.35.192.8	from smiles, 2.34.89.7
specific icm commands, 5.9.2.4	substructure, 2.34.35.4
center, 2.13.1, 2.34.9	mask, 2.34.65.21
cgi programming with icm, 2.11	superposition, 2.22.7, 2.35.133, 3.15
chain breaks, 2.23.5.7, 2.23.5.8, 2.35.137.1	table, 2.25
symbol, 2.34.89.9	text format, 5.6.11
change atom position, 2.34.89.3	topological descriptors, 2.35.40
sequence position in multiple alignment, 2.34.72.7	view, 2.34.89.54
unix directory, 2.34.89.21	chemistry, 2.25, 2.35.27
changing local stick radii, 2.34.89.86	chiral isomer generation, 2.34.30
surface dot size, 2.23.5.54	chirality, 2.20.16, 2.34.30
channel, 2.23.14.2	choosing ligands, 3.13.1.2
charge, 2.23.14.4, 5.3.2	chroma, 2.35.90.4

circular permutation of coordinates, 2.34.69	unique, 2.34.13.4.1
clamp values to range, 2.35.178	label, 2.34.13.5
clashThreshold, 2.19.5	map, 2.34.13.6
clashes, 2.34.65.16	by value, 2.34.23.16
labels, 2.35.166	molecule, 2.34.13.1
classification, 2.35.44.6	names, 2.35.29
clear, 2.34.10	object, 2.34.11.2
graphical selection, 2.34.10	preference, 2.19.10
screen, 2.34.10	specification, 2.34.11.1
click and lock, 5.9.2.4	surface by conservation, 2.34.13.3
clipping plane, 2.23.5.9, 2.23.5.10, 2.23.5.11, 2.34.72.6, 5.3.3	table, 2.35.29.3
closer than threshold, 2.35.44.9	volume, 2.34.13.7
closest sequence, 2.35.99.3	column, 5.3.5
value, 2.35.56.1	correlation, 2.34.91.3
cluster, 2.35.154.1	function, 2.34.7.2
center, 2.35.70.9	names, 2.34.85.1, 2.34.88.2
centers, 2.13.1	of grobs, 2.35.109
selection, 2.35.70.9	selection, 2.35.99
tree, 2.35.99.5	combiRIDGE, 3.13.1.22
size, 2.35.102.1	combinatorial compounds, 2.35.27
clustering, 2.13, 2.34.65.37, 2.34.65.38, 2.34.92.7	libraries, 2.34.65.33, 2.35.102.4
clusters, 2.13, 2.13.1	PDB, 2.37.92
cnMethodAverage, 2.22.6	transformations, 3.10.4
cnWeight, 2.19.6	combining plots, 2.34.65.32
code, 2.35.44.6	receptor and ligand stacks, 2.34.4.2
coil, 5.3.4	command, 2.35.99.4, 5.3.10
collection, 2.12, 5.3.6	line editing, 2.2
color, 2.23.5.33, 2.34.11	help, 2.34.45
accessibility, 2.34.13	options, 2.1
background, 2.34.13.2	word list, 3.1.5
example, 3.2.7	commands, 2.22.11, 5.1.1
accessibility, 3.2.11	communication protocols, 2.32
alignment, 2.34.13.3	comp, 2.35.105
atom contributions, 2.34.12	comp_matrix, 2.34.89.20, 2.34.90.16, 5.3.11
bfactor, 3.2.9	compare, 2.18.12, 2.18.15, 2.34.14
charge, 3.2.12	angles, 2.34.14.2
electrostatic potential, 2.18.5	atom, 2.34.14.1
hydrophobicity, 3.2.10	by rmsd without superposition, 2.34.14.1
pharmacophore, 2.34.12	chemical tables, 2.34.35.10
potential, 2.37.25	patch only, 2.34.14.3
shape depth, 2.34.13	rmsd, 2.34.14.1
chemical, 2.34.12, 2.34.88.1	surface, 2.34.14.3
choice, 2.19.9	variables, 2.34.14.2
file, 2.38.15	compareMethod, 2.22.7
grob, 2.34.13.4	comparing two sarrays, 2.35.105
by atom selection, 2.34.13.4.3	comparison, 2.35.70.10
atoms, 2.23.7.1	operations, 2.14.5
map, 2.34.13.4.4	complete view, 2.35.144
matrix, 2.34.13.4.2	compound accessibilities, 3.14.4.1
potential, 2.34.13.4.5	array, 2.25

compress, 2.34.15	and reroot, 2.34.18.4
alignment, 2.34.15.1	chemical 3D, 2.37.82
binary, 2.34.15.4	and optmimize geometry, 2.37.83
conf, 2.34.15.3	comp, 2.34.18.1
grob, 2.34.15.2	comparison, 2.34.18.1
in place, 2.34.15.4	fragments, 2.34.18.2
objects, 2.34.15	mol, 2.34.18.3
stack, 2.34.15.3	object 3D and optmimize geometry, 2.37.85
compressed table view, 2.34.89.24	macro, 2.37.13
conditional buttons, 5.5.5	pdb, 3.8.2
string, 2.35.156.7	to 3D, 2.34.89.8
conf, 2.34.89.61, 2.34.110.41, 2.35.160.6, 5.3.12, 5.8.9	ICM object, 2.37.86
data, 2.35.160.6	iarray, 2.35.166
confgen, 3.17	icm-object, 2.34.18
configuration, 2.38.14	integer, 2.35.166
file, 2.34.110.42	convert2Dto3D, 2.37.85
memory usage, 2.18.7	convert3Dto3D, 2.37.86
conformation comparison, 2.22.7	convertObject, 2.37.13
conformational ensemble, 2.34.7.6.2	converting a chemical, 2.34.18.3
generator, 2.34.66.1, 3.17	alignment to table, 2.35.160.2
interpolation, 2.34.23.6	chemicals, 3.13.1.8
stack, 2.34.110.41, 5.3.12, 5.8.9	table columns into matrix, 2.35.90.6
compression, 2.34.15.3	to, 2.35.123
file, 2.38.7	cool, 2.37.40
transition, 2.37.38	pictures, 2.23.5.30
conformer, 3.13.1.20	cooling schedule, 2.19.46
storage, 2.34.63.5, 2.34.94.2	coordinate frame, 2.19.4, 2.34.23.4
conformers, 3.17	coordinates, 2.23.14.7
connect, 2.34.16, 2.34.54	copy, 2.34.19
chains with alignments, 2.34.57	chemical image, 2.23.9.15
molcart, 2.34.16.1	file, 2.21.26
consensus, 2.19.7	site, 2.34.89.28
coloring, 2.19.12, 2.23.2	correlation matrix, 2.35.163
definitions, 2.23.1	covalent bound count, 2.35.137.3
consensusStrength, 2.19.7	neighbors, 2.35.101.1
conservation, 2.35.122.5, 2.35.136.8	covalently attached molecule, 2.35.101.1
constant, 2.5	cpk, 2.19.35, 5.3.13
constants, 2.5	create a covalent bond, 2.34.65.2
contact areas, 2.35.90	pharmacophore, 2.37.87
continue, 2.34.17	creating a local patch object, 2.34.18.2
contour lines, 2.35.32	credits, 4.5
surfaces, 2.23.7.5	crypt, 2.34.20
contouring density, 2.34.65.14	crystal axis vectors, 2.35.16
contrast, 2.23.5.33	symmetry transformation, 3.10.2
conversion, 5.1.6	transformations, 2.35.176
to real array, 2.35.168	crystallographic cell, 2.34.69
convert, 2.34.18, 2.34.18.2	occupancy, 2.35.107
3D to chemical, 2.35.27	symmetry intro, 1.4.2.4
3D/0D to 2D, 2.34.65.9	crystallography, 2.35.129
ICM object to PDB, 2.34.96	csv format, 2.34.84.44

cube, 2.23.14.2	class, 2.34.22
current, 5.3.9	column table, 2.34.22.16
map, 5.3.7	conf, 2.34.22.17
object, 5.3.8	directory, 2.34.22.8
working directory, 2.35.108	disulfide bond, 2.34.22.27
cursor action, 5.9.2.4	drestraint, 2.34.22.18
custom alignment color, 2.23.5.1	element, 2.34.22.31
field, 2.34.89.51	file, 2.34.22.9
interaction, 2.34.90.37	from array, 2.34.22.6
menu, 2.33, 2.34.84.3	hydrogen, 2.34.22.11
customization, 3.1.2	label, 2.34.22.19, 2.34.22.20
environment, 2.33	chemical, 2.34.22.20
and paste chemicals, 2.23.9.14, 2.23.9.15	link, 2.34.22.21
cyclic temperature protocol, 2.19.46	map, 2.34.22.22
cylinder, 2.23.14.2	molcart, 2.34.22.3
cz32, 4.5	molecule, 2.34.22.13
data visualization, 2.34.65.38	object, 2.34.22.12
database, 5.4.1	parray, 2.34.22.36
browser, 2.34.63.3	element, 2.34.22.36
connection, 2.34.16.1	peptide bond, 2.34.22.28
file, 3.5.1	plot, 2.34.22.4
import, 2.34.65.26	salts, 2.34.70.3
date, 2.34.21, 2.35.156.2	selection, 2.34.22.5
array, 2.34.21	selftether, 2.34.22.34
dcMethod, 2.22.8	sequence, 2.34.22.23
dcWeight, 2.19.8	session, 2.34.22.10
decomposition, 2.34.65.27, 2.34.92.2, 2.34.92.3	shell object, 2.34.22.1
deep learning, 2.34.53	site, 2.34.22.24
defCell, 2.24.1	alignment, 2.34.22.26
defSymGroup, 2.18.2	sstructure, 2.34.22.25
default atom colors, 2.34.89.16	stack, 2.34.22.29
color of label, 2.19.11	object, 2.34.22.30
parameters, 2.22.1	system, 2.34.22.9
value, 5.8.2	table, 2.34.22.32
define axis, 3.10.3	rows, 2.34.22.32
defining space box, 2.35.21	term, 2.34.22.33
dehtml, 2.35.126.3	tether, 2.34.22.35
del, 2.34.22.9	tree, 2.34.22.36
delete, 2.34.22	variable, 2.34.22.6
3D graphics panel, 2.34.105	views, 2.34.22
alias, 2.34.22.2	backbone, 2.35.137.1
array element, 2.34.22.6	restraint, 2.34.22.18
index, 2.34.22.6	deleting, 2.34.22.26
selection, 2.34.22.1	sites by number, 2.34.22.24
atom, 2.34.22.7	delphi, 2.37.25
bond, 2.34.22.14	density correlation, 2.19.8, 3.11.3
boundary, 2.34.22.15	fitting, 2.22.8
chemical, 2.34.22.37	in unit cell, 2.34.65.23
fragment, 2.34.22.37	densityCutoff, 2.19.13
selection, 2.34.22.37	dependent columns, 2.34.1.1.1

depth-cueing, 2.19.17	distance, 2.23.5.24, 2.35.41, 5.4.3
desolvation, 2.22.25	averaging, 2.22.6
detecting bad covalent geometry, 2.34.90.12	contact-based, 2.35.23, 2.35.23.1
proximity, 2.35.44.9	geometry, 5.4.4
diagram, 2.34.65.32	matrix, 2.35.160.5, 2.37.7
dialog generation, 2.35.11	between stack conformations, 2.35.90.11
in html documents, 2.34.44	restraint, 5.4.6
tables, 2.34.44	file, 2.38.9
scripting, 2.35.11	type file, 2.38.8
dielConst, 2.19.14	restraints, 2.34.89.22
dielConstExtern, 2.19.15	distances, 2.35.102.3
dielectric constant, 2.19.14	distribution, 1.3, 2.34.65.32
diff, 2.35.105	comparison, 2.35.136
dihedral, 2.37.4	disulfide bond, 5.4.5
angle, 2.34.65.19	diverse subset, 3.14.6.4
calculation, 3.3.10	dividing chemical into individual molecules, 2.35.154.4
directory, 2.34.22.8, 2.34.65.5, 2.35.135	dna to protein sequence translation, 2.35.175.1
display, 2.34.23	rna conversion, 2.35.138.1
GUI window, 2.34.23.26	translate, 2.35.175.1
box, 2.34.23.7	dockBatch, 3.13.1.7
clash, 2.19.5, 2.34.23.8	dockScan, 3.13.1.18
contact, 2.34.65.16	docking, 2.37.89
drestraint, 2.34.23.9	intro, 3.13.1.5
field, 2.23.5.3	result viewing, 2.37.28
from script, 2.34.23.3	simple models, 3.14.3
gradient, 2.34.23.10	timing, 3.13.1.3
grob, 2.34.23.11	with template, 3.13.1.23
label, 2.34.23.12	docksub, 3.13.1.19
gui, 2.34.23.26	docksyb.icm, 3.13.1.19
hbond, 2.34.23.13	documents, 5.5.8
label, 2.34.23.15	dollar separated file, 2.34.84.44
map, 2.23.5.13, 2.34.23.16	dominant color, 2.35.29.2
model, 2.34.23.1	donor, 3.6.1
new, 2.34.23.2	plot intro, 1.4.3.2
off-screen, 2.34.23.3	dots, 2.34.78
offscreen, 2.34.23.3	dotted surface, 2.23.5.56
origin, 2.34.23.4	double click action, 5.9.2.4
ribbon, 2.34.23.18	drestraint, 2.34.90.18, 5.4.6
rotate, 2.34.23.5	generate from structure, 2.34.65.7
site, 2.34.23.19	global weight, 2.19.6
skin, 2.34.23.20	set, 2.34.89.22
slide, 2.34.23.21	type, 5.4.7
stack, 2.34.23.6	drop, 2.19.16
string, 2.34.23.22	drug, 2.12
surface, 2.34.23.20	ds3D, 2.37.31
area, 2.23.5.3	dsCellBox, 2.37.15
tethers, 2.34.23.23	dsChem, 2.37.17
trajectory, 2.34.23.17	dsCustom, 2.37.18
volume, 2.34.23.24	dsPocket, 2.37.28
window, 2.3, 2.34.23.25	dsPropertySkin, 2.37.19

dsRebel, 2.18.5, 2.23.14.6, 2.37.25	library, 2.34.32
dsSeqPdbOutput, 2.37.26	tautomer, 2.34.31
dsSkinLabel, 2.37.27	enumeration, 2.35.27
dsStackConf, 2.37.29	eps files, 2.21.23
dsVarLabels, 2.37.30	equipotential surface, 2.35.32
dsXyz, 2.37.32	error SOAP services, 2.35.49
dump database, 2.34.110.7	ignoring, 2.21.25
dynamic gui, 5.5.5	error/warning bits cleanup, 2.34.10
ecepp, 5.5.1	errorAction, 2.22.10
edit, 2.34.24	vrestraint vs_var, 2.34.89.82
files, 2.23.14.1	evalSidechainFlex, 2.37.90
eigen value factorization, 2.35.45	evol tree intro, 1.4.3.5
eigendecomposition of a matrix, 2.35.45	evolutionary tree intro, 1.4.3.5
eigenvalues, 2.35.45	exact, 2.34.35.9, 2.34.35.10
eigenvectors, 2.35.45	match, 2.35.126.1
electro intro, 1.4.2.9	example scripts, 3.14
electroMethod, 2.22.9	excel, 2.34.84.44, 2.34.110.10
density, 2.23.7.5, 2.34.89.36, 2.34.90.21, 2.37.42, 2.37.43	exit, 2.34.34
around selection, 2.19.25	exitSeslogStyle, 2.22.11
map generation, 2.19.1	expanding substructure match, 2.34.89.70
maps, 2.23.14.1	export, 2.34.110.7
electrostatic boundary matrix, 2.35.90.10	animation, 2.34.110.31
coloring, 2.23.14.6	pdb, 2.23.14.14
isopotential surfaces, 2.34.65.13	exporting sdf, 2.34.110.11
potential, 2.34.13.4.5	expression shortcuts, 2.10.1.2
solvation, 3.7.2	tags, 2.24.9
surface, 2.37.25	comparison, 2.14.5
troubleshooting, 5.7.13	arithmetics, 2.14.2
electrostatics, 2.23.14.6	assignment, 2.14.1
intro, 1.4.2.9	comparison, 2.14.5
elements, 2.23.9.16	logical, 2.14.3
ellipsoid, 2.35.163	extending to bonded hydrogens, 2.35.137.6
elseif, 2.34.25	terminal atoms, 2.35.137.6
empty model, 2.35.109	external process, 2.34.65.1
enamine, 3.19	extracting from Markush, 2.34.55
endfor, 2.34.26	icm script arguments, 2.35.59
endif, 2.34.27	stack from object, 2.34.63.5
endmacro, 2.34.28	ez25, 3.7
endwhile, 2.34.33	factor, 5.8.13
energetics, 3.7	false negatives, 2.35.136.5
function, 2.23.14.3	family, 2.34.89.38.1
profile, 2.37.84	faq, 1.3
terms, 2.17	cheminformatics, 3.14.6
ensemble, 2.34.63.1, 2.34.94.1	chemsuper, 3.14.5
average, 3.7.5	mac gui preferences, 3.14.6.2
entropy of alignment, 2.35.136.8	molcart dump, 3.14.6.3
atom, 2.34.18.4	query, 3.14.6.1
enumerate, 2.34.29, 2.34.30, 2.34.31, 2.34.32	multiple chem overlay, 3.14.5.1
charge, 2.34.29	residue table, 3.14.4.1
chiral, 2.34.30	fast Fourier transform, 2.34.65.24

fasta, 2.23.12.15, 5.5.2	flattening 3D molecule, 2.37.17
format, 2.34.110.1	flexible superimpose, 2.37.50
feature table, 5.8.6.1	flow control, 2.15
in sequences, 2.34.89.26	fog, 2.19.17, 2.34.13.7, 2.34.23.24, 5.4.2
ffMethod, 2.22.12	color, 2.19.17
field, 2.34.89.35	fogStart, 2.19.17
name, 2.35.99.2	fold search, 5.8.4
file, 2.34.110.24	foldbank.db, 2.38.3
exists, 2.35.50	folding procedure, 3.14.1
list, 2.35.59	font, 2.34.58.1
length, 2.35.55	size, 2.34.89.38.1, 2.38.14
object origin, 2.35.55	sizes, 3.14.6.2
permissions, 2.35.55	specification, 2.34.89.38.1
time modified, 2.35.55	for, 2.34.37
type, 2.35.55	fork, 2.34.38, 2.35.70.1
files, 2.38	formal charge, 2.23.5.20, 2.34.89.12, 5.3.2
filling volume, 2.23.5.11	formatdb, 2.34.110.25
filter, 2.34.35.10, 2.34.63.3	fprintf, 2.34.39
functions, 5.5.4	fractional coordinates, 2.35.192.4
filtering table rows, 5.5.4	to abs coordinates, 2.35.16
find, 2.34.35	fragment, 3.13.1.22, 3.13.1.24
alignment, 2.34.35.1	fragmented molecule, 2.34.18.2
and replace a chemical pattern, 2.34.70.1	frame, 2.34.94, 2.34.110.31
chemical fragment, 2.34.70	free starin, 2.35.136.3
chemical, 2.34.35.5	fullscreen, 2.34.89.85
pattern, 2.34.70	function, 2.34.40, 2.34.64
substructure, 2.35.70.2	columns, 2.34.1.1.1
database, 2.19.2, 2.34.35.2	functions, 5.1.1
fast, 2.34.35.3	selecting in objects, 2.8.10
family of commands, 2.34.35	gamess, 5.5.6
in sarray, 2.35.70.8	expansion, 2.35.146.4
molcart, 2.34.35.9, 3.5	gapExtension, 2.19.18
molecule, 2.34.35.4	gapFunction, 2.24.3
motifs, 2.24.9	gapOpen, 2.19.19
pattern, 2.34.35.8	gaussian averaging, 2.35.146.2
pdb, 2.34.35.6	gcMethod, 2.22.13
pharmacophore, 2.34.35.11	genbank, 2.23.12.15
prosite, 2.34.35.7	generalized arrays, 5.1.6
scaffold, 2.35.179	generate intermediate conformers, 2.37.38
table, 2.34.35.10	generating movie images, 3.9.2.1
findFuncMin, 2.37.33, 2.37.34	genomics, 1.4.3.1
findFuncZero, 2.37.35	clustering, 2.34.43.2
findSymNeighbors, 2.37.16	intro, 1.4.3.1
find_related_sequences, 2.37.33	geometry optimization, 2.34.66.1
finding long covalent bonds, 2.35.137.1	started, 1.7
fingerprint, 2.35.41	getting data from outside, 2.32
fingerprints, 2.9	started, 1.7
to density, 2.22.8	giga, 3.18, 3.19
fix, 2.34.36	sized, 3.18, 3.19
fixed branches, 2.35.137.2	giga-sized, 3.18, 3.19

global, 2.34.41	haze, 2.19.17
glossary, 5	hb, 2.19.21
go, 2.35.44.6	hbCutoff, 2.19.21
goto, 2.34.42	hbond, 2.23.5.25, 2.23.5.26, 2.34.22.6, 5.5.7
term, 2.19.20, 2.34.89.73	color, 2.34.23.14
gpWeights, 2.19.20	display, 2.23.5.27, 2.23.5.28
gpu, 3.13.1.21	energy, 2.34.23.14
graph matching, 2.35.133	list, 2.35.160.10
graphical box, 2.34.23.7	show, 2.34.90.23
row selection, 2.35.70.5	hbondMinStrength, 2.23.5.25
selection, 2.35.137.5	faq, 3.3.4
graphics, 2.19.9, 2.34.89.4, 2.35.188, 3.2, 5.3.3	how to, 3.3.4
card, 2.23.5.52	header, 2.34.1.1
controls, 2.3, 2.38.15, 5.4.2	helical axis, 2.37.36
exists, 2.35.50	cylinders, 2.23.5.42
intro, 1.4.1, 1.4.1.4	helicity, 3.7.6
learning, 3.2.1	content calculation, 3.7.6
attributes, 2.19.4	help, 2.34.45, 2.34.45.1, 2.34.45.2
fogStart, 2.19.17	browser, 2.34.45.1
view vector, 2.34.89.80	commands, 2.34.45.3
graphviz, 2.35.160.7	functions, 2.34.45.4
greedy matching, 2.10.1.4	getting, 3.1.1
grid energy, 2.34.90.21	word, 2.34.45.2
potentials, 2.34.65.25	getting, 3.1.1
grob, 2.34.54, 5.5.3	heterogenous environment, 2.23.14.2
coloring, 2.34.13	hidden blocks, 5.1.1.1
files, 2.38.10	display, 2.34.23.3
inside-out flip, 2.34.89.42	hydrogens, 2.23.5.32
normal directions, 2.34.89.42	stack in object, 2.34.94.2
vertex, 2.23.5.21	hierarchical, 2.13
translate, 2.34.103	highEnergyAction, 2.22.14
group, 2.34.43	his-tags, 2.35.180
by column, 2.34.43.4	histogram, 2.34.65.32
column, 2.34.43.4	2D, 2.35.90
rename of table columns, 2.34.85.1	history, 2.34.46, 2.34.110.40
replacement, 2.34.68	delete, 2.34.22.10
select of table columns, 2.34.88.2	of ICM, 1.2
sequence, 2.34.43.1	hitlist, 3.13.1.17
unique, 2.34.43.2	homodel, 2.37.41
table, 2.34.43.3	homology modeling, 1.4.2.2, 2.34.7.6, 2.34.89.68, 2.34.89.69, 2.36.1, 3.14.4
grouping table by a column, 2.34.89.24	faq, 3.14.4
gui, 2.34.44, 5.9.2.4	intro, 1.4.2.2
exists, 2.35.50	output, 2.34.7.6.3
functions, 5.5.5	steps, 2.34.7.6.1
panels, 2.34.105	to export a molcart table, 3.14.6.3
programming, 2.33, 2.34.44, 2.34.89.24	html, 2.11, 2.34.44, 2.35.99.4, 5.5.8
gvim text editor, 5.8.2	document order, 2.34.89.40
gzip files, 2.34.15.4	tag removal, 2.35.126.3
hash, 2.12, 5.3.6	html-formatted text, 5.5.8
table, 5.3.6	html5, 2.11

hydration, 2.23.14.2, 2.35.7	cmp, 2.38.33
parameters, 2.38.13	cn, 2.38.9
hydrogen bond, 2.23.5.25, 2.23.5.26, 2.34.65.17, 5.5.7	cnf, 2.38.7
bonding parameters, 2.38.12	cnt, 2.38.8
cutoff, 2.19.21	cod, 2.38.4
bonds, 2.35.102.3	col, 2.38.24
display, 2.23.5.32	gro, 2.38.10
placement, 2.34.89.25	gui, 2.33
hydrophobicity profile, 3.3.12	hbt, 2.38.12
iSee, 5.8.14	hdt, 2.38.13
i_2out, 2.18.4	htm, 2.38.11
i_out, 2.18.3	iar, 2.38.35
iarray, 2.34.22.6, 2.35.56.1, 2.35.66.2, 2.35.70.8, 5.6.1	lps, 2.34.7.6.2
making, 2.35.66.1	map, 2.38.16
icb files, 5.8.14	mat, 2.38.37
GUI, 2.34.89.40	ob, 2.38.18
algorithms, 4.3	pdb, 2.38.28
application refs, 4.4	prf, 2.38.34
literature, 4.3	rar, 2.38.38
archive, 2.34.84.2	res, 2.38.20
arguments, 2.35.59	rs, 2.38.23
binary, 2.35.108	rst, 2.38.22
branching, 2.15.2	sar, 2.38.36
commands, 2.34	se, 2.38.30
controls, 2.15	seq, 2.38.29
flags, 2.1	tab, 2.38.25
functions, 2.35	tot, 2.38.26
graphics, 3.2	trj, 2.38.17
history, 1.2	var, 2.38.21
jumps, 2.15.3	vwt, 2.38.27
learning, 3.1.4	icmCavityFinder, 2.37.14
loops, 2.15.1	icmMacroShape, 2.37.88
macros, 2.37	icmPmfProfile, 2.37.23
main refs, 4.2	icmPocketFinder, 2.37.89
menus, 2.23.10.1	icmscript, 2.34.84.4
method literature, 4.4	arguments, 2.35.59
molecules, 2.16	if, 2.34.47
object file, 2.38.18	ignoring swiss secondary structure, 2.24.10
preferences, 2.22.1	illegal smiles, 2.35.70.2
session, 2.22.11	image, 3.2.6
shell, 3.1	annotation, 3.2.5
functions, 2.36	center, 3.2.8
support, 1.3	format, 5.9.3
table, 2.23	high quality, 3.2.2
ali, 2.38.31	parray, 5.7.3.3
all, 2.38.32	resolution, 3.2.2
bbt, 2.38.5	rotation, 3.2.3
bst, 2.38.6	implicit continuous solvation, 2.38.13
cfg, 2.38.14	solvation, 2.34.89.72
clr, 2.38.15	imposing tether, 2.34.89.68, 2.34.89.69

ops, 2.14.4	l_antiAlias, 2.20.1
incidence, 2.35.90.13	l_autoLink, 2.20.2
increasing the number of shell variables, 2.38.14	l_bpmc, 2.20.3
increment charge, 2.34.89.10	l_breakRibbon, 2.20.4
index expressions, 2.6	l_bufferedOutput, 2.20.5
in array, 2.35.70.4	l_bug, 2.20.6
substring, 2.35.70.3	l_caseSensitivity, 2.20.7
table, 2.34.110.24	l_commands, 2.20.8
entry, 2.35.135.1	l_confirm, 2.20.9
sdf-file path, 2.35.108	l_easyRotate, 2.20.10
indices of labeled table rows, 2.35.70.6	l_info, 2.20.11
selected table rows, 2.35.70.5	l_minRedraw, 2.20.12
infinity, 2.35.168	l_neutralAcids, 2.20.13
info, 2.34.48	l_out, 2.20.14
molcart, 2.34.48.1	l_print, 2.20.15
inner join, 2.34.50	l_racemicMC, 2.20.16
insert rows, 2.34.1.4	l_readMolArom, 2.20.17
integer, 5.6.2	l_showAccessibility, 2.20.18
array, 2.35.66, 5.6.1	l_showMC, 2.20.19
output, 2.18.4	l_showMinSteps, 2.20.20
shell variables, 2.18	l_showResCodeInSelection, 2.20.21
intensity, 2.35.90.4	l_showSites, 2.20.23
interaction cutoff, 2.20.27	l_showSpecialChar, 2.20.22
lists, 2.20.27, 2.23.14.3	l_showSstructure, 2.20.24
interactive docking, 1.4.2.8	l_showTerms, 2.20.26
interatomic distance, 2.19.10, 2.34.65.16, 2.35.151	l_showWater, 2.20.25
potential, 2.34.89.51, 2.34.90.37	l_updateLists, 2.20.27
interface comparison, 2.34.14.3	l_warn, 2.20.28
residues, 3.3.5	l_wrapLine, 2.20.29
torsions, 3.3.7	l_writeStartObjMC, 2.20.30
view, 2.37.28	l_xrUseHydrogen, 2.20.31
intermolecular bond, 2.34.72.3	label, 2.34.23.22, 5.6.3
internal coordinate file, 2.38.21	fonts, 2.38.15
coordinates, 2.8.9	large text, 2.34.84.40
positional restraints, 5.9.4	latent, 2.35.102.6
interplanar angle, 2.37.4	learn, 2.34.51, 2.34.53, 2.35.109
interpolate, 2.35.29.1	ann, 2.34.53
interpolation, 2.35.29.1	atom, 2.34.51.1
interruptAction, 2.22.15	chemical, 2.34.51.2
inverting array order, 2.35.66.2, 2.35.122.2	left join, 2.34.50
italic, 2.34.89.38.1	triangle of a matrix, 2.35.90.3
iterative overlay, 2.34.97	library to replacement groups, 2.34.65.27, 2.34.92.2, 2.34.92.3
superposition, 2.23.14, 2.34.98	ligand based screening, 3.15
javascript, 2.11	binding, 2.37.28
join, 2.34.50	docking, 3.13, 3.13.1
tables, 2.34.50	intro, 1.4.2.6
keep, 2.34.49	editing, 1.4.2.8
kernel models quality, 2.35.136.5	editor, 2.37.37
mapping, 2.38.15	fit, 3.13
kmz, 5.5.3	view, 2.23.5.31

light, 2.23.5.34	library, 2.34.7.6.2
lightness, 2.35.90.4	modeling, 1.4.2.3
limits, 2.38.14	intro, 1.4.2.3
line thickness, 2.23.12.5	search, 2.34.7.6.2
in 2D chemicals, 2.23.9.14	resolution shape, 2.37.88
lineWidth, 2.19.22	lower case, 2.35.167
linear chemical notation, 2.26	ma29, 3.11
regression, 2.35.84	macro, 2.34.64, 5.6.5
grob, 2.34.54	macro_def, 5.6.5
group, 2.34.55	main ICM references, 4.2
internal variables of molecular object, 2.34.56	concepts, 3.10.1
ms2ali, 2.34.57	make, 2.34.65
sequences to 3D objects, 2.34.57	3d label, 2.34.65.15
to alignment, 2.34.57	angle, 2.34.65.18
variable, 2.34.56	background, 2.34.65.1
variables, 2.34.56	blast index, 2.34.110.25
linked alignment, 2.35.99	bond, 2.34.65.2
sequence, 2.35.99	chain, 2.34.65.3
linux shell, 2.34.99, 5.10.2	multi, 2.34.65.3
list, 2.34.58	boundary, 2.34.65.4
binary, 2.34.59	directory, 2.34.65.5
database, 2.34.60	distance, 2.34.65.16
directory, 2.34.61	disulfide bond, 2.34.65.6
font, 2.34.58.1	drestraint, 2.34.65.7
html documents, 2.35.99	factor, 2.34.65.8
molcart, 2.34.62	flat, 2.34.65.9
database, 2.34.62	chem_array, 2.34.65.9
of files, 2.35.135	grob, 2.37.36
updates, 2.34.66	from image, 2.34.65.11
listUpdateThreshold, 2.19.23	matrix, 2.34.65.12
literature, 4.1	image, 2.34.65.11
load, 2.34.63	map, 2.34.65.10
conf, 2.34.63.1	matrix, 2.34.65.12
frame, 2.34.63.2	potential, 2.34.65.13
molcart, 2.34.63.3	skin, 2.34.65.14
object, 2.34.63.6	hbond, 2.34.65.17
solution, 2.34.63.4	image, 2.34.65.20
stack object, 2.34.63.5	index fasta, 2.34.84.24, 2.34.110.24
loadEDS, 2.37.42	key, 2.34.65.21
loadEDSweb, 2.37.43	map, 2.34.65.22
local, 3.5.1	cell, 2.34.65.23
logarithm, 2.35.85	factor, 2.34.65.24
logical, 5.6.4	potential, 2.34.65.25
operations, 2.14.3	xray, 2.34.65.31
variables, 2.20	molcart, 2.34.65.26
logical_ops, 2.14.3	molsar, 2.34.65.27
logicals, 2.20	pca, 2.34.65.29
long axes, 2.35.163	peptide bond, 2.34.65.30
loop database rebuilding, 2.34.110.28	plot, 2.34.65.32
interrupt, 2.19.47	reaction, 2.34.65.33

alignment, 2.34.65.34	mcBell, 2.19.26
from alignment, 2.34.65.34	mcJump, 2.19.27
random, 2.34.65.36	mcShake, 2.19.28
torsion, 2.34.65.19	mcStep, 2.19.29
tree, 2.34.65.37	mean force, 2.34.89.51, 2.34.90.37
object, 2.34.65.38	median value, 2.35.93
unique, 2.34.65.39	membrane, 2.23.14.2, 3.20
makeAxisArrow, 2.37.36	memorizing positions, 3.2.4
makeIndexChemDb, 2.37.44	menu, 2.34.67
makeIndexSwiss, 2.37.45	script, 3.1.3
makePdbFromStereo, 2.37.46	merge PDB, 2.37.92
makePharma, 2.37.87	arrays to table, 2.34.43.3
makeSimpleDockObj, 2.37.47	continuation lines, 2.34.84.39
makeSimpleModel, 2.37.48	objects, 2.34.72.2
making predictive models, 2.34.51	parts of molecule, 2.34.72.3
manual style, 1.5	pdb, 3.4.4
map, 2.19.25, 2.23.5.13, 2.23.6.1, 5.6.6	sarray into string, 2.35.158
aa property to sequence, 2.35.122.1	stacks, 3.7.7
averaging, 2.35.146.5	tables, 2.34.4.3, 2.34.50
calculation, 2.34.65.24	merge2, 3.8.7
conversion, 2.34.65.31	mergePdb, 2.37.92
file, 2.38.16	several chemical, 2.35.158.1
fitting, 2.22.8	merging into one molecule, 2.34.72.3
format, 5.6.6	mesh, 2.35.109, 2.35.189
mean value, 2.35.94	point radius, 2.23.5.21
min value, 2.35.95	score, 3.13.1.12
name, 2.35.86	mfMethod, 2.22.16
operations, 5.6.6	mfWeight, 2.19.30
transformations, 2.35.146.5	mimel, 5.6.8
trimming, 2.35.22	mimelDepth, 2.19.31
value sigma, 2.35.133	mimelMolDensity, 2.19.32
on atoms, 2.34.89.36	minNumGrad, 2.34.66
contouring, 2.34.65.14	minTetherWindow, 2.18.8
mapAtomMargin, 2.19.25	minimization exit criteria, 2.34.66
mapSigmaLevel, 2.19.24	minimize, 2.18.10, 2.34.66
mapping chemical equivalences, 2.35.70	cartesian, 2.34.66.1
properties to sequence, 2.35.122.4	loop, 2.34.66.2
and factors, 3.11	stack, 2.34.66.3
margin, 2.23.6.1	tether, 2.18.8, 2.34.66.4
mass-spectrometry functions, 2.34.30, 2.34.31, 2.34.32	drop, 2.19.16
matching chemicals, 2.35.70.2	minimizeMethod, 2.22.17
hydrogens, 2.34.89.70	missing bonds, 2.34.72.3
matrix, 5.6.7	loop, 2.23.5.7, 2.23.5.8
derivatives, 2.35.80	residues, 2.35.54.1
new, 2.35.90.1	triangles, 2.35.189
plot, 2.35.32	mkUniqPdbSequences, 2.37.49
map value, 2.35.91	mlr, 2.34.52
maxColorPotential, 2.18.5, 2.37.25	mm26, 3.8
maxMemory, 2.18.7	mmcif, 5.6.10
movie, 3.9.2	mmff, 5.6.9

show atom types, 2.34.90.11	monte carlo, 2.34.71
mnSolutions, 2.18.9	montecarlo, 2.18.11, 2.18.13, 2.18.14, 2.18.15, 2.18.19, 2.22.7, 2.34.71
mncalls, 2.18.10	local, 2.18.16
mncallsMC, 2.18.11	trajectory, 2.34.23.17
mnconf, 2.18.12	moprphing, 2.37.38
mnhighEnergy, 2.18.13	more, 5.6.13
mnreject, 2.18.14	morph, 2.34.23.6
mnvisits, 2.18.15	to tether target, 2.37.38
model reliability, 2.37.23	morph2tz, 2.37.38
modify, 2.34.68	morphing, 2.34.23.6, 2.34.89.68, 2.34.89.69, 2.34.94.3
and reroot, 2.34.18.4	mouse controls, 2.3
chem, 2.34.70	file, 2.34.110.31
charge, 2.34.70.2	move, 2.34.72
delete salt, 2.34.70.3	alignment sequence, 2.34.72.7
normalize, 2.34.70.4	atoms, 2.34.89.3
chemical column, 2.34.70.3	bonding, 2.34.72.3
find replace, 2.34.70.1	column, 2.34.72.5
molcart, 2.34.70.5	element, 2.34.72.4
rotate, 2.34.69	file, 2.21.28, 2.34.85.3
modifyGroupSmiles, 2.37.37	fragments together, 2.34.72.3
modules, 1.4.4	ligand out, 2.34.92.6
mol, 2.34.84.49, 2.34.84.50, 2.34.110.11, 2.34.110.24, 5.6.11	molecule, 2.34.72.1
file, 2.35.156.3	ms_molecule, 2.34.72.1
to icm, 2.34.18.3	multiple molecules, 2.34.72.2
translation, 3.2.4	object, 2.34.72.2
mol-file to chem-table element, 2.35.109	plane, 2.34.72.6
mol-format, 2.23.14.7	sequence, 2.34.72.7
mol2, 5.6.12	table column, 2.34.72.5
molcart, 2.27, 2.34.16.1, 3.5	movie, 2.34.94.3
connection options, 3.5.2	images by frame, 3.9.2.2
molecular, 2.35.58, 5.7.3.1	molecular simulation, 3.9.2
arrays, 5.7.3	rotate view, 3.9.1
dynamics, 3.20	zooming, 3.9.1
manipulations, 3.8	moving grobs with molecules or objects, 2.34.54
modifications, 3.8.5	selection to another object, 2.35.137.8
object, 5.7.1	mpeg, 2.34.110.31
objects, 2.16	ms_, 2.8.6
surface, 2.34.90.9, 5.8.7	multi center drestraint, 2.22.6
views, 1.4.1.1	multi-part molecule, 2.34.18.2
volume, 2.35.114	multicore, 2.35.70.1
molecule, 2.7, 2.34.54	multiline input, 2.34.84.5
create, 3.8.4	multiple NMR models, 2.23.14.5
properties, 2.34.89.34	alignment, 2.34.3.3
rotation, 3.2.3	to pairwise similarities, 2.37.7
translation, 3.2.3, 3.2.4	conformation storage, 5.8.9
create, 1.7.2	conformations, 2.34.63.1, 2.34.94.1
intro, 1.7.2, 2.7	linear regression, 2.34.52
sort/reorder, 2.34.91.5	mol as text, 2.35.156.3
selecting, 2.8.6	object file, 2.34.84.2
molt, 2.27, 3.5.1	sequence alignment intro, 1.4.3.4

multiprocessor, 2.34.38	obsolete, 2.19.54
mutate residue, 2.34.68	occlusion shading, 2.34.13
mutating residue, 3.8.5	octanol transfer, 2.35.114
mute, 5.6.15	off, 2.34.84.22
mysql, 2.34.16.1	format, 5.5.3
nLocalDeformVar, 2.18.16	oligonucleotide melting, 2.35.164
nProc, 2.18.18	on-line help, 2.34.45.1, 2.34.45.2
nSsearchStep, 2.18.17	third, 2.35.37
name, 2.35.79	only, 5.7.2
atom fields, 2.34.89.34	ontology, 2.35.44.6
naming compounds, 2.34.89.47	openGL window, 2.34.105
nearest sequence, 2.35.95	operating system, 2.34.22.9, 2.34.99, 2.35.188, 5.10.2
neato, 2.35.160.7	optimal chemical superposition, 3.14.5.1
neighbor joining, 2.34.65.38	optimization, 2.34.71
neighbors, 2.35.151	Hbond, 2.37.91
nested script, 5.8.2	hydrogen bond, 2.37.91
neural network, 2.34.53	optimizeHbonds, 2.37.91
real array, 2.35.122	or, 2.14.3
nice, 2.37.39	order, 2.34.3.1, 2.34.72.7
image, 3.2.2	original sequence names, 2.23.12.15
non-redundant, 3.4.3	os_, 2.8.5
normal distribution, 2.35.121	other variables, 2.24
normalize chemicals, 2.34.70.4	out-of density atoms, 2.34.90.21
defined, 2.35.168	output, 2.18.3
nota, 1.5	outside penalty, 2.23.6.1
notational conventions, 1.5	overlap, 2.35.70.10
nproc, 2.34.38	by atom pairs, 2.34.97
nucleotides, 2.21.24	chemical substructure, 2.37.22
number, 2.18.18	overview, 1.4
of dots, 2.23.5.55	pK shift, 3.7.3
elements, 2.35.102	pKa, 2.34.22.20, 2.34.89.11, 2.34.89.12
hydrogen bonds, 2.34.90.23	model, 2.34.89.12
molecules in objects, 2.35.137.4	packing density, 3.3.8
occurrences, 2.35.102	pair-distances, 2.34.22.6
residues in molecules, 2.35.137.4	pairdistance parray, 2.23.5.24
van der Waals contacts, 2.34.90.13	pairwise interactions, 2.34.89.51
transfer from sequence, 2.34.3.2	panel layout, 2.23.8.6
nvis, 2.35.66.6	paragraphs, 2.34.110.24
object, 2.34.13.1, 2.34.54, 5.7.1	parallel, 2.18.18
in table, 2.35.109	computing, 2.35.70.1
parray, 5.7.3.1	processing, 2.34.38
properties, 2.34.89.34	parallelization, 2.35.70.1
stack, 5.8.9	parameter list file, 3.14.6.2
to chemarray, 2.35.27	parray, 2.34.22.6, 5.7.3
user fields, 2.35.54.1	parrayTo3D, 2.37.83
assign comment, 2.34.89.17	parrayToMol, 2.37.82
source file, 2.35.55	parse SOAP message, 2.35.186
translate, 2.34.103	parsing, 2.35.89
merge, 3.8.6	web pages, 2.34.84.47
selecting, 2.8.5	partial least squares, 2.34.51

sum, 2.35.77	plotSeqProperty, 2.37.60
passing arguments, 5.8.2	3d, 1.4.3.7
by reference, 2.34.64	plotting van der Waals, 3.7.1
pattern, 5.7.4	faq, 3.7.1
search, 2.34.35.2	pls, 2.34.51
pause, 2.34.73	column contributions, 2.35.160.8, 2.35.160.9
pdb, 5.6.10, 5.7.6	model, 2.35.160.8, 2.35.160.9
file creation time, 2.35.38	weights, 2.35.160.8, 2.35.160.9
files, 2.38.28	pmf, 2.22.16
format, 2.34.84.48	residue profile, 2.37.23
merge, 3.4.4	pmf-file, 2.38.19
sequence generation, 3.4.3	pmffile, 2.38.19
pdbDirStyle, 2.22.18	png, 2.34.110.22, 2.34.110.36, 5.7.5
peptide, 5.7.7	pocket, 2.37.28, 2.37.89, 3.13.1.1
docking, 3.12.5	point coordinates, 2.35.192.1
folding, 1.4.2.1	size, 2.23.5.21
intro, 1.4.2.1	pointer array, 5.7.3
personal gui controls, 3.1.2	polar hydrogens, 2.23.5.32
setup, 3.1.2	surface area, 2.35.114
ph30, 3.12	polarization charge, 3.7.2, 5.7.13
ph4, 5.7.8	positional constraint, 2.23.14.12
object faq, 3.6.1	postscript, 2.21.23
pharmacophore, 2.34.12, 3.5, 5.7.8	potential surface, 2.23.14.6
faq, 3.6	coloring, 5.7.13
grid type definitions, 2.34.89.73	pov-ray, 2.34.110.38
object, 3.6.1	pow, 2.35.37
objects, 3.6	precision, 2.35.136.5
pharmacophores, 3.6	predict, 2.34.76
psi plot, 2.37.58	predictSeq, 2.37.61
pipe, 2.27, 2.34.84.43	prediction model, 2.35.84
piping, 2.27	quality, 2.35.136
placeLigand, 2.37.50	score, 2.35.136
planar angle, 2.34.65.18	predictive models, 2.34.51.2
plot, 2.34.65.32, 2.34.74	preference, 2.22
3D 2Dfunction, 3.12.3	system, 2.22.1
shape, 3.12.4	preferences, 3.1.2.3
area, 2.34.75	prepSwiss, 2.37.62
grid line width, 2.23.12.5	previous atom, 2.35.101.1
histogram, 3.12.2	principal axes, 2.35.163
how to, 3.12	component analysis, 3.3.9
simple, 3.12.1	inertia moments, 2.35.88
plot2DSeq, 2.37.51	print, 2.34.77
plotBestEnergies, 2.37.54	bar, 2.34.78
plotCluster, 2.37.56	image, 2.34.80
plotFlexibility, 2.37.55	to string, 2.34.93
plotMatrix, 2.37.57	printMatrix, 2.37.63
plotRama, 2.37.58	printPostScript, 2.37.64
plotRose, 2.37.59	printTorsions, 2.37.65
plotSeqDotMatrix, 2.37.52	printf, 2.34.79
plotSeqDotMatrix2, 2.37.53	problem, 3.14.6.2

profile, 2.35.136.3, 5.7.9	rdBlastOutput, 2.37.68
program overview, 1.4	rdSeqTab, 2.37.69
progress bar, 2.34.78	reaction, 2.34.65.33
progression, 2.34.78	group file, 2.34.55
project setup, 3.13.1.6	read, 2.34.84, 2.34.84.56, 2.34.84.57
projected alignment, 2.35.99.3	FILTER, 2.34.84.6
projecting surface charge, 3.7.2	alignment, 2.34.84.12
property, 2.34.89.52, 2.34.89.53, 2.34.89.54	all, 2.34.84.7
grids, 2.19.20	binary, 2.34.84.2
map, 2.34.89.73	blob, 2.34.84.38
superposition, 2.34.89.73	color, 2.34.84.13
prosite, 5.7.10	column, 2.34.84.51
pattern, 5.7.4	comp_matrix, 2.34.84.14
protac, 3.16	conf, 2.34.84.15
protein docking, 2.35.192.3	csd, 2.34.84.16
intro, 1.4.2.5	csv, 2.34.84.44
engineering, 2.24.9	database, 2.34.84.17
grid docking, 3.14.2	drestraint, 2.34.84.18
health, 2.37.58	type, 2.34.84.19
topology, 2.23.5.42	entries from database, 2.34.84.8
protonation states table, 2.35.160.11	factor, 2.34.84.20
psa, 5.7.12	file by chunk, 2.34.84.40
purple box, 2.35.21	from file, 2.34.84.1
qstat, 3.13.1.19	string, 2.34.84.5
qsub, 3.13.1.19	fromstring, 2.34.84.5
quadratic equation, 2.35.147	ftp http, 2.34.84.9
quantum mechanics, 2.34.84.21, 2.34.110.17	gamess, 2.34.84.21
qubic equation, 2.35.148	grob, 2.34.84.22
query, 3.14.6.1	gui, 2.34.84.3
molcart, 2.34.81	html, 2.34.84.4
question mark operator, 2.35.156.7	file, 2.34.84.4
quit, 2.34.82	iarray, 2.34.84.23
property transfer via alignment, 2.35.122.3	index, 2.34.84.24
r_2out, 2.19.34	table, 2.34.84.8
r_out, 2.19.33	json, 2.34.84.57
radii.electrostatic, 2.35.120	library, 2.34.84.25
van der Waals, 2.35.120	mmff, 2.34.84.26
rainbow, 2.35.29.1	librarymmff, 2.34.84.26
ramachandran faq, 3.3.3	map, 2.34.84.27
how to, 3.3.3	matrix, 2.34.84.28
random array, 2.35.121	menu file, 2.34.84.3
order, 2.35.139	mol, 2.20.13, 2.34.84.8, 2.34.84.29
sequence, 2.34.65.36	mol2, 2.34.84.8, 2.34.84.30
randomSeed, 2.18.19	object, 2.34.84.32
randomize, 2.18.19, 2.34.83	parray, 2.34.84.32.1
angles, 2.34.83.1	pdb, 2.23.14.4, 2.23.14.5, 2.34.84.2, 2.34.84.33
coordinates, 2.34.83	sequence, 2.34.84.34
torsions, 2.34.83	profile, 2.34.84.35
rarray, 2.34.22.6, 2.35.56.1, 2.35.70.8, 2.35.122.2, 5.7.11	prosite, 2.34.84.36
properties, 2.35.122.4	rarray, 2.34.84.37

sequence, 2.34.84.8, 2.34.84.41	syntax, 2.10.1
database, 2.34.84.41.1	regression, 2.34.51
smiles, 2.34.84.46	regul, 2.37.67
stack, 2.34.84.42	regular expression, 2.10, 2.35.70.4, 2.35.89
string, 2.34.84.43	filter, 2.34.84.1
table, 2.34.84.44	expression, 2.35.126.3
chunk, 2.34.84.45	regularization, 2.18.8, 2.34.66.4, 5.7.15
csv, 2.34.84.44	procedure, 3.8.3
html, 2.34.84.47	rejectAction, 2.22.19
mmcif, 2.34.84.48	relational database, 2.35.149
mol, 2.34.84.50	relative accessible area of atoms, 2.22.2
mol2, 2.34.84.49	release notes, 1.1
text, 2.34.84.40	remarkObj, 2.37.70
trajectory, 2.34.84.31	remove columns, 2.34.22.16
and save a fragment, 2.34.84.31.1	expression tags, 2.35.180
write, 2.34.84.31.1	file, 2.34.22.9
unix, 2.34.84.10	trailing blanks, 2.35.178
cat, 2.34.84.11	removing html tags, 2.34.84.47
variable, 2.34.84.52	outliers, 2.35.178
view, 2.34.84.53	rename, 2.34.3.1, 2.34.85
vrestraint, 2.34.84.54	chemicals, 2.34.89.47
type, 2.34.84.55	column table, 2.34.85.1
with filter, 2.34.84.6	file, 2.34.85.3
xml, 2.34.84.56	molcart, 2.34.85.2
readMolNames, 2.24.11	system, 2.34.85.3
readcomp_matrix, 2.34.84.14	renaming, 2.23.12.15
reading external tool output, 2.34.65.1	reorder, 2.34.72.7
from standard input, 2.34.84.43	alignment sequences, 2.34.110.1
pdb from ftp, 2.21.18	array, 2.35.139
web, 2.21.19	columns by function, 2.34.91.3
restraint, 2.34.84.54	objects, 2.34.91.4
real, 3.19, 5.7.14	replace matching array element, 2.35.126.1
array, 5.7.11	without interpretation, 2.35.126.2
shell variables, 2.19	replacing scaffold in a library, 2.34.70.1
space refinement, 2.34.65.31	reproducible randomness, 2.18.19
reals, 2.19	reroot, 2.34.18.4
rebel, 2.18.5, 2.23.14.6, 5.7.13	selections, 3.3.6
rebuild molcart index, 2.34.7.11	resLabelShift, 2.19.35
recalculate dependent values, 2.34.7.2	resLabelStyle, 2.22.20
values, 2.34.1.1.1	reserved names, 2.24
receptor, 3.13.1.1	residue, 2.34.13.1, 5.7.16
preparation, 3.13.1.1	accumulators, 2.35.63
redefine hydrogen coordinates, 2.34.89.25	alignment, 2.34.89.68, 2.34.89.69
references, 4	conservation, 2.35.122.5
refineModel, 2.37.66	contact area matrix, 2.35.90.8
reflections, 2.23.5.33	areas, 2.35.7.1
refresh view, 2.34.23.2	field, 2.34.89.34
refs, 4.1	gap, 2.23.5.7, 2.23.5.8
regexp, 2.10, 2.35.89	label, 2.19.35, 2.34.3.2
back references, 2.10.1.3	library file, 2.38.20

translation, 2.23.14.14	chem, 2.34.87.4
number, 2.35.66.5	grob, 2.34.87.2
table, 2.35.160.3	object, 2.34.87.1
property averaging, 2.35.146.3	view, 2.34.87.3
calculation, 2.35.63	rotation, 2.34.23.5
proximity, 2.35.90.8	angle, 2.35.17
ranges, 2.8.11	rounding, 2.35.122
selection, 2.20.21	a real, 2.35.156
as string, 2.35.156.8	output, 2.34.90.45
function, 2.35.127	rsWeight, 2.19.36
table, 3.14.4.1	rs_, 2.8.7
tethering, 2.34.89.68, 2.34.89.69	ruler, 2.19.10
user field, 2.35.54.1	script, 2.34.8
residue_selections, 2.8.11	running a docking job, 3.13.1.18
selecting, 2.8.7	dock job, 3.13.1.9
resizing, 2.35.68	script from html, 5.8.2
resorting nodes edges, 2.35.160.7	s-s bond, 5.4.5
restore, 3.14.6.2	s_alignment_rainbow, 2.21.1
defaults, 2.34.85.4	s_blastdbDir, 2.21.2
preference, 2.34.85.4	s_editor, 2.21.3
restraining molecules to shapes, 2.23.14.12	s_entryDelimiter, 2.21.4
restraint, 3.20	s_errorFormat, 2.21.5
restraints, 2.17, 2.34.89.68, 2.34.89.69	s_fieldDelimiter, 2.21.6
torsion, 2.34.89.81	s_helpEngine, 2.21.7
return, 2.34.86	s_icmPrompt, 2.21.10
reverse complement, 2.35.138.2	s_icmhome, 2.21.8, 3.1.2.1
lighting, 2.34.89.42	s_imageViewer, 2.21.11
normals, 2.34.89.42	s_inxDir, 2.21.9
reversing order, 2.35.66.2	s_javaCodeBase, 2.21.12
rgb, 2.35.90.4, 5.7.17	s_labelHeader, 2.21.13
matrix, 2.35.29	s_lib, 2.21.14
ribbon, 5.7.18	s_logDir, 2.21.15
bullets, 2.23.5.7	s_out, 2.21.16
diagram, 2.23.5.42, 2.23.5.43	s_pdbDir, 2.21.17
ribbonColorStyle, 2.22.21	s_pdbDirFtp, 2.21.18
ribbonStyle, 2.22.22	s_pdbDirWeb, 2.21.19
ride, 3.19	s_printCommand, 2.21.21
ridge, 3.13.1.21	s_projectDir, 2.21.20
right join, 2.34.50	s_prositeDat, 2.21.22
rigid chemical superposition, 2.34.97	s_psViewer, 2.21.23
ring, 2.35.130	s_reslib, 2.21.24
center coordinates, 2.35.192.2	s_skipMessages, 2.21.25
sampling, 3.17	s_sysCp, 2.21.26
templates, 2.34.89.8	s_sysLs, 2.21.27
rm, 2.34.22.9	s_sysMv, 2.21.28
rocking, 2.34.23.5	s_sysRm, 2.21.29
root mean square deviation, 2.35.136.5	s_tempDir, 2.21.30
roots, 2.35.147, 2.35.148	s_translateString, 2.21.31
rotate, 2.34.87	s_userDir, 2.21.32
2D-chem in a table column, 2.34.87.4	s_usrlib, 2.21.33

s_webViewer, 2.21.35	coordinates, 2.35.137.7
s_xpdbDir, 2.21.36	iarray, 2.35.137
sa23, 3.3	length, 2.35.137.13
sampling grid, 2.35.192.3	occupancy, 2.35.137.7
sarray, 2.34.22.6, 5.8.1	user field, 2.35.137.7
transformation in place, 2.34.102.1	chemical, 2.34.88.1
save preferences, 2.34.110.42	column table, 2.34.88.2
print, 3.2.6	lines, 2.34.84.1
sdf file, 2.34.110.11	tether partners, 2.35.137.12
saving graphics to album, 2.34.65.20	vw partners, 2.35.137.12
image, 2.34.110.36	selectMinGrad, 2.19.37
scaffold, 2.35.178	selectSphereRadius, 2.19.38
scaffolds, 2.34.55	selected stack conformations, 2.34.22.17
scanMakeHitlist, 3.13.1.17	selecting by b-factor, 2.35.137
scoring, 3.13.1.4	y z, 2.35.137
screen X, 2.35.190	columns, 5.9.1
coordinates, 2.35.190	from clusters, 3.14.6.4
script, 2.35.99.4, 5.8.2	neighboring elements, 2.35.101
file name, 2.35.55	residues, 3.3.6
inside ICM, 5.8.2	saving, 2.35.66.4
name, 5.8.2	selection, 2.8, 2.35.137, 2.35.137.6
image generation, 2.34.23.3	elements, 2.8.4
scripting molecular movements, 3.2.4	examples, 2.8.3
sdf, 2.23.14.7, 2.27, 2.34.110.24, 5.6.11	functions, 2.8.10
file, 2.34.84.49, 2.34.84.50, 2.34.89.47, 2.34.110.11, 2.35.156.3, 5.7.3	gap patching, 2.35.137, 2.35.137.11
to chem-table, 2.35.109	level, 2.8, 2.35.182
search for chemical pattern, 2.35.56.3	levels, 2.8.2
pdb headers, 3.4.5	simplification, 2.35.137.11
prosite, 3.4.1	transfer, 2.35.137, 2.35.156.8
sequence pattern, 2.34.35.8	type, 2.8
searchObjSegment, 2.37.73	types, 2.8.1
searchPatternDb, 2.37.71	variable, 2.24.12
searchPatternPdb, 2.37.72	atoms, 2.8.8
searchSeqDb, 2.37.74	functions, 2.8.10
searchSeqFullPdb, 2.37.76	molecules, 2.8.6
searchSeqPdb, 2.37.75	objects, 2.8.5
searchSeqProsite, 2.37.77	output, 2.24.15
searchSeqSwiss, 2.37.78	residues, 2.8.7
searches and alignments, 3.4	torsions, 2.8.9
second moments, 2.35.163	variables, 2.8.9
secondary structure derivation from 3D, 2.34.5.1	selections, 2.34.89.34
schematic, 2.23.5.42	in molecular objects, 2.8
segMinLength, 2.18.20	selftether, 2.23.14.12, 5.9.4
segment, 5.8.4	seq_ali_project, 2.35.156.6
select, 2.34.88	sequence, 2.35.172, 2.35.173, 5.8.3
atoms by number of bonded atoms, 2.35.137.3	alignment, 2.35.5.1, 2.37.1
of the fixed torsions, 2.35.137.2	intro, 1.4.3.3
based on alignment, 2.35.137.14	analysis intro, 1.4.3
bfactor, 2.35.137.7	assembly, 2.34.43.2
center of mass, 2.35.137.15	belongs to alignment, 2.35.70

distance, 2.35.137	comp_matrix, 2.34.89.20
matrix from alignment, 2.35.90.9	current map, 2.34.89.45
dotplot, 1.4.3.2	object, 2.34.89.48
from alignment, 2.34.22.23	directory, 2.34.89.21
pdb, 2.34.65.35	drestraint, 2.34.89.22
identity, 2.37.7, 2.37.8	type, 2.34.89.23
intro, 1.4.3	electrostatic radii, 2.34.89.79
modification, 2.35.180	error, 2.34.89.33
neighbor, 2.35.99.3	field, 2.34.89.34
parray, 5.7.3.2	alignment, 2.34.89.35
pattern, 5.7.4	map, 2.34.89.36
position correspondence, 2.35.160.3	name, 2.34.89.37
positional weights, 2.34.89.1	font, 2.34.89.38
redundancy removal, 2.34.43.2	grob, 2.34.89.39
search, 2.34.35.2	foreground, 2.34.89.40
selection, 2.34.22.23	format, 2.34.89.41
structure alignment, 2.36.1	grob, 2.34.89.42
to alignment transfer, 2.35.122.3	coordinates, 2.34.89.42
type, 5.8.3	label, 2.34.89.42
sequence-alignment mapping, 2.35.156.5, 2.35.156.6	group, 2.34.89.63
sequence-structure alignment, 2.35.5.1	column, 2.34.89.24
output format, 2.18.21, 2.18.22	hydrogen, 2.34.89.25
sequenceBlock, 2.18.21	key, 2.34.89.43
sequenceColorScheme, 2.22.23	label, 2.34.89.44
sequenceLine, 2.18.22	3d label, 2.34.89.44.4
sequences, 3.4	chemical, 2.34.89.44.3
not in alignments, 2.34.22.23	distance, 2.34.89.44.1
set, 2.34.89	table, 2.34.89.44.2
alternative atom, 2.34.89.18	map, 2.34.89.45
area, 2.34.89.1	molcart, 2.34.89.46
atom, 2.34.89.3	molecular variables, 2.34.89.83
ball label, 2.34.89.2	name, 2.34.89.47
background image, 2.34.89.4	sequence, 2.34.89.47.1
bfactor, 2.34.89.5	object, 2.34.89.48
biological symmetry, 2.34.89.64	occupancy, 2.34.89.49
bond topology, 2.34.89.7	plane, 2.34.89.50
type, 2.34.89.6	pmf, 2.34.89.51
and formal charges, 2.34.89.7	property, 2.34.89.52, 2.34.89.54, 2.34.89.55
cartesian, 2.34.89.8	alignment, 2.34.89.55
chain, 2.34.89.9	chemical view, 2.34.89.54
charge, 2.34.89.10	column, 2.34.89.53
formal, 2.34.89.11	radii graphical, 2.34.89.86
auto, 2.34.89.12	randomSeed, 2.34.89.56
mmff, 2.34.89.13	randomize, 2.34.89.56
chargemmff, 2.34.89.13	resolution, 2.34.89.57
chiral, 2.34.89.14	selftether, 2.34.89.68
chemical, 2.34.89.15	similarity, 2.35.44.8, 2.35.136.2
color, 2.34.89.16	site, 2.34.89.26
comment, 2.34.89.17, 2.34.89.18	alignment, 2.34.89.27
sequence, 2.34.89.19	residue, 2.34.89.29

sstructure backbone, 2.34.89.59	warning message, 2.35.191
sequence, 2.34.89.60	shineStyle, 2.22.24
to sequence, 2.34.89.60	shininess, 2.19.40
stack, 2.34.89.61	show, 2.34.90, 2.34.90.39
energy, 2.34.89.61, 2.34.94.1	alias, 2.34.90.7
stereo, 2.34.89.58	aliases, 2.34.90.7
swiss, 2.34.89.62	alignment, 2.34.90.8
name, 2.34.89.62	area, 2.34.90.9
symmetry, 2.34.89.65	atom, 2.34.90.10
bio, 2.34.89.64	type, 2.34.90.11
crystal, 2.34.89.63	atoms, 2.34.90.10
group, 2.34.89.63	bond, 2.34.90.12
to a torsion, 2.34.89.65	clash, 2.34.90.13
table, 2.34.89.66	color, 2.34.90.14
tautomer, 2.34.89.31	column, 2.34.90.15
terms, 2.34.89.67	comp_matrix, 2.34.90.16
tether, 2.34.89.69	database, 2.34.90.17
append, 2.34.89.70	drestraint, 2.34.90.18
texture, 2.34.89.32	type, 2.34.90.19
type, 2.34.89.71	energy, 2.34.90.20
mmff, 2.34.89.77	atom, 2.34.90.21
molecule, 2.34.89.75	gradient, 2.34.90.22
object, 2.34.89.74	hbond, 2.34.90.23
property, 2.34.89.73	exact, 2.34.90.24
sequence, 2.34.89.76	hbondexact, 2.34.90.24
surface, 2.34.89.72	html, 2.34.90.25
variable grid, 2.34.89.84	iarray, 2.34.90.26
variablegrid, 2.34.89.84	integer, 2.34.90.27
view, 2.34.89.80	key, 2.34.90.4
vrestraint, 2.34.89.81	label, 2.34.90.28
vrestraintvs_var, 2.34.89.82	library, 2.34.90.29
radii, 2.34.89.78	link, 2.34.90.30
vwelradii, 2.34.89.79	logical, 2.34.90.31
vwradii, 2.34.89.78	map, 2.34.90.5
window, 2.34.89.85	mol, 2.34.90.32
xstick, 2.34.89.86	mol2, 2.34.90.33
radii, 2.34.89.86	molecule, 2.34.90.34
setResLabel, 2.37.80	molecules, 2.34.90.6
setcomp_matrix, 2.34.89.20	object, 2.34.90.35
seticmff, 2.37.79	pdb, 2.34.90.36
setting conf properties, 2.34.89.61	pharmacophore type, 2.34.90.54
setvs_var, 2.34.89.83	pmf, 2.34.90.37
sf-term, 2.34.89.72	preferences, 2.34.90.38
sfWeight, 2.19.39	profile, 2.34.90.39
sh24, 3.4	residue, 2.34.90.40
shadows, 2.23.5.34	type, 2.34.90.41
shell, 3.1, 5.8.5	residuetype, 2.34.90.41
functions, 2.34.40	segment, 2.34.90.42
intro, 1.7.1	selftether, 2.34.90.1
progression, 2.34.78	sequence, 2.34.90.43

site, 2.34.90.2	smart, 2.23.14.7
stack, 2.34.90.44	smarts, 2.35.70.2
svariable, 2.34.90.3	smiles, 2.23.14.7, 2.26, 2.27
table, 2.34.90.45	to chem-table element, 2.35.109
as database, 2.34.90.17	smooth alignment, 2.35.146.4
term, 2.34.90.46	interpolation, 2.34.94.3
tethers, 2.34.90.47	map, 2.35.146.5
uniprot, 2.34.90.48	rarray, 2.35.146.1
entry, 2.34.90.48	surface, 2.37.88
version, 2.34.90.49	soap, 2.32
volume, 2.34.90.52	soft trim, 2.35.178
map, 2.34.90.53	solid sphere, 2.23.5.11
volumemap, 2.34.90.53	solubility, 2.35.114
vrestraint, 2.34.90.50	solvation, 2.22.25, 2.23.14.2
type, 2.34.90.51	energy, 2.19.39, 2.22.25
vrestraints, 2.34.90.50	solvent accessible area, 2.18.23
showcomp_matrix, 2.34.90.16	surface, 2.23.5.55, 2.23.5.56, 2.34.90.9
showing weak hydrogen bonds, 2.23.5.25	sort, 2.34.91, 2.34.91.4
side chain, 2.37.90	array, 2.34.91.1
flexibility, 2.37.90	arrays, 2.34.91.1
sigma function, 2.35.44.8, 2.35.136.2	column, 2.34.91.3
level, 2.23.7.5	table, 2.34.91.3
signal recognition measure, 2.37.21	molecules, 2.34.91.5
similar chains, 2.35.137.13	object, 2.34.91.4
similarity, 2.34.35.9, 2.34.35.10	stack, 2.34.91.6
simple expressions, 2.10.1.1	table, 2.34.91.2
string substitution, 2.35.126.2	sortSeqByLength, 2.37.81
simplified representation, 2.23.5.16	space group, 2.34.69
compound, 2.35.179	transformations, 2.35.176
mesh structure, 2.34.15.2	sparse atoms, 2.23.14.3
simulation duration, 2.19.47	spawn background job, 2.34.65.1
temperature, 2.19.46	special values, 2.35.168
intro, 1.4.2	specificity, 2.35.136.5
sinking number, 2.19.35	spectral decomposition, 2.35.45
site, 2.34.11.2, 5.8.6	split, 2.34.92
arrows, 2.34.89.26	column values, 2.34.92.5
table, 5.8.6.1	grob, 2.34.92.1
sites, 2.34.22.26	group, 2.34.92.2
by residue selection, 2.34.22.24	array, 2.34.92.3
sequences, 5.8.6.1	into chains, 2.34.92.6
sixthe power, 2.22.6	molsar, 2.34.65.28
skin, 2.19.35, 5.8.7	object, 2.34.92.6
intro, 1.4.1.2	to molecules, 2.34.92.6
slide, 2.34.1.3, 2.35.144, 5.8.14	sequence, 2.34.92.4
transition time, 2.34.23.21	table cell, 2.34.92.5
slides, 2.35.190	tree, 2.34.92.7
slideshow, 2.34.1.3, 2.34.23.21, 2.35.144	splitting selection, 2.8.11
sln, 5.8.8	spreadsheet, 2.34.84.44
slurm, 3.13.1.19	sprintf, 2.34.93
smallest set of smallest rings, 2.35.130	sql, 2.34.81, 2.34.89.46, 2.35.50.1, 2.35.99.12, 2.35.102.5, 2.35.182.2

sqrt, 2.35.37	factors, 3.11.1
square matrix to element pairs, 2.35.160.5	structure, 3.11.1
ssThreshold, 2.19.41	sub-alignment to selection, 2.35.128
ssWeight, 2.19.42	sub-matrix, 2.35.90.2
ssbond, 5.4.5	subalignment, 2.35.5.3, 5.1.1
ssearch, 2.18.17, 2.34.95	submap, 2.35.86
ssearchStep, 2.19.43	subroutine, 2.34.64
ssign sstructure segment, 2.34.5.2	subset, 2.6
stack, 2.18.12, 2.18.13, 2.18.15, 2.22.7, 2.34.89.61, 2.34.94, 2.34.94.1, 2.35.66.6, 2.35.160.6, 5.3.12, 5.8.9	substring, 2.35.89, 2.35.156, 2.35.156.1
bin size, 2.34.14	substructure, 2.34.35.9, 2.34.35.10
cleaning, 2.34.22.17	search, 2.34.35.4
extension, 2.34.4.2	grid engine, 3.13.1.19
multiplication, 2.34.4.2	superimpose, 2.23.14, 2.34.97
merge, 3.7.7	faq, 3.3.1
standard chemical form, 2.34.70.4	how to, 3.3.1
deviation, 2.35.133	minimize, 2.34.98
standardization, 2.34.22.11	support, 1.3
chemical, 2.34.70	suppressing view changes, 2.34.23.21
startup, 3.1.2.3	surface, 2.19.35, 2.35.109, 5.8.15
static RMSD, 2.35.155	accessibility, 2.34.90.9
and dynamic hbonds, 2.23.5.24	area, 2.37.2, 5.8.15
statistical thermodynamics, 2.35.47	charge, 5.7.13
stereo, 2.23.5.52, 2.34.30, 2.34.89.58	color, 2.34.89.16
reconstruction, 3.8.9	dot density, 2.23.5.55
stereo-specific hydrogens, 2.34.22.11	energy, 2.22.25, 2.34.89.72
stereoisomer, 2.34.30	mesh, 2.35.192.3
stereoisomers, 2.20.16	point selection, 2.35.192
stick, 5.8.10	term, 2.19.39
store, 2.34.94	surfaceAccuracy, 2.18.23
conf, 2.34.94, 2.34.94.1	surfaceMethod, 2.22.25
frame, 2.34.94.3	surfaceTension, 2.19.44
image, 2.34.65.20	svariable, 5.8.12
stack object, 2.34.94.2	svg, 2.34.110.22
torsion type, 2.34.94	export, 2.23.9.14
strength of hydrogen bond, 2.34.23.14	map, 2.35.160.7
string, 5.8.11	swapping protein fragments, 3.8.7
array, 2.35.135, 5.8.1	swiss, 2.34.89.62
filtering, 2.35.178	swissFields, 2.24.10
inversion, 2.35.156.1	swissprot, 2.34.89.26
label, 2.34.23.12	symmetrization of a matrix, 2.35.90.3
matching, 2.10, 2.35.89	symmetry, 2.35.176
variables, 2.21	faq, 3.10
strings, 2.21	group, 2.18.2
strip, 2.34.96	problem, 2.34.69
struct, 2.35.99.2	syntax highlighting, 5.8.2
structural alignment, 2.34.3.5, 2.35.5.2	sys, 2.34.99
optimization, 2.34.35.1	system, 5.10.2
superposition, 2.34.3.5	command, 2.34.99
analysis, 3.3	copy, 2.21.26
comparison, 2.35.23.2	file move, 2.21.28

remove, 2.21.29	thumbnails, 2.35.68
table, 2.34.22.4, 2.34.89.52, 2.34.89.53, 2.34.89.54, 2.34.91.3, 5.9.1	tif, 5.9.6
actions, 5.9.2.4	time, 2.35.38, 2.35.156.2
column, 2.35.99	timeLimit, 2.19.47
format, 2.34.89.41	tolFunc, 2.19.49
plot, 2.34.65.32	tolGrad, 2.19.48
transformations, 2.35.104	topological psa, 5.7.12
creation, 2.34.43.3	torScan, 2.37.84
display style, 5.9.1	torsion, 2.35.136.3
expression, 5.9.2	rmsd comparison, 2.34.14.2
from matrix, 2.35.160.4	scan, 2.37.84
grid view, 5.9.1	torsions, 2.35.102.3
of atoms and distances, 2.35.160.10	score, 2.36.2
operations, 5.9.2.1	tpsa, 5.7.12
plot, 5.9.2.3	trajectory, 2.34.63.2, 2.34.94, 2.34.94.3, 5.6.14
principal component analysis, 2.34.65.29	file, 2.38.17
print, 2.34.90.45	frame writing, 2.34.23.17
row, 2.34.72.4	smoothing, 2.34.23.17
label mark, 2.34.89.44.2	transform, 2.34.102, 2.34.102.2
mark, 2.35.79	general, 2.34.102
selected row numbers, 2.35.70	grob coordinates, 2.34.102.2
subset, 5.9.2.2	molecules, 2.34.102.2
show html, 2.34.108.1	sarray, 2.34.102.1
targa, 5.9.3	transformation, 2.35.122, 5.9.7
target coordinates, 5.9.4	vector, 5.9.7
tautomer, 2.34.31	and symmetry, 3.10
tempCycle, 2.19.46	transforming points, 2.35.192.5
tempLocal, 2.19.45	translate, 2.34.54, 2.34.103
temperature, 2.19.46	transparency, 2.34.89.42, 5.5.3
variations in optimizer, 2.19.46	background, 2.34.110.36
template docking, 3.13.1.23	grob, 2.34.23.11
tensor product of two vectors, 2.35.90	grobs, 2.23.5.57
terminal font, 2.38.14	tree, 2.34.65.37, 2.35.99.5
window, 2.34.44	cluster, 2.13
terms, 2.17	delete, 2.34.22.36
hydrogen bonding, 2.19.21	label format, 2.35.99.5
test, 2.34.100	representatives, 2.13.1
binary, 2.34.100.1	trim string array, 2.34.102.1
testing if argument exists, 2.35.59	trimming grid map values, 2.35.178
tether, 2.23.14.12, 2.34.110.9, 5.9.4, 5.9.5	true positives, 2.35.136.5
text, 2.35.89	truncate alignment, 2.34.65.34
search in tables, 2.35.56.2	values, 2.35.178
to script, 5.8.2	grob, 2.23.5.9, 2.23.5.10
texture, 5.5.3	tsShapeData, 2.23.14.12
tga, 5.9.3	table format, 2.34.84.44
then, 2.34.101	two alignments, 2.35.44.13
thickness, 2.23.9.14	dimensional plot, 2.35.146.2
thread to template, 2.34.66.4	set comparison, 2.35.44.8, 2.35.136.2
threading, 2.35.5.1	sets, 2.35.70.10
letter code, 2.35.172, 2.35.173	txdoc browser, 2.34.84.4

tzMethod, 2.22.26	transformation, 2.35.104
tzWeight, 2.19.50	vertex, 2.34.13.4.2
ultra large libraries, 3.13.1.24	connectivity, 2.35.90.13
uncharge functional groups, 2.34.70.2	vertexes, 2.34.13.4.2
unclip, 2.34.23.2	vertical alignment block, 2.34.65.34
underline, 2.34.89.38.1	workspace, 2.23.8.6
undisplay, 2.34.104	vertices, 2.34.13.4.2
graphics, 2.34.105	vicinity, 2.19.51
window, 2.34.105	video, 2.34.110.31
unfix, 2.34.106	view, 2.23.5.9, 2.23.5.10, 2.34.89.55
union, 2.35.70.10	point, 2.35.190
unique, 2.34.13.1, 5.10.1	restoration, 2.35.73
atomic order, 2.34.65.39	transition, 2.34.89.80
column values, 2.34.43.4	views, 5.8.14
names, 2.35.99	virtual, 5.10.3
new object name, 2.35.99	arrays, 2.34.1.1.1
smiles, 2.34.65.39	chemistry, 2.34.70, 2.35.102.4
unix, 2.34.99, 5.10.2	field, 2.34.7.2
grep, 2.34.84.1	ligand screening, 3.13, 3.13.1
unlink alignments, 2.34.22.21	intro, 1.4.2.7
sequences, 2.34.22.21	screening, 3.18, 3.19
variables, 2.34.22.21	visitsAction, 2.22.28
update database, 2.34.70.5	vls, 3.13, 3.13.1
speadsheet, 2.34.1.1.1	cluster, 3.13.1.15
updates, 1.1	intro, 1.4.2.7
updating atom pairs, 2.20.27	job queueing, 3.13.1.15
upper case, 2.35.171	overview, 3.13.1
url string parsing, 2.35.160	parallelization, 3.13.1.14
user atom display, 2.23.5.3	results, 3.13.1.17
commands, 2.34.84.3	scores storage, 3.13.1.16
defaults, 2.34.110.42	threshold, 3.13.1.11
environment, 3.1.2.2	vls_intro, 3.13.1.10
menu, 2.23.10.1	volume, 5.10.4
menus, 2.33	vrestraint, 5.10.5
user-defined properties, 2.34.89.34	file, 2.38.23
solvation parameters, 2.35.7	type, 5.10.6
user_startup, 3.1.2.4	file, 2.38.22
icm, 3.1.2	vs_, 2.8.9
guide, 3	vs_out, 2.24.15
v-synthes, 3.13.1.24	vwCutoff, 2.19.52
v_, 2.8.1	vwExpand, 2.19.53
van der Waals surface, 2.23.5.56	vwExpandDisplay, 2.19.54
varLabelStyle, 2.22.27	vwMethod, 2.22.29
variable restraint, 2.34.89.81	vwSoftMaxEnergy, 2.19.55
selection, 2.8.9	wait, 2.34.107
vdW gap, 2.35.151	warning, 2.23.14.3
vector, 2.35.102.6	message, 2.35.191
dot product, 2.35.187.1	suppression, 2.20.28
length, 2.35.103	water.dielectric constant, 2.19.15
product, 2.35.187.1	waterRadius, 2.19.56

web, 2.11, 2.34.108	png, 2.34.110.36
table, 2.34.108.1	postscript, 2.34.110.37
webEntrezOption, 2.22.30	pov, 2.34.110.38
weighted rmsd, 2.23.14	povray, 2.34.110.38
while, 2.34.109	project, 2.34.110.2
whole string, 2.35.126.1	rarray, 2.34.110.4
window averaging, 2.35.146.1	sarray, 2.34.110.5
layout, 2.35.156.9	sequence, 2.34.110.39
width and height, 2.35.190	session, 2.34.110.40
windowSize, 2.18.24	several array, 2.34.110.8
movie, 2.34.110.31	simple object, 2.34.110.33
wire, 5.10.7	stack, 2.34.110.41
wireBondSeparation, 2.19.57	system preference, 2.34.110.42
wireStyle, 2.22.31	table, 2.34.110.10
workspace, 2.34.105	mol, 2.34.110.11
write, 2.34.110	with links, 2.34.110.19
album, 2.34.110.21	tether, 2.34.110.9
alignment, 2.34.110.1	tethers, 2.34.110.9
array, 2.34.110.8	trajectory, 2.34.23.17
table, 2.34.110.8	vs_var, 2.34.110.43
binary, 2.34.110.2	writevs_var, 2.34.110.43
blast, 2.34.110.25	x-ray crystallography, 2.34.90.21
column, 2.34.110.12	xlsx, 2.34.84.44, 2.34.110.10
database, 2.34.110.13	xml, 2.34.84.56, 2.35.89, 5.1.6
drestraint, 2.34.110.14	drugbank example, 2.12
type, 2.34.110.15	xpdb, 2.34.84.2
factor, 2.34.110.16	xplor format, 2.34.84.27
gamess, 2.34.110.17	xrMethod, 2.22.32
grob, 2.34.110.18	xrWeight, 2.19.58
html, 2.34.110.19	xray density to rectangular energy map, 2.34.65.31
iarray, 2.34.110.3	xstick, 5.10.8
image, 2.34.110.20	radii, 2.34.89.2
alignment, 2.34.110.23	xyz morphing, 3.8.8
chemical, 2.34.110.22	zega, 5.10.9
parray, 2.34.110.21	intro, 1.4.3.6
index, 2.34.84.24, 2.34.110.24	\|, 2.14.3
blast, 2.34.110.25
fasta, 2.34.110.24
library, 2.34.110.26
map, 2.34.110.27
matrix, 2.34.110.6
model, 2.34.110.28
mol, 2.34.110.29
mol2, 2.34.110.30
molcart, 2.34.110.7
movie, 2.34.110.31
object, 2.34.110.32
parray, 2.34.110.34
simple, 2.34.110.33
pdb, 2.23.14.14, 2.34.110.35

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