ICM Manual v.3.6 by Ruben Abagyan
Copyright © 2011, Molsoft LLC
Jan 30 2012

Contents


Introduction
Reference Guide
User's Guide
References
Glossary

Index

Index

&, 2.12.3	CONSENSUS_strength, 2.17.9
2D labels, 2.27.53.1	Cad, 2.28.22, 2.28.22.1, 2.28.22.2
to 3D, 3.13.2.3	Cad1, 2.28.22.1
smooth, 2.28.137.2	Cadalign, 2.28.22.2
3D chemical builder, 1.4.2.8	Ceil, 2.28.23
font size, 2.27.23.12	Cell, 2.28.24
label, 2.27.23.12, 2.27.83.33	Charge, 2.28.25
labels, 2.27.53.1	Chemical, 2.28.26
mol file, 2.29.84	Cluster, 2.28.27
plots intro, 1.4.3.7	Collada, 5.5.3
smoothing, 2.28.137.3	Collection, 2.28.27.1
superposition, 2.29.22	Color, 2.28.28
transformations, 2.27.96.2	from gradient, 2.28.28.1
chemical similarity, 2.28.127	image, 2.28.28.2
pharmacophore comparison, 2.28.127.2	Connolly surface, 5.8.7
3dxml, 5.5.3	Consensus, 2.28.29
=, 2.12.1	Corr, 2.28.30
A, 5.1	Cos, 2.28.31
APF distance, 2.28.127	Cosh, 2.28.32
Abs, 2.28.1	Count, 2.28.33
Acc, 2.28.2	CubicRoot, 2.28.34
Acos, 2.28.3	D, 5.4
Acosh, 2.28.4	DAE, 5.5.3
Adobe, 2.19.23	DE, 2.27.34.2
Align, 2.28.5	DNA Representation, 1.4.1.3
sequence, 2.28.5.1	alignment, 2.27.3.3
Angle, 2.28.6	melting temperature, 2.28.155
Apple, 3.14.6.2	views, 1.4.1.3
Area, 2.28.7	Date, 2.28.35
residue contacts, 2.28.7.1	Deletion, 2.28.36
Asin, 2.28.8	Descriptor, 2.28.37
Asinh, 2.28.9	Det, 2.28.38
Ask, 2.28.10	Disgeo, 2.28.39
Askg, 2.28.11	Distance, 2.28.40
Atan, 2.28.12	2 alignments, 2.28.40.11
Atan2, 2.28.13	matrices, 2.28.40.7
Atanh, 2.28.14	Dayhoff, 2.28.40.9
Atom, 2.28.15	Tanimoto, 2.28.40.6
Augment, 2.28.16	alignment, 2.28.40.10
Axis, 2.28.17	as_, 2.28.40.3
B, 5.2	rarray, 2.28.40.4
BPMC, 5.2.5	atoms, 2.28.40.3
Bfactor, 2.28.18	chemical, 2.28.40.6, 2.28.40.13
Boltzmann, 2.28.19	dayhoff, 2.28.40.9
Box, 2.28.20	iarray, 2.28.40.1
Bracket, 2.28.21	alignment, 2.28.40.10
C, 5.3	matrix, 2.28.40.5, 2.28.40.7
CCP4, 5.6.6	multiple atomic, 2.28.40.4
CONSENSUS, 2.21.1	rarray, 2.28.40.2
CONSENSUSCOLOR, 2.21.2	tether, 2.28.40.8

cluster, 2.28.40.12	hbondAngleSharpness, 2.21.5.21
H, 5.5	hbondBallPeriod, 2.21.5.22
EDS server, 2.29.42	hbondBallStyle, 2.21.5.23
EST-alignment, 2.27.3.3	hbondMinStrength, 2.21.5.20
Eigen, 2.28.41	hbondRebuild, 2.21.5.19
Energy, 2.28.42	hbondStyle, 2.21.5.18
Error, 2.28.43	hbondWidth, 2.21.5.24
soap, 2.28.44	hetatmZoom, 2.21.5.26
Exist, 2.28.45	hydrogenDisplay, 2.21.5.27
molcart, 2.28.45.1	light, 2.21.5.28
Existenv, 2.28.46	lightPosition, 2.21.5.29
Exp, 2.28.48	mapLineWidth, 2.21.5.30
Extension, 2.28.47	occupancyDisplay, 2.21.5.31
FILTER, 2.21.3	occupancyRadiusRatio, 2.21.5.32
Z, 2.21.3.1	quality, 2.21.5.33, 2.28.83.1
gz, 2.21.3.2	rainbowBarStyle, 2.21.5.34
uue, 2.21.3.3	resLabelDrag, 2.21.5.35
FTP, 2.21.4	resLabelShift, 2.21.5.36
createFile, 2.21.4.1	ribbonCylinderRadius, 2.21.5.37
keepFile, 2.21.4.2	ribbonGapDistance, 2.21.5.38
proxy, 2.21.4.3	ribbonRatio, 2.21.5.39
Field, 2.28.49, 2.28.49.1	ribbonWidth, 2.21.5.40
user, 2.28.49.1	ribbonWorm, 2.21.5.41
File, 2.28.50	rocking, 2.21.5.42
Find, 2.28.51	rockingRange, 2.21.5.43
chemical, 2.28.51.3	rockingSpeed, 2.21.5.44
pattern, 2.28.51.3	selectionLevel, 2.21.5.45
in array, 2.28.51.1	selectionStyle, 2.21.5.46
table, 2.28.51.2	sketchAccents, 2.21.5.25
FlexLM license info, 2.28.178	stereoMode, 2.21.5.47
Floor, 2.28.52	stickRadius, 2.21.5.26, 2.21.5.48
Formula, 2.28.53	surfaceDotDensity, 2.21.5.50
GRAPHICS, 2.21.5	surfaceDotSize, 2.21.5.49
atomLabelShift, 2.21.5.1	surfaceProbeRadius, 2.21.5.51
atomValueCircles, 2.21.5.2	transparency, 2.21.5.52
ballRadius, 2.21.5.3, 2.21.5.26	wormRadius, 2.21.5.53
ballStickRatio, 2.21.5.4	GRID, 2.21.6
chainBreakLabelDisplay, 2.21.5.7	gcghExteriorPenalty, 2.21.6.1
chainBreakStyle, 2.21.5.6	gpGaussianRadius, 2.21.6.6
clashWidth, 2.21.5.5	margin, 2.21.6.2
cpkClipCaps, 2.21.5.8	maxEl, 2.21.6.3
displayLineLabels, 2.21.5.9	maxVw, 2.21.6.5
displayMapBox, 2.21.5.10	minEl, 2.21.6.4
dnaBallRadius, 2.21.5.11	GROB, 2.21.7
dnaRibbonRatio, 2.21.5.12	arrowRadius, 2.21.7.3
dnaRibbonWidth, 2.21.5.13	atomSphereRadius, 2.21.7.1
dnaRibbonWorm, 2.21.5.14	contourSigmaIncrement, 2.21.7.5
dnaStickRadius, 2.21.5.15	relArrowHead, 2.21.7.4
formalChargeDisplay, 2.21.5.16	relArrowSize, 2.21.7.2
grobLineWidth, 2.21.5.17	GUI, 2.21.8

dialog customize programming, 2.26	I_out, 2.22.4
plot, 2.27.59.31	Iarray, 2.28.61, 2.28.61.4, 2.28.61.5
tableRowMarkColors, 2.21.8.4	atom numbers, 2.28.61.4
windowLayout, 2.21.8.5	bits to integers, 2.28.61.3
workspaceFolderStyle, 2.21.8.8	inverse, 2.28.61.2
workspaceStyle, 2.21.8.6	residue numbers, 2.28.61.5
workspaceTabStyle, 2.21.8.7	reverse, 2.28.61.2
Getarg, 2.28.54	stack, 2.28.61.6
Getenv, 2.28.55	Icm Options, 2.1
Gradient, 2.28.56	IcmSequence, 2.28.62
Graphics, 1.4.1	Image, 2.28.63
Grob, 2.28.57	collection, 3.9.2.1
Group, 2.28.58	frame by frame, 3.9.2.2
HTTP.proxy, 2.21.4.4	Index, 2.28.64
Hartree-Fock, 2.27.78.20, 2.27.104.17	chemical, 2.28.64.1
Hash, 2.28.27.1	compare, 2.28.64.9
Header, 2.28.59	element in array, 2.28.64.7
Histogram, 2.28.60	regexp, 2.28.64.3
N, 5.6	string, 2.28.64.2
ICM desktop, 2.21.8.5	table label, 2.28.64.5
documents, 2.27.78.3	selection, 2.28.64.4
modules, 1.4.4	tree, 2.28.64.8
object, 2.29.13	unique elements, 2.28.64.6
residue library, 2.19.24	Indexx, 2.28.65
ICM-shell, 3.1, 5.8.5	Info, 2.28.67
intro, 1.7.1	image, 2.28.68
script, 2.27.8	Insertion, 2.28.66
ICMFF force field, 2.29.78	Integer, 2.28.69
ICMHOME, 3.1.2.1	Integral, 2.28.70
shell variable, 3.1.2.1	Interrupt, 2.28.71
IMAGE, 2.21.9	Introduction, 1
bondLength2D, 2.21.9.15	JSON, 2.27.78.54
color, 2.21.9.8	LIBRARY, 2.21.10
compress, 2.21.9.9	men, 2.21.10.1
gammaCorrection, 2.21.9.7	res, 2.21.10.2
generateAlpha, 2.21.9.10	Label, 2.28.72
lineWidth, 2.21.9.3	Laplacian, 2.28.73
lineWidth2D, 2.21.9.14	Latent, 2.28.177.3
orientation, 2.21.9.16	LatentVector, 2.28.177.3
paperSize, 2.21.9.17	Length, 2.28.74
previewResolution, 2.21.9.13	LinearFit, 2.28.75
previewer, 2.21.9.12	LinearModel, 2.28.76
printerDPI, 2.21.9.2	Log, 2.28.77
quality, 2.21.9.1	LogP, 2.28.105
rgb2bw, 2.21.9.18	LogS, 2.28.105
scale, 2.21.9.4	M_out, 2.22.5
stereoAngle, 2.21.9.6	Mac, 3.14.6.2
stereoBase, 2.21.9.5	Map, 2.28.78
stereoText, 2.21.9.11	Markush structures, 2.27.50
writeScale, 2.21.9.19	Mass, 2.28.79

Mathews, 2.28.127.3	soap, 2.28.93.7
Matrix, 2.28.82	tree, 2.28.93.1
alignment, 2.28.82.8	Norm, 2.28.94
boundary, 2.28.82.9	Normalize, 2.28.95
grob connectivity, 2.28.82.12	NotInList, 2.28.96
histogram, 2.28.82.11	R, 5.7
new, 2.28.82.1	OBJECT, 2.21.11
residue areas, 2.28.82.7	Obj, 2.28.97
comparison, 2.28.82.4	Occupancy, 2.28.98
stack, 2.28.82.10	PBS, 3.13.3.6
sub, 2.28.82.2	PLOT, 2.21.12
symmetrical, 2.28.82.3	Yratio, 2.21.12.5
table, 2.28.82.5	box, 2.21.12.13
tensor, 2.28.82.6	color, 2.21.12.7
Max, 2.28.83	font, 2.21.12.10
image graphic, 2.28.83.1	fontSize, 2.21.12.2
MaxHKL, 2.28.84	labelFont, 2.21.12.11
Mean, 2.28.85	lineWidth, 2.21.12.3
Method, 2.20.12	logo, 2.21.12.6
Min, 2.28.86	markSize, 2.21.12.4
Mod, 2.28.88	numberOffset, 2.21.12.1
Mol, 2.28.89	orientation, 2.21.12.8
MolPSA, 5.7.12	rainbowStyle, 2.21.12.12
Moment, 2.28.80	seriesLabels, 2.21.12.9
of Inertia, 2.28.80	PLS, 2.28.93.6
Money, 2.28.87	error, 2.28.127.3
NOE averaging, 2.20.5	models, 2.28.127.3
Name, 2.28.90	Parray, 2.28.100
chemical, 2.28.90.6	Parray-object, 2.28.100
property, 2.28.90.1	Path, 2.28.99
close sequence, 2.28.90.3	Pattern, 2.28.101
image, 2.28.90.10	Pi, 2.28.102
molcart, 2.28.90.11	Polar Surface Area, 5.7.12
object parray, 2.28.90.9	Potential, 2.28.103
sequence, 2.28.90.7	Power, 2.28.104
soap, 2.28.90.2	Predict, 2.28.105
string, 2.28.90.4	Probability, 2.28.106
tree, 2.28.90.5	Profile, 2.28.107
Namex, 2.28.91	Property, 2.28.108
image, 2.28.91.2	Putarg, 2.28.109
sequence, 2.28.91.1	Putenv, 2.28.110
Newick tree format, 2.28.147.3	R-groups, 2.27.50
Next, 2.28.92, 2.28.92.1	REBEL, 3.7.2
covalent neighbors, 2.28.92.1	faq, 3.7.2
Nof, 2.28.93	file, 2.27.50
chemical, 2.28.93.2	R_2out, 2.22.7
distance, 2.28.93.3	R_out, 2.22.6
latent, 2.28.93.6	Radius, 2.28.111
library, 2.28.93.4	Random, 2.28.112
molcart, 2.28.93.5	string, 2.28.112.1

reverse, 2.28.113.2	overlap, 2.28.127.1
sequence projection, 2.28.113.1	predictions, 2.28.127.4
alignment projection, 2.28.113.3	sequence, 2.28.127.5
strength, 2.28.113.5	Select, 2.28.128
property assignment, 2.28.113.4	break, 2.28.128.1
RarrayAlignment, 2.28.113.5	atom property, 2.28.128.7
Rarrayinverse, 2.28.113.2	nmembers, 2.28.128.4
Real, 2.28.114	string, 2.28.128.9
array, 2.28.113	expand, 2.28.128.6
Reference, 2.28.116	fix, 2.28.128.2
Guide, 2	graphical, 2.28.128.5
Remainder, 2.28.115	neighbors, 2.28.128.3
Replace, 2.28.117	Select_by atom numbers, 2.28.128.10
chemical, 2.28.117.4	Select_by_sequence, 2.28.128.13
exact, 2.28.117.1	Select_by_text, 2.28.128.9
regexp, 2.28.117.3	Select_lists, 2.28.128.12
simple, 2.28.117.2	Select_patching, 2.28.128.11
Res, 2.28.118, 2.28.119	Select_projection, 2.28.128.8
Resali, 2.28.119	Sequence, 2.28.129
Resolution, 2.28.120	array, 2.28.129.2
Rfactor, 2.28.122	Sequence(dna reverse), 2.28.129.1
Rfree, 2.28.123	Shuffle, 2.28.130
Ring, 2.28.121	Sign, 2.28.131
Rmsd, 2.28.124	Simulations, 1.4.2
of subset, 2.21.14	Sin, 2.28.132
Rot, 2.28.125	Sinh, 2.28.133
S, 5.8	Site, 2.28.134
SAR analysis, 2.27.59.27, 2.27.86.2	Slide, 2.28.135
SC, 2.27.34.2	Smiles, 2.28.136
SEQUENCE.restoreOrigNames, 2.21.12.14	Smooth, 2.16.23, 2.28.137, 2.28.137.1, 2.28.137.3
SITE, 2.21.13	matrix, 2.28.137.2
defSelect, 2.21.13.2	Smoothrs, 2.28.137.3
labelOffset, 2.21.13.3	SoapMessage, 2.28.143
labelStyle, 2.21.13.4	SolveQuadratic, 2.28.138
labelWrap, 2.21.13.5	SolveQubic, 2.28.139
showSeqSkip, 2.21.13.6	Sort, 2.28.144
wrapComment, 2.21.13.7	Sphere, 2.21.14.3, 2.28.142
SLN notation, 2.28.147.9	Split, 2.28.145
SMARTS, 2.24, 2.27.10, 2.28.93.2	chemical, 2.28.145.4
SOAP, 2.28.90.2, 2.28.93.7, 2.28.172.1	multisep, 2.28.145.3
request message, 2.28.143	regexp, 2.28.145.2
SSSR, 2.28.121	tree, 2.28.145.1
S_out, 2.22.8	Sql, 2.28.140
Sarray, 2.28.126	Sqrt, 2.28.141
index, 2.28.126.1	Srmsd, 2.28.146
Score, 2.28.127	Sstructure, 2.28.148
alignment, 2.28.127.7	String, 2.28.147, 2.28.147.7
apf, 2.28.127.2	alternative, 2.28.147.6
conservation, 2.28.127.6	mol, 2.28.147.2
model, 2.28.127.3	selection, 2.28.147.7

substring, 2.28.147.1	sequence, 2.28.170
chemical formula, 2.28.147.9	Turn, 2.28.171
Sum, 2.28.149	Type, 2.28.172
chemical, 2.28.149.1	molcart, 2.28.172.2
image, 2.28.149.2	soap, 2.28.172.1
Swissprot, 2.27.104.23	Z, 5.10
Symgroup, 2.28.150	Unique, 2.28.173
T, 5.9	Unix, 2.28.174
TOOLS, 2.21.14	Uppsala, 2.29.42
edsDir, 2.21.14.1	server, 2.29.43
membrane, 2.21.14.2	V_, 2.8.1
minSphereCubeSize, 2.21.14.3	Value, 2.28.175
pdbReadNmrModels, 2.21.14.4	soap, 2.28.176
superimposeMaxDeviation, 2.21.14.7	Vector, 2.28.16, 2.28.177, 2.28.177.1, 2.28.177.3
superimposeMaxIterations, 2.21.14.5	symmetry transformation, 2.28.177.2
superimposeMinAtomFraction, 2.21.14.6	Vectorproduct, 2.28.177.1
tsShape, 2.21.14.9	Vectorsymmetrytransformation, 2.28.177.2
tsWeight, 2.21.14.10	Version, 2.28.178
writePdbRenameRes, 2.21.14.11	View, 2.28.180
Table, 2.28.151	Volume, 2.28.179
alignment numbers, 2.28.151.3	WEBAUTOLINK, 2.21.16
distance, 2.28.151.9	WEBLINK, 2.21.15
matrix, 2.28.151.4	Warning, 2.28.181
model, 2.28.151.7	Wavefront format, 2.27.78.21
pairs, 2.28.151.5	XML, 2.10
stack, 2.28.151.6	Xyz, 2.28.182
url_decoder, 2.28.151.1	axes, 2.28.182.7
Table(alignment), 2.28.151.2	chemical match, 2.28.182.5
Table(stack), 2.28.151.6	fract, 2.28.182.3
Tan, 2.28.152	mesh, 2.28.182.2
Tanh, 2.28.153	points, 2.28.182.1
Tanimoto, 2.28.61.3	transformed xyz, 2.28.182.4
distance, 2.27.59.35	vector2matrix, 2.28.182.6
matrix, 2.28.40.6	ZEGA, 5.10.9
Temperature, 2.28.155	intro, 1.4.3.6
Tensor, 2.28.154	_NAME, 2.27.83.41
Time, 2.28.156	_chemBatch, 3.1.2.5
Tointeger, 2.28.157	_confGen, 3.13.2.3
Tolower, 2.28.158	_dockScan, 3.13.2.6
Toreal, 2.28.159	_macro, 2.30.1
Torsion, 2.28.160	file, 2.30.1
Tostring, 2.28.161	_startup, 3.1.2.3
Toupper, 2.28.162	file, 2.30.2
Tr123, 2.28.163	icm, 2.30.2
Tr321, 2.28.164	a_, 2.8.1
Trace, 2.28.165	abbr, 1.6
Trans, 2.28.166	abbreviations, 1.6
Transform, 2.28.167	absolute to cell x y z, 2.28.182.3
Transpose, 2.28.168	accFunction, 2.22.2
Trim, 2.28.169	acceptor, 3.6.1

accessMethod, 2.20.1	block length, 2.16.21
accessible residues, 3.3.6	secondary structure, 2.29.1
surface, 2.27.59.14, 5.8.15	cleaning, 2.28.137.4
accessing sections, 2.27.104.23	color by property, 2.27.83.30
accuracy, 2.28.127.3	coloring, 2.19.1
activate fog, 2.27.23.24	distance, 2.28.128.13
alignment, 2.27.83.34	editor, 2.4
document, 2.27.83.34	extraction, 2.28.5
tab, 2.27.83.34	gap format, 5.1.1.1
table, 5.9.2.4	intro, 1.4.3.4
add, 2.27.1	projection, 2.28.147, 2.28.147.4, 2.28.147.5
column, 2.27.1.1	score, 2.28.127.6
function, 2.27.1.1.1	sequence reordering, 2.28.5
matrix, 2.27.1.2	strength, 2.28.113.5
slide, 2.27.1.3	structural, 2.27.3.4, 2.28.5
table, 2.27.1.4	to sequence transfer, 2.28.113.1
row, 2.27.1.4	text conversion, 2.28.147.3
addBfactor, 2.17.1	weighted, 2.28.5
adding atoms to non-ICM objects, 2.27.7.1	gapExtension, 2.17.15
columns to table, 2.27.1.1	gapOpen, 2.17.16
hydrogens, 2.29.13	alignment_as_text, 2.28.147.3
in place, 2.12.4	aliphatic amines, 2.27.64.2
to slideshow, 2.27.1.3	all, 5.1.2
admet selection, 3.13.3.4	torsions table, 3.3.11
advanced chemical search, 3.6	alpha, 2.21.5.52, 2.27.83.36, 5.1.3
operations, 2.12.6	channel, 2.21.9.10
ops, 2.12.6	alternative flag, 2.27.83.15
ali_seq_project, 2.28.147.4	amber, 5.1.4
alias, 2.27.2	amino acid, 2.19.24, 2.28.163, 2.28.164
align, 2.27.3	labels, 2.27.3.1
3D, 2.27.3.4	and, 2.12.3
faq, 3.3.2	angles, 2.28.93.3
heavy, 2.27.3.5	angular hbond dependence, 2.21.5.21
how to, 3.3.2	animated story, 5.8.14
chemical, 2.27.82.1	animation, 2.27.23.5, 2.27.23.6, 3.9
fragments, 2.27.3.3	annotation, 2.27.83.23
intro, 1.4.3.3	append, 5.1.5
number, 2.27.3.1	a tables, 2.27.1.4
res numbers, 2.27.3.1	column, 2.27.4.3
sequence, 2.27.3.2	command, 2.27.4
sequences, 2.27.3.2	sequence, 2.27.4.1
alignMethod, 2.20.2	to group, 2.27.4.1
alignMinCoverage, 2.17.2	stack, 2.27.4.2
alignMinMethod, 2.17.2	tables, 2.27.48
alignOldStatWeight, 2.17.3	by shared column, 2.27.4.3
alignSS, 2.29.1	appending, 2.27.1.1
alignTwoSequences, 2.29.2	an element, 2.12.4
aligned residues, 2.28.119	menu items, 2.21.10.1
alignment, 5.1.1	representations to a slide, 2.27.23.21
as table, 2.28.151.2	rows to matrix, 2.27.1.2

arguments, 2.27.58	base, 5.2.1
arithmetic operations, 2.12.2	basis set, 2.27.78.20, 2.27.104.17
arithmetics, 2.12	batch chemical processing, 3.1.2.5
array, 2.27.66.4, 5.1.6, 5.7.3.1	docking, 3.13.2.6
assignment, 2.12.1	beta, 5.2.3
derivative, 2.28.137.1	bfactor circles, 2.21.5.2
overlap, 2.28.127.1	biased probability monte carlo, 2.27.65
parray, 2.27.22.29	binary file table of contents, 2.27.78.2
size, 2.28.93	files, 2.27.104.2
subset, 2.6	key, 2.27.83.37
arrow from selection, 2.29.36	binding energy, 3.7.4
length, 2.27.83.23	pocket finding, 3.4.2
as2_out, 2.22.13	pockets, 2.27.86.1
as_, 2.8.8	site analysis, 3.4.2
as_graph, 2.21.5.45, 2.21.5.46, 2.28.128.5	biological symmetry, 2.27.83.8
as_out, 2.22.12	vector, 2.28.61.3
assign, 2.27.5	to integers compression, 2.28.61.3
ring conformation to template, 2.27.60.4	blast files, 2.27.104.24
sstructure, 2.27.5.1	blast-formatted database, 2.27.34.3, 2.27.104.24
segment, 2.16.19, 2.27.5.2	blending, 2.27.104.30
assignment, 2.12.1	images, 2.28.149.2
atom, 2.27.13.1, 5.1.7	bold, 2.27.83.32.1
code file, 2.30.4	bond angle bending, 2.30.5
coordinates, 2.28.182.1	errors, 2.27.84.11
flickering, 2.27.83.2	stretching, 2.30.6
label font, 2.30.15	to protein, 2.27.66.3
name, 2.28.72	bonded atoms, 2.28.92.1
pairs, 2.27.83.61, 2.27.83.62, 2.28.151.9	born radii, 2.27.84.8
proximity to surface, 2.27.84.8	boundary element, 5.2.4
selection by number, 2.28.61.4	matrix, 2.28.82.9
type, 2.28.172	box, 2.28.20
user field, 2.28.49.1	break, 2.27.6
atomLabelStyle, 2.20.3	brightness, 2.21.5.28
atomSingleStyle, 2.20.4	build, 2.27.7
atomic contributions, 2.27.84.19	atom, 2.27.7.1
coordinate transfer, 2.27.83.2	column, 2.27.7.2
solvation contributions, 2.28.7	faq, 3.8.1
in residue, 2.28.58	from string, 2.27.7.8
alternative position, 2.27.83.15	helix, 3.10.5
selecting, 2.8.8	how to, 3.8.1
translate, 2.27.83.2	hydrogen, 2.27.7.9
attenuation by occupancy, 2.27.59.25	loop, 2.27.7.6
auc enrichment, 2.29.21	model, 2.27.7.5, 2.27.104.9
auto saving log, 2.20.10	molcart, 2.27.7.10
autoSavePeriod, 2.16.1	sequence, 2.27.7.3
avi, 2.27.104.30	smiles, 2.27.7.7
axis, 5.1.8	string, 2.27.7.8
axisLength, 2.17.4	tautomer, 2.27.7.4
background, 2.28.28.2	built-in functions, 5.5.5
ball, 5.2.2	plot, 2.27.83.47

contact surface, 2.27.14	drawing, 2.21.9.14
molecule, 2.27.13.1	quality, 2.21.9.15
number of bonds, 2.28.128.3	formula, 2.28.147.9
variables, 2.27.14	fragment counting, 2.28.93.2
calcArea, 2.29.3	keys, 2.27.59.21
calcBindingEnergy, 2.29.4	match coordinates, 2.28.182.5
calcDihedralAngle, 2.29.5	matching, 2.27.34.4, 2.27.78.46, 2.27.78.47, 2.28.124, 2.28.146
calcEnergyStrain, 2.29.20	models, 2.28.90.1
calcEnsembleAver, 2.29.6	modification, 2.27.62, 2.27.64, 2.29.37
calcMaps, 2.29.7	name, 2.28.90.6
calcPairSeqIdsFromAli, 2.29.8	normalization, 2.27.64
calcPepHelicity, 2.29.9	rules, 2.27.64.4
calcProtUnfoldingEnergy, 2.29.10	pattern, 2.24, 2.27.82.1
calcRmsd, 2.29.11	search, 2.28.51.3
calcSeqContent, 2.29.12	reaction product generation, 2.27.59.32
calc_nosauc, 2.29.21	search, 2.27.34.10, 2.27.82.1, 2.28.93.2
calculate phases, 3.11.2	similarity, 3.5
call, 2.27.8	spreadsheet, 2.27.12, 2.27.78.45, 2.27.78.46, 2.27.78.47, 2.27.83.41, 2.27.104.11
carboxylic acid, 2.27.64.2	structure from smiles, 2.27.83.6
cartesian cooridnates, 2.28.182	substructure, 2.27.34.4
cartridge, 3.5	mask, 2.27.59.21
cavities, 2.27.86.1	superposition, 2.20.6, 2.28.124
cavity, 5.3.1	table, 2.23
analysis, 3.3.13	view, 2.27.83.48
ccp4 maps, 2.27.78.26	chemistry, 2.23, 2.28.26
cd, 2.27.83.18	chiral isomer generation, 2.27.29
cell axis vectors, 2.28.182.7	chirality, 2.18.16, 2.27.29
specific icm commands, 5.9.2.4	choosing ligands, 3.13.1.2
center, 2.11.1, 2.27.9	cif, 2.27.78.45
chain breaks, 2.21.5.6, 2.21.5.7, 2.28.128.1	circular permutation of coordinates, 2.27.63
symbol, 2.27.83.8	clamp values to range, 2.28.169
change atom position, 2.27.83.2	clashThreshold, 2.17.5
sequence position in multiple alignment, 2.27.66.6	labels, 2.28.157
unix directory, 2.27.83.18	clear, 2.27.10
changing local stick radii, 2.27.83.79	graphical selection, 2.27.10
surface dot size, 2.21.5.49	screen, 2.27.10
channel, 2.21.14.2	click and lock, 5.9.2.4
charge, 5.3.2	clipping plane, 2.21.5.8, 5.3.3
compounds, 2.27.64.2	closer than threshold, 2.28.40.7
change, 2.27.83.9	closest sequence, 2.28.90.3
chem formula, 2.28.147.9	value, 2.28.51.1
chemSuper3D, 2.29.22	cluster, 2.28.145.1
chemical, 2.23, 2.27.34.9	center, 2.28.64.8
2D drawings, 2.27.59.9	centers, 2.11.1
SMARTS search, 2.27.34.5	selection, 2.28.64.8
database, 3.5	tree, 2.28.90.5
decomposition, 2.27.59.27, 2.27.86.2	size, 2.28.93.1
descriptors, 2.28.37, 5.7.12	clustering, 2.11, 2.27.59.35, 2.27.86.7
distance, 2.28.127.2	clusters, 2.11, 2.11.1
diversity, 3.14.6.4	cnMethodAverage, 2.20.5

coil, 5.3.4	comp, 2.28.96
collection, 2.10, 5.3.6	comp_matrix, 2.27.83.17, 2.27.84.15, 5.3.11
color, 2.21.5.28, 2.27.11	compare, 2.16.11, 2.16.14, 2.27.14
accessibility, 2.27.13	angles, 2.27.14.2
background, 2.27.13.2	atom, 2.27.14.1
example, 3.2.7	by rmsd without superposition, 2.27.14.1
accessibility, 3.2.11	chemical tables, 2.27.34.10
alignment, 2.27.13.3	patch only, 2.27.14.3
atom contributions, 2.27.12	rmsd, 2.27.14.1
bfactor, 3.2.9	surface, 2.27.14.3
charge, 3.2.12	variables, 2.27.14.2
electrostatic potential, 2.16.5	compareMethod, 2.20.6
hydrophobicity, 3.2.10	comparing two sarrays, 2.28.96
pharmacophore, 2.27.12	comparison operations, 2.12.5
potential, 2.29.25	complete view, 2.28.135
shape depth, 2.27.13	compound accessibilities, 3.14.4.1
chemical, 2.27.12, 2.27.82.1	array, 2.23
file, 2.30.15	compress, 2.27.15
grob, 2.27.13.4	binary, 2.27.15.3
by atom selection, 2.27.13.4.3	conf, 2.27.15.2
atoms, 2.21.7.1	grob, 2.27.15.1
map, 2.27.13.4.4	in place, 2.27.15.3
matrix, 2.27.13.4.2	objects, 2.27.15
potential, 2.27.13.4.5	stack, 2.27.15.2
unique, 2.27.13.4.1	compressed table view, 2.27.83.21
label, 2.27.13.5	conditional buttons, 5.5.5
map, 2.27.13.6	string, 2.28.147.6
by value, 2.27.23.16	conf, 2.27.83.54, 2.27.104.40, 2.28.151.6, 5.3.12, 5.8.9
molecule, 2.27.13.1	data, 2.28.151.6
names, 2.28.28	confgen, 3.13.2.3
object, 2.27.11.2	configuration, 2.30.14
specification, 2.27.11.1	memory usage, 2.16.6
surface by conservation, 2.27.13.3	conformation comparison, 2.20.6
volume, 2.27.13.7	conformational generator, 2.27.60.1, 3.13.2.3
column, 5.3.5	interpolation, 2.27.23.6
function, 2.27.7.2	stack, 2.27.104.40, 5.3.12, 5.8.9
selection, 2.28.90	compression, 2.27.15.2
combinatorial compounds, 2.28.26	file, 2.30.7
libraries, 2.27.59.32, 2.28.93.4	transition, 2.29.38
PDB, 2.29.90	conformer storage, 2.27.57.5, 2.27.88.2
transformations, 3.10.4	conformers, 3.13.2.3
combining plots, 2.27.59.31	connect, 2.27.16
receptor and ligand stacks, 2.27.4.2	chains with alignments, 2.27.52
command, 2.28.90.4, 5.3.10	molcart, 2.27.16.1
line editing, 2.2	consensus, 2.17.7
help, 2.27.43	coloring, 2.17.9, 2.21.2
options, 2.1	definitions, 2.21.1
word list, 3.1.5	consensusStrength, 2.17.7
commands, 2.20.10	conservation, 2.28.113.5, 2.28.127.6
communication protocols, 2.25	constant, 2.5

contact areas, 2.28.82	creating a local patch object, 2.27.18.2
continue, 2.27.17	credits, 4.5
contour surfaces, 2.21.7.5	crypt, 2.27.20
contouring density, 2.27.59.14	crystal axis vectors, 2.28.16
contrast, 2.21.5.28	symmetry transformation, 3.10.2
conversion, 5.1.6	transformations, 2.28.167
to real array, 2.28.159	crystallographic cell, 2.27.63
convert, 2.27.18, 2.27.18.2, 3.13.2	occupancy, 2.28.98
3D to chemical, 2.28.26	symmetry intro, 1.4.2.4
3D/0D to 2D, 2.27.59.9	crystallography, 2.28.120
ICM object to PDB, 2.27.90	csv format, 2.27.78.42
and reroot, 2.27.18.4	csym, 1.4.2.4
chemical 3D, 2.29.81	cube, 2.21.14.2
and optmimize geometry, 2.29.82	current, 5.3.9
comp, 2.27.18.1	icm-process number, 2.16.4
comparison, 2.27.18.1	map, 5.3.7
fragments, 2.27.18.2	object, 5.3.8
mol, 2.27.18.3	working directory, 2.28.99
object 3D and optmimize geometry, 2.29.83	cursor action, 5.9.2.4
macro, 2.29.13	custom field, 2.27.83.45
pdb, 3.8.2	interaction, 2.27.84.35
to 3D, 2.27.83.7	customization, 3.1.2
ICM object, 2.29.84	and paste chemicals, 2.21.9.14, 2.21.9.15
iarray, 2.28.157	cyclic temperature protocol, 2.17.43
icm-object, 2.27.18	cylinder, 2.21.14.2
integer, 2.28.157	cz32, 4.5
convert2Dto3D, 2.29.83	database, 5.4.1
convert3Dto3D, 2.29.84	browser, 2.27.57.3
convertObject, 2.29.13	connection, 2.27.16.1
converting a chemical, 2.27.18.3	file, 3.5.1
pdb-chemical, 3.13.2	import, 2.27.59.26
alignment to table, 2.28.151.2	date, 2.27.21
chemicals, 3.13.2.4	array, 2.27.21
table columns into matrix, 2.28.82.5	dcMethod, 2.20.7
to, 2.28.114	dcWeight, 2.17.8
cool, 2.29.40	decomposition, 2.27.59.27, 2.27.86.2
pictures, 2.21.5.25	defCell, 2.22.1
cooling schedule, 2.17.43	defSymGroup, 2.16.2
coordinate frame, 2.17.4, 2.27.23.4	default atom colors, 2.27.83.13
copy, 2.27.19	value, 5.8.2
chemical image, 2.21.9.15	define axis, 3.10.3
file, 2.19.26	defining space box, 2.28.20
site, 2.27.83.24	dehtml, 2.28.117.3
correlation matrix, 2.28.154	delete, 2.27.22
covalent bound count, 2.28.128.3	3D graphics panel, 2.27.99
neighbors, 2.28.92.1	alias, 2.27.22.2
covalently attached molecule, 2.28.92.1	array element, 2.27.22.6
cpk, 5.3.13	index, 2.27.22.6
create a covalent bond, 2.27.59.2	selection, 2.27.22.1
pharmacophore, 2.29.85	atom, 2.27.22.7

boundary, 2.27.22.15	dependent columns, 2.27.1.1.1
chemical, 2.27.22.35	depth cueing, 2.27.13.7, 5.4.2
fragment, 2.27.22.35	depth-cueing, 2.17.14
selection, 2.27.22.35	desolvation, 2.20.24
class, 2.27.22	detecting bad covalent geometry, 2.27.84.11
conf, 2.27.22.16	proximity, 2.28.40.7
directory, 2.27.22.8	dialog generation, 2.28.11
disulfide bond, 2.27.22.25	in html documents, 2.27.42
drestraint, 2.27.22.17	tables, 2.27.42
element, 2.27.22.29	scripting, 2.28.11
file, 2.27.22.9	dielConst, 2.17.11
from array, 2.27.22.6	dielConstExtern, 2.17.12
hydrogen, 2.27.22.11	dielectric constant, 2.17.11
label, 2.27.22.18, 2.27.22.19	diff, 2.28.96
chemical, 2.27.22.19	dihedral angle, 2.27.59.19
link, 2.27.22.20	calculation, 3.3.10
map, 2.27.22.21	directory, 2.27.22.8, 2.27.59.5, 2.28.126
molcart, 2.27.22.3	display, 2.27.23
molecule, 2.27.22.13	GUI window, 2.27.23.26
object, 2.27.22.12	box, 2.27.23.7
parray, 2.27.22.34	clash, 2.17.5, 2.27.23.8
element, 2.27.22.34	drestraint, 2.27.23.9
peptide bond, 2.27.22.26	field, 2.21.5.2
plot, 2.27.22.4	from script, 2.27.23.3
salts, 2.27.64.3	gradient, 2.27.23.10
selection, 2.27.22.5	grob, 2.27.23.11
selftether, 2.27.22.32	label, 2.27.23.12
sequence, 2.27.22.22	gui, 2.27.23.26
session, 2.27.22.10	hbond, 2.27.23.13
shell object, 2.27.22.1	label, 2.27.23.15
site, 2.27.22.23	map, 2.21.5.10, 2.27.23.16
sstructure, 2.27.22.24	model, 2.27.23.1
stack, 2.27.22.27	new, 2.27.23.2
object, 2.27.22.28	off-screen, 2.27.23.3
system, 2.27.22.9	offscreen, 2.27.23.3
table, 2.27.22.30	origin, 2.27.23.4
rows, 2.27.22.30	ribbon, 2.27.23.18
term, 2.27.22.31	rotate, 2.27.23.5
tether, 2.27.22.33	site, 2.27.23.19
tree, 2.27.22.34	skin, 2.27.23.20
variable, 2.27.22.6	slide, 2.27.23.21
views, 2.27.22	stack, 2.27.23.6
backbone, 2.28.128.1	string, 2.27.23.22
restraint, 2.27.22.17	surface, 2.27.23.20
deleting sites by number, 2.27.22.23	area, 2.21.5.2
delphi, 2.29.25	tethers, 2.27.23.23
density correlation, 2.17.8, 3.11.3	trajectory, 2.27.23.17
fitting, 2.20.7	volume, 2.27.23.24
in unit cell, 2.27.59.23	window, 2.3, 2.27.23.25
densityCutoff, 2.17.10	distance, 2.21.5.19, 5.4.3

contact-based, 2.28.22, 2.28.22.1	dump database, 2.27.104.7
geometry, 5.4.4	dynamic gui, 5.5.5
matrix, 2.28.151.5, 2.29.8	ecepp, 5.5.1
between stack conformations, 2.28.82.10	edit, 2.27.24
restraint, 5.4.6	files, 2.21.14.1
file, 2.30.9	electro intro, 1.4.2.9
type file, 2.30.8	electroMethod, 2.20.8
restraints, 2.27.83.19	density, 2.21.7.5, 2.29.42, 2.29.43
distances, 2.28.93.3	around selection, 2.17.22
distribution, 1.3	map generation, 2.17.1
comparison, 2.28.127	maps, 2.21.14.1
disulfide bond, 5.4.5	electrostatic boundary matrix, 2.28.82.9
diverse subset, 3.14.6.4	isopotential surfaces, 2.27.59.13
dividing chemical into individual molecules, 2.28.145.4	potential, 2.27.13.4.5
dna to protein sequence translation, 2.28.166.1	solvation, 3.7.2
translate, 2.28.166.1	surface, 2.29.25
dockScan, 3.13.2.6	troubleshooting, 5.7.13
docking, 2.29.87	intro, 1.4.2.9
intro, 3.13.2.1	ellipsoid, 2.28.154
result viewing, 2.29.28	elseif, 2.27.25
simple models, 3.14.3	endfor, 2.27.26
timing, 3.13.1.3	endif, 2.27.27
with template, 3.13.2.7	endmacro, 2.27.28
documents, 5.5.8	endwhile, 2.27.32
dominant color, 2.28.28.2	energetics, 3.7
donor, 3.6.1	function, 2.21.14.3
plot intro, 1.4.3.2	terms, 2.15
dots, 2.27.72	ensemble average, 3.7.5
dotted surface, 2.21.5.51	entropy of alignment, 2.28.127.6
double click action, 5.9.2.4	atom, 2.27.18.4
drestraint, 2.27.84.17, 5.4.6	enumerate, 2.27.29, 2.27.30, 2.27.31
generate from structure, 2.27.59.7	chiral, 2.27.29
global weight, 2.17.6	library, 2.27.31
set, 2.27.83.19	tautomer, 2.27.30
type, 5.4.7	enumeration, 2.28.26
drop, 2.17.13	eps files, 2.19.23
drug, 2.10	error SOAP services, 2.28.44
ds3D, 2.29.31	ignoring, 2.19.25
dsCellBox, 2.29.15	error/warning bits cleanup, 2.27.10
dsChem, 2.29.17	errorAction, 2.20.9
dsCustom, 2.29.18	vrestraint vs_var, 2.27.83.75
dsPocket, 2.29.28	evalSidechainFlex, 2.29.88
dsPropertySkin, 2.29.19	evol tree intro, 1.4.3.5
dsPrositePdb, 2.29.24	evolutionary tree intro, 1.4.3.5
dsRebel, 2.16.5, 2.29.25	exact, 2.27.34.9, 2.27.34.10
dsSeqPdbOutput, 2.29.26	match, 2.28.117.1
dsSkinLabel, 2.29.27	example scripts, 3.14
dsStackConf, 2.29.29	exit, 2.27.33
dsVarLabels, 2.29.30	exitSeslogStyle, 2.20.10
dsXyz, 2.29.32	expanding substructure match, 2.27.83.63

animation, 2.27.104.30	and replace a chemical pattern, 2.27.64.1
pdb, 2.21.14.11	chemical fragment, 2.27.64
exporting sdf, 2.27.104.11	chemical, 2.27.34.5
expression shortcuts, 2.9.1.2	pattern, 2.27.64
comparison, 2.12.5	substructure, 2.28.64.1
arithmetics, 2.12.2	database, 2.17.2, 2.27.34.2
assignment, 2.12.1	fast, 2.27.34.3
comparison, 2.12.5	family of commands, 2.27.34
logical, 2.12.3	in sarray, 2.28.64.7
extending to bonded hydrogens, 2.28.128.6	molcart, 2.27.34.9, 3.5
terminal atoms, 2.28.128.6	molecule, 2.27.34.4
external process, 2.27.59.1	pattern, 2.27.34.8
extracting from Markush, 2.27.50	pdb, 2.27.34.6
icm script arguments, 2.28.54	pharmacophore, 2.27.34.11
stack from object, 2.27.57.5	prosite, 2.27.34.7
ez25, 3.7	table, 2.27.34.10
factor, 5.8.13	findFuncMin, 2.29.33, 2.29.34
false negatives, 2.28.127.3	findFuncZero, 2.29.35
family, 2.27.83.32.1	findSymNeighbors, 2.29.16
faq, 1.3	find_related_sequences, 2.29.33
cheminformatics, 3.14.6	finding long covalent bonds, 2.28.128.1
chemsuper, 3.14.5	to density, 2.20.7
mac gui preferences, 3.14.6.2	fix, 2.27.35
molcart dump, 3.14.6.3	fixed branches, 2.28.128.2
query, 3.14.6.1	flattening 3D molecule, 2.29.17
multiple chem overlay, 3.14.5.1	flow control, 2.13
residue table, 3.14.4.1	fog, 2.17.14, 2.27.13.7, 2.27.23.24, 5.4.2
fast Fourier transform, 2.27.59.24	color, 2.17.14
sequence search, 2.27.34.3	fogStart, 2.17.14
fasta, 2.21.12.14, 5.5.2	fold search, 5.8.4
format, 2.27.104.1	foldbank.db, 2.30.3
feature table, 2.28.151.8	folding procedure, 3.14.1
in sequences, 2.27.83.23	font, 2.27.53.1
ffMethod, 2.20.11	size, 2.27.83.32.1, 2.30.14
field name, 2.28.90.2	sizes, 3.14.6.2
file, 2.27.104.23	specification, 2.27.83.32.1
exists, 2.28.45	for, 2.27.36
list, 2.28.54	fork, 2.27.37
length, 2.28.50	formal charge, 2.21.5.16, 5.3.2
object origin, 2.28.50	formatdb, 2.27.104.24
permissions, 2.28.50	fprintf, 2.27.38
time modified, 2.28.50	fractional coordinates, 2.28.182.3
type, 2.28.50	to abs coordinates, 2.28.16
files, 2.30	fragmented molecule, 2.27.18.2
filling volume, 2.21.5.8	frame, 2.27.88, 2.27.104.30
filter, 2.27.34.10, 2.27.57.3	fullscreen, 2.27.83.78
functions, 5.5.4	function, 2.27.58
filtering table rows, 5.5.4	columns, 2.27.1.1.1
find, 2.27.34	selecting in objects, 2.8.10
alignment, 2.27.34.1	gamess, 5.5.6

gapExtension, 2.17.15	gui, 2.27.42, 5.9.2.4
gapFunction, 2.22.3	exists, 2.28.45
gapOpen, 2.17.16	functions, 5.5.5
gaussian averaging, 2.28.137.2	panels, 2.27.99
gcMethod, 2.20.12	programming, 2.26, 2.27.42, 2.27.83.21
genbank, 2.21.12.14	gvim text editor, 5.8.2
generalized arrays, 5.1.6	gzip files, 2.27.15.3
generate intermediate conformers, 2.29.38	hash, 2.10, 5.3.6
generating movie images, 3.9.2.1	table, 5.3.6
genomics, 1.4.3.1	haze, 2.17.14
clustering, 2.27.41.2	hb, 2.17.18
intro, 1.4.3.1	hbCutoff, 2.17.18
geometry optimization, 2.27.60.1	hbond, 2.21.5.20, 2.21.5.21, 2.27.22.6, 5.5.7
started, 1.7	color, 2.27.23.14
getting data from outside, 2.25	display, 2.21.5.22, 2.21.5.23
started, 1.7	energy, 2.27.23.14
global, 2.27.39	list, 2.28.151.9
glossary, 5	show, 2.27.84.21
goto, 2.27.40	hbondMinStrength, 2.21.5.20
term, 2.17.17, 2.27.83.66	faq, 3.3.4
gpWeights, 2.17.17	how to, 3.3.4
graph matching, 2.28.124	header, 2.27.1.1
graphical box, 2.27.23.7	helical axis, 2.29.36
row selection, 2.28.64.4	cylinders, 2.21.5.37
selection, 2.28.128.5	helicity, 3.7.6
graphics, 2.27.83.3, 2.28.178, 3.2, 5.3.3	content calculation, 3.7.6
card, 2.21.5.47	help, 2.27.43, 2.27.43.1, 2.27.43.2
controls, 2.3, 2.30.15, 5.4.2	browser, 2.27.43.1
exists, 2.28.45	commands, 2.27.43.3
intro, 1.4.1, 1.4.1.4	functions, 2.27.43.4
learning, 3.2.1	getting, 3.1.1
attributes, 2.17.4	word, 2.27.43.2
fogStart, 2.17.14	getting, 3.1.1
view vector, 2.27.83.73	heterogenous environment, 2.21.14.2
greedy matching, 2.9.1.4	hidden blocks, 5.1.1.1
grid potentials, 2.27.59.25	display, 2.27.23.3
grob, 5.5.3	hydrogens, 2.21.5.27
coloring, 2.27.13	stack in object, 2.27.88.2
files, 2.30.10	hierarchical, 2.11
inside-out flip, 2.27.83.36	highEnergyAction, 2.20.13
normal directions, 2.27.83.36	his-tags, 2.28.170
translate, 2.27.97	histogram, 2.27.59.31
group, 2.27.41	2D, 2.28.82
by column, 2.27.41.4	history, 2.27.44, 2.27.104.39
column, 2.27.41.4	delete, 2.27.22.10
replacement, 2.27.62	of ICM, 1.2
sequence, 2.27.41.1	homodel, 2.29.41
unique, 2.27.41.2	homology modeling, 1.4.2.2, 2.27.7.5, 2.27.83.61, 2.27.83.62, 2.29.1, 3.14.4
table, 2.27.41.3	faq, 3.14.4
grouping table by a column, 2.27.83.21	intro, 1.4.2.2

steps, 2.27.7.5.1	bbt, 2.30.5
to export a molcart table, 3.14.6.3	bst, 2.30.6
html, 2.27.42, 2.28.90.4, 5.5.8	cfg, 2.30.14
document order, 2.27.83.34	clr, 2.30.15
tag removal, 2.28.117.3	cmp, 2.30.33
html-formatted text, 5.5.8	cn, 2.30.9
hydration, 2.21.14.2, 2.28.7	cnf, 2.30.7
parameters, 2.30.13	cnt, 2.30.8
hydrogen bond, 2.21.5.20, 2.21.5.21, 2.27.59.17, 5.5.7	cod, 2.30.4
bonding parameters, 2.30.12	col, 2.30.24
cutoff, 2.17.18	gro, 2.30.10
bonds, 2.28.93.3	hbt, 2.30.12
display, 2.21.5.27	hdt, 2.30.13
placement, 2.27.83.22	htm, 2.30.11
hydrophobicity profile, 3.3.12	iar, 2.30.35
iProc, 2.16.4	map, 2.30.16
iSee, 5.8.14	mat, 2.30.37
i_out, 2.16.3	ob, 2.30.18
iarray, 2.27.22.6, 2.28.51.1, 2.28.61.2, 2.28.64.7, 5.6.1	pdb, 2.30.28
making, 2.28.61.1	prf, 2.30.34
icb files, 5.8.14	rar, 2.30.38
GUI, 2.27.83.34	res, 2.30.20
algorithms, 4.3	rs, 2.30.23
application refs, 4.4	rst, 2.30.22
literature, 4.3	sar, 2.30.36
archive, 2.27.78.2	se, 2.30.30
arguments, 2.28.54	seq, 2.30.29
binary, 2.28.99	tab, 2.30.25
branching, 2.13.2	tot, 2.30.26
commands, 2.27	trj, 2.30.17
controls, 2.13	var, 2.30.21
flags, 2.1	vwt, 2.30.27
functions, 2.28	icmCavityFinder, 2.29.14
graphics, 3.2	icmMacroShape, 2.29.86
history, 1.2	icmPmfProfile, 2.29.23
jumps, 2.13.3	icmPocketFinder, 2.29.87
learning, 3.1.4	icmscript, 2.27.78.3
loops, 2.13.1	arguments, 2.28.54
macros, 2.29	if, 2.27.45
main refs, 4.2	ignoring swiss secondary structure, 2.22.9
menus, 2.21.10.1	illegal smiles, 2.28.64.1
method literature, 4.4	image, 3.2.6
molecules, 2.14	annotation, 3.2.5
object file, 2.30.18	center, 3.2.8
session, 2.20.10	format, 5.9.3
shell, 3.1	high quality, 3.2.2
support, 1.3	parray, 5.7.3.3
table, 2.21	resolution, 3.2.2
ali, 2.30.31	rotation, 3.2.3
all, 2.30.32	implicit continuous solvation, 2.30.13

imposing tether, 2.27.83.61, 2.27.83.62	l_breakRibbon, 2.18.4
place, 2.12.4	l_bufferedOutput, 2.18.5
ops, 2.12.4	l_bug, 2.18.6
incidence, 2.28.82.12	l_caseSensitivity, 2.18.7
increasing the number of shell variables, 2.30.14	l_commands, 2.18.8
increment charge, 2.27.83.9	l_confirm, 2.18.9
index expressions, 2.6	l_easyRotate, 2.18.10
in array, 2.28.64.3	l_info, 2.18.11
substring, 2.28.64.2	l_minRedraw, 2.18.12
table, 2.27.104.23	l_neutralAcids, 2.18.13
entry, 2.28.126.1	l_out, 2.18.14
sdf-file path, 2.28.99	l_print, 2.18.15
indices of labeled table rows, 2.28.64.5	l_racemicMC, 2.18.16
selected table rows, 2.28.64.4	l_readMolArom, 2.18.17
infinity, 2.28.159	l_showAccessibility, 2.18.18
info, 2.27.46	l_showMC, 2.18.19
molcart, 2.27.46.1	l_showMinSteps, 2.18.20
inner join, 2.27.48	l_showResCodeInSelection, 2.18.21
insert rows, 2.27.1.4	l_showSites, 2.18.23
integer, 5.6.2	l_showSpecialChar, 2.18.22
array, 2.28.61, 5.6.1	l_showSstructure, 2.18.24
shell variables, 2.16	l_showTerms, 2.18.26
interaction cutoff, 2.18.27	l_showWater, 2.18.25
lists, 2.18.27, 2.21.14.3	l_updateLists, 2.18.27
interactive docking, 1.4.2.8	l_warn, 2.18.28
interatomic potential, 2.27.83.45, 2.27.84.35	l_wrapLine, 2.18.29
interface comparison, 2.27.14.3	l_writeStartObjMC, 2.18.30
residues, 3.3.5	l_xrUseHydrogen, 2.18.31
torsions, 3.3.7	label, 2.27.23.22, 5.6.3
view, 2.29.28	fonts, 2.30.15
intermolecular bond, 2.27.66.3	large text, 2.27.78.38
internal coordinate file, 2.30.21	latent, 2.28.93.6
coordinates, 2.8.9	learn, 2.27.49
positional restraints, 5.9.4	atom, 2.27.49.1
interpolate, 2.28.28.1	left join, 2.27.48
interpolation, 2.28.28.1	triangle of a matrix, 2.28.82.3
interruptAction, 2.20.14	library to replacement groups, 2.27.59.27, 2.27.86.2
inverting array order, 2.28.61.2, 2.28.113.2	ligand binding, 2.29.28
italic, 2.27.83.32.1	dock faq, 3.13.2
iterative overlay, 2.27.91	docking, 3.13, 3.13.1, 3.13.2
superposition, 2.21.14, 2.27.92	intro, 1.4.2.6
join, 2.27.48	editing, 1.4.2.8
tables, 2.27.48	editor, 2.29.37
keep, 2.27.47	fit, 3.13
kernel models quality, 2.28.127.3	setting, 3.13.2
mapping, 2.30.15	view, 2.21.5.26
kmz, 5.5.3	light, 2.21.5.29
l_antiAlias, 2.18.1	limits, 2.30.14
l_autoLink, 2.18.2	line thickness in 2D chemicals, 2.21.9.14
l_bpmc, 2.18.3	lineWidth, 2.17.19

regression, 2.28.76	make, 2.27.59
group, 2.27.50	3d label, 2.27.59.15
internal variables of molecular object, 2.27.51	angle, 2.27.59.18
ms2ali, 2.27.52	background, 2.27.59.1
sequences to 3D objects, 2.27.52	bond, 2.27.59.2
to alignment, 2.27.52	chain, 2.27.59.3
variable, 2.27.51	multi, 2.27.59.3
variables, 2.27.51	boundary, 2.27.59.4
linked alignment, 2.28.90	directory, 2.27.59.5
sequence, 2.28.90	distance, 2.27.59.16
linux shell, 2.27.93, 5.10.2	disulfide bond, 2.27.59.6
list, 2.27.53	drestraint, 2.27.59.7
binary, 2.27.54	factor, 2.27.59.8
database, 2.27.55	flat, 2.27.59.9
font, 2.27.53.1	chem_array, 2.27.59.9
html documents, 2.28.90	grob, 2.29.36
molcart, 2.27.56	from image, 2.27.59.11
database, 2.27.56	matrix, 2.27.59.12
of files, 2.28.126	image, 2.27.59.11
updates, 2.27.60	map, 2.27.59.10
listUpdateThreshold, 2.17.20	matrix, 2.27.59.12
literature, 4.1	potential, 2.27.59.13
load, 2.27.57	skin, 2.27.59.14
conf, 2.27.57.1	hbond, 2.27.59.17
frame, 2.27.57.2	image, 2.27.59.20
molcart, 2.27.57.3	key, 2.27.59.21
object, 2.27.57.6	map, 2.27.59.22
solution, 2.27.57.4	cell, 2.27.59.23
stack object, 2.27.57.5	factor, 2.27.59.24
loadEDS, 2.29.42	potential, 2.27.59.25
loadEDSweb, 2.29.43	xray, 2.27.59.30
local, 3.5.1	molcart, 2.27.59.26
logarithm, 2.28.77	molsar, 2.27.59.27
logical, 5.6.4	pca, 2.27.59.28
operations, 2.12.3	peptide bond, 2.27.59.29
variables, 2.18	plot, 2.27.59.31
logical_ops, 2.12.3	reaction, 2.27.59.32
logicals, 2.18	sequence, 2.27.59.34
long axes, 2.28.154	alignment, 2.27.59.33
loop database rebuilding, 2.27.104.27	from alignment, 2.27.59.33
interrupt, 2.17.44	torsion, 2.27.59.19
modeling, 1.4.2.3	tree, 2.27.59.35
intro, 1.4.2.3	unique, 2.27.59.36
search, 2.27.7.5.2	makeAxisArrow, 2.29.36
resolution shape, 2.29.86	makeIndexChemDb, 2.29.44
ma29, 3.11	makeIndexSwiss, 2.29.45
macro, 2.27.58, 5.6.5	makePdbFromStereo, 2.29.46
macro_def, 5.6.5	makePharma, 2.29.85
main ICM references, 4.2	makeSimpleDockObj, 2.29.47
concepts, 3.10.1	makeSimpleModel, 2.29.48

manual style, 1.5	mergePdb, 2.29.90
map, 2.17.22, 2.21.5.10, 5.6.6	several chemical, 2.28.149.1
aa property to sequence, 2.28.113.1	merging into one molecule, 2.27.66.3
averaging, 2.28.137.5	mesh, 2.28.179
calculation, 2.27.59.24	score, 3.13.3.3
conversion, 2.27.59.30	mfMethod, 2.20.15
file, 2.30.16	mfWeight, 2.17.27
fitting, 2.20.7	mimel, 5.6.8
format, 5.6.6	mimelDepth, 2.17.28
mean value, 2.28.85	mimelMolDensity, 2.17.29
min value, 2.28.86	minNumGrad, 2.27.60
name, 2.28.78	minTetherWindow, 2.16.7
operations, 5.6.6	minimization exit criteria, 2.27.60
transformations, 2.28.137.5	minimize, 2.16.9, 2.27.60
trimming, 2.28.21	cartesian, 2.27.60.1
value sigma, 2.28.124	loop, 2.27.60.2
contouring, 2.27.59.14	stack, 2.27.60.3
mapAtomMargin, 2.17.22	tether, 2.16.7, 2.27.60.4
mapSigmaLevel, 2.17.21	drop, 2.17.13
mapping properties to sequence, 2.28.113.4	minimizeMethod, 2.20.16
and factors, 3.11	missing bonds, 2.27.66.3
mass-spectrometry functions, 2.27.29, 2.27.30, 2.27.31	loop, 2.21.5.6, 2.21.5.7
matching chemicals, 2.28.64.1	residues, 2.28.49.1
hydrogens, 2.27.83.63	triangles, 2.28.179
matrix, 5.6.7	mkUniqPdbSequences, 2.29.49
derivatives, 2.28.73	mm26, 3.8
new, 2.28.82.1	mmcif, 5.6.10
map value, 2.28.83	mmff, 5.6.9
maxColorPotential, 2.16.5	type, 2.28.172
maxMemory, 2.16.6	show atom types, 2.27.84.10
movie, 3.9.2	mnSolutions, 2.16.8
mcBell, 2.17.23	mncalls, 2.16.9
mcJump, 2.17.24	mncallsMC, 2.16.10
mcShake, 2.17.25	mnconf, 2.16.11
mcStep, 2.17.26	mnhighEnergy, 2.16.12
mean force, 2.27.83.45, 2.27.84.35	mnreject, 2.16.13
membrane, 2.21.14.2	mnvisits, 2.16.14
memorizing positions, 3.2.4	model reliability, 2.29.23
menu, 2.27.61	modify, 2.27.62
script, 3.1.3	and reroot, 2.27.18.4
merge PDB, 2.29.90	chem, 2.27.64
arrays to table, 2.27.41.3	charge, 2.27.64.2
continuation lines, 2.27.78.37	delete salt, 2.27.64.3
objects, 2.27.66.2	normalize, 2.27.64.4
parts of molecule, 2.27.66.3	chemical find replace, 2.27.64.1
pdb, 3.4.4	molcart, 2.27.64.5
sarray into string, 2.28.149	rotate, 2.27.63
stacks, 3.7.7	modifyGroupSmiles, 2.29.37
tables, 2.27.4.3, 2.27.48	modules, 1.4.4
merge2, 3.8.7	mol, 2.27.78.46, 2.27.78.47, 2.27.104.11, 2.27.104.23, 5.6.11

to icm, 2.27.18.3	movie, 2.27.88.3
translation, 3.2.4	images by frame, 3.9.2.2
mol-file to chem-table element, 2.28.100	molecular simulation, 3.9.2
mol2, 5.6.12	rotate view, 3.9.1
molcart, 2.27.16.1, 3.5	zooming, 3.9.1
connection options, 3.5.2	moving selection to another object, 2.28.128.8
molecular, 2.28.53, 5.7.3.1	mpeg, 2.27.104.30
arrays, 5.7.3	ms_, 2.8.6
manipulations, 3.8	multi center drestraint, 2.20.5
modifications, 3.8.5	multi-part molecule, 2.27.18.2
object, 5.7.1	multiple NMR models, 2.21.14.4
objects, 2.14	alignment, 2.27.3.2
surface, 2.27.84.8, 5.8.7	to pairwise similarities, 2.29.8
views, 1.4.1.1	conformation storage, 5.8.9
volume, 2.28.105	mol as text, 2.28.147.2
molecule, 2.7	object file, 2.27.78.2
create, 3.8.4	sequence alignment intro, 1.4.3.4
properties, 2.27.83.30	smiles file format, 2.27.78.43
rotation, 3.2.3	mutate residue, 2.27.62
translation, 3.2.3, 3.2.4	mutating residue, 3.8.5
create, 1.7.2	mute, 5.6.15
intro, 1.7.2, 2.7	mysql, 2.27.16.1
sort/reorder, 2.27.85.4	nLocalDeformVar, 2.16.15
selecting, 2.8.6	nProc, 2.16.17
monte carlo, 2.27.65	nSsearchStep, 2.16.16
montecarlo, 2.16.10, 2.16.12, 2.16.13, 2.16.14, 2.16.18, 2.20.6, 2.27.65	name, 2.28.72
local, 2.16.15	atom fields, 2.27.83.30
trajectory, 2.27.23.17	naming compounds, 2.27.83.41
moprphing, 2.29.38	nearest sequence, 2.28.86
more, 5.6.13	nested script, 5.8.2
morph, 2.27.23.6	nice, 2.29.39
to tether target, 2.29.38	image, 3.2.2
morph2tz, 2.29.38	non-redundant, 3.4.3
morphing, 2.27.23.6, 2.27.83.61, 2.27.83.62, 2.27.88.3	normal distribution, 2.28.112
mouse controls, 2.3	normalize chemicals, 2.27.64.4
file, 2.27.104.30	defined, 2.28.159
move, 2.27.66	nota, 1.5
alignment sequence, 2.27.66.6	notational conventions, 1.5
atoms, 2.27.83.2	nucleotides, 2.19.24
bonding, 2.27.66.3	number of dots, 2.21.5.50
column, 2.27.66.5	elements, 2.28.93
element, 2.27.66.4	hydrogen bonds, 2.27.84.21
file, 2.19.28, 2.27.79.3	molecules in objects, 2.28.128.4
fragments together, 2.27.66.3	occurrences, 2.28.93
molecule, 2.27.66.1	residues in molecules, 2.28.128.4
ms_molecule, 2.27.66.1	van der Waals contacts, 2.27.84.12
multiple molecules, 2.27.66.2	transfer from sequence, 2.27.3.1
object, 2.27.66.2	nvis, 2.28.61.6
sequence, 2.27.66.6	object, 2.27.13.1, 5.7.1
table column, 2.27.66.5	parray, 5.7.3.1

stack, 5.8.9	sum, 2.28.70
to chemarray, 2.28.26	passing arguments, 5.8.2
user fields, 2.28.49.1	by reference, 2.27.58
assign comment, 2.27.83.14	pattern, 5.7.4
source file, 2.28.50	search, 2.27.34.2
translate, 2.27.97	pause, 2.27.67
merge, 3.8.6	pdb, 5.6.10, 5.7.6
selecting, 2.8.5	file creation time, 2.28.35
obsolete, 2.17.51	files, 2.30.28
occlusion shading, 2.27.13	format, 2.27.78.45
octanol transfer, 2.28.105	merge, 3.4.4
off, 2.27.78.21	sequence generation, 3.4.3
format, 5.5.3	pdbDirStyle, 2.20.17
oligonucleotide melting, 2.28.155	peptide, 5.7.7
on-line help, 2.27.43.1, 2.27.43.2	docking, 3.12.5
third, 2.28.34	folding, 1.4.2.1
only, 5.7.2	intro, 1.4.2.1
openGL window, 2.27.99	personal gui controls, 3.1.2
operating system, 2.27.93, 2.28.178, 5.10.2	setup, 3.1.2
optimal chemical superposition, 3.14.5.1	ph30, 3.12
optimization, 2.27.65	ph4, 5.7.8
Hbond, 2.29.89	object faq, 3.6.1
hydrogen bond, 2.29.89	pharmacophore, 2.27.12, 3.5, 5.7.8
optimizeHbonds, 2.29.89	faq, 3.6
or, 2.12.3	grid type definitions, 2.27.83.66
order, 2.27.66.6	object, 3.6.1
original sequence names, 2.21.12.14	objects, 3.6
os_, 2.8.5	pharmacophores, 3.6
other variables, 2.22	psi plot, 2.29.57
output, 2.16.3	pipe, 2.27.78.41
overlay by atom pairs, 2.27.91	planar angle, 2.27.59.18
chemical substructure, 2.29.22	plot, 2.27.68
overview, 1.4	3D 2Dfunction, 3.12.3
pK shift, 3.7.3	shape, 3.12.4
packing density, 3.3.8	area, 2.27.69
pair-distances, 2.27.22.6	histogram, 3.12.2
pairdistance parray, 2.21.5.19	how to, 3.12
pairwise interactions, 2.27.83.45	simple, 3.12.1
panel layout, 2.21.8.5	plot2DSeq, 2.29.50
paragraphs, 2.27.104.23	plotBestEnergies, 2.29.53
parallelization, 2.16.4, 2.16.17	plotCluster, 2.29.55
parameter list file, 3.14.6.2	plotFlexibility, 2.29.54
parray, 2.27.22.6, 5.7.3	plotMatrix, 2.29.56
parrayTo3D, 2.29.82	plotRama, 2.29.57
parrayToMol, 2.29.81	plotRose, 2.29.58
parse SOAP message, 2.28.176	plotSeqDotMatrix, 2.29.51
parsing, 2.28.81	plotSeqDotMatrix2, 2.29.52
web pages, 2.27.78.44	plotSeqProperty, 2.29.59
partial least squares, 2.27.49	3d, 1.4.3.7
slide display, 2.27.23.21	plotting van der Waals, 3.7.1

pls, 2.27.49	grids, 2.17.17
column contributions, 2.28.151.7	map, 2.27.83.66
model, 2.28.151.7	superposition, 2.27.83.66
weights, 2.28.151.7	prosite, 5.7.10
pmf, 2.20.15	pattern, 5.7.4
residue profile, 2.29.23	protein docking, 2.28.182.2
pmf-file, 2.30.19	intro, 1.4.2.5
pmffile, 2.30.19	grid docking, 3.14.2
png, 2.27.104.35, 5.7.5	health, 2.29.57
pocket, 2.29.28, 2.29.87, 3.13.1.1	topology, 2.21.5.37
point coordinates, 2.28.182.1	psa, 5.7.12
pointer array, 5.7.3	purple box, 2.28.20
polar hydrogens, 2.21.5.27	quadratic equation, 2.28.138
surface area, 2.28.105	quantum mechanics, 2.27.78.20, 2.27.104.17
polarization charge, 3.7.2, 5.7.13	qubic equation, 2.28.139
positional constraint, 2.21.14.9	query, 3.14.6.1
postscript, 2.19.23	molcart, 2.27.75
potential surface coloring, 5.7.13	question mark operator, 2.28.147.6
pov-ray, 2.27.104.37	quit, 2.27.76
pow, 2.28.34	property transfer via alignment, 2.28.113.3
precision, 2.28.127.3	r_2out, 2.17.31
predict, 2.27.70	r_out, 2.17.30
predictSeq, 2.29.60	radii.electrostatic, 2.28.111
prediction model, 2.28.76	van der Waals, 2.28.111
quality, 2.28.127	rainbow, 2.28.28.1
score, 2.28.127	ramachandran faq, 3.3.3
preference, 2.20	how to, 3.3.3
preferences, 3.1.2.3	random array, 2.28.112
prepSwiss, 2.29.61	order, 2.28.130
previous atom, 2.28.92.1	randomSeed, 2.16.18
principal axes, 2.28.154	randomize, 2.16.18, 2.27.77
component analysis, 3.3.9	angles, 2.27.77.1
inertia moments, 2.28.80	coordinates, 2.27.77
print, 2.27.71	torsions, 2.27.77
bar, 2.27.72	rarray, 2.27.22.6, 2.28.51.1, 2.28.113.2, 5.7.11
image, 2.27.74	properties, 2.28.113.4
to string, 2.27.87	rdBlastOutput, 2.29.67
printMatrix, 2.29.62	rdSeqTab, 2.29.68
printPostScript, 2.29.63	reaction, 2.27.59.32
printTorsions, 2.29.64	group file, 2.27.50
printf, 2.27.73	read, 2.27.78, 2.27.78.53, 2.27.78.54
problem, 3.14.6.2	FILTER, 2.27.78.5
profile, 5.7.9	alignment, 2.27.78.11
program overview, 1.4	all, 2.27.78.6
progress bar, 2.27.72	binary, 2.27.78.2
progression, 2.27.72	color, 2.27.78.12
project setup, 3.13.2.2	column, 2.27.78.48
projected alignment, 2.28.90.3	comp_matrix, 2.27.78.13
projecting surface charge, 3.7.2	conf, 2.27.78.14
property, 2.27.83.46, 2.27.83.47, 2.27.83.48	csd, 2.27.78.15

database, 2.27.78.16	variable, 2.27.78.49
drestraint, 2.27.78.17	view, 2.27.78.50
type, 2.27.78.18	vrestraint, 2.27.78.51
entries from database, 2.27.78.7	type, 2.27.78.52
factor, 2.27.78.19	with filter, 2.27.78.5
file by chunk, 2.27.78.38	xml, 2.27.78.53
from file, 2.27.78.1	readMolNames, 2.22.10
string, 2.27.78.4	readcomp_matrix, 2.27.78.13
fromstring, 2.27.78.4	reading external tool output, 2.27.59.1
ftp http, 2.27.78.8	from standard input, 2.27.78.41
gamess, 2.27.78.20	pdb from ftp, 2.19.18
grob, 2.27.78.21	web, 2.19.19
html, 2.27.78.3	restraint, 2.27.78.51
file, 2.27.78.3	real, 5.7.14
iarray, 2.27.78.22	array, 5.7.11
index, 2.27.78.23	shell variables, 2.17
table, 2.27.78.7	space refinement, 2.27.59.30
json, 2.27.78.54	reals, 2.17
library, 2.27.78.24	rebel, 2.16.5, 5.7.13
mmff, 2.27.78.25	rebuild molcart index, 2.27.7.10
librarymmff, 2.27.78.25	recalculate dependent values, 2.27.7.2
map, 2.27.78.26	values, 2.27.1.1.1
matrix, 2.27.78.27	receptor, 3.13.1.1
mol, 2.18.13, 2.27.78.7, 2.27.78.28	preparation, 3.13.1.1
mol2, 2.27.78.7, 2.27.78.29	redefine hydrogen coordinates, 2.27.83.22
object, 2.27.78.31	references, 4
parray, 2.27.78.31.1	refineModel, 2.29.65
pdb, 2.21.14.4, 2.27.78.2, 2.27.78.32	reflections, 2.21.5.28
sequence, 2.27.78.33	refresh view, 2.27.23.2
profile, 2.27.78.34	refs, 4.1
prosite, 2.27.78.35	regexp, 2.9, 2.28.81
rarray, 2.27.78.36	back references, 2.9.1.3
sarray, 2.27.78.37, 2.27.78.38	syntax, 2.9.1
sequence, 2.27.78.7, 2.27.78.39	regression, 2.27.49
database, 2.27.78.39.1	regul, 2.29.66
smiles, 2.27.78.43	regular expression, 2.9, 2.28.64.3, 2.28.81
stack, 2.27.78.40	filter, 2.27.78.1
string, 2.27.78.41	expression, 2.28.117.3
table, 2.27.78.42	regularization, 2.16.7, 2.27.60.4, 5.7.15
csv, 2.27.78.42	procedure, 3.8.3
html, 2.27.78.44	rejectAction, 2.20.18
mmcif, 2.27.78.45	relational database, 2.28.140
mol, 2.27.78.47	relative accessible area of atoms, 2.20.1
mol2, 2.27.78.46	release notes, 1.1
text, 2.27.78.38	remarkObj, 2.29.69
trajectory, 2.27.78.30	remove expression tags, 2.28.170
and save a fragment, 2.27.78.30.1	file, 2.27.22.9
write, 2.27.78.30.1	trailing blanks, 2.28.169
unix, 2.27.78.9	removing html tags, 2.27.78.44
cat, 2.27.78.10	outliers, 2.28.169

chemicals, 2.27.83.41	restraints, 2.15, 2.27.83.61, 2.27.83.62
file, 2.27.79.3	torsion, 2.27.83.74
molcart, 2.27.79.2	return, 2.27.80
object, 2.27.79.1	reverse complement, 2.28.129.1
system, 2.27.79.3	lighting, 2.27.83.36
atom, 2.27.79.1	normals, 2.27.83.36
molecule, 2.27.79.1	reversing order, 2.28.61.2
residue, 2.27.79.1	rgb, 5.7.17
renaming, 2.21.12.14	matrix, 2.28.28
reorder, 2.27.66.6	ribbon, 5.7.18
alignment sequences, 2.27.104.1	bullets, 2.21.5.6
array, 2.28.130	diagram, 2.21.5.37, 2.21.5.38
objects, 2.27.85.3	ribbonColorStyle, 2.20.20
replace matching array element, 2.28.117.1	ribbonStyle, 2.20.21
without interpretation, 2.28.117.2	right join, 2.27.48
replacing scaffold in a library, 2.27.64.1	rigid chemical superposition, 2.27.91
reproducible randomness, 2.16.18	ring, 2.28.121
reroot, 2.27.18.4	sampling, 3.13.2.3
selections, 3.3.6	templates, 2.27.83.7
resLabelShift, 2.17.32	rocking, 2.27.23.5
resLabelStyle, 2.20.19	root mean square deviation, 2.28.127.3
reserved names, 2.22	roots, 2.28.138, 2.28.139
residue, 2.27.13.1, 5.7.16	rotate, 2.27.81
accumulators, 2.28.58	grob, 2.27.81.2
alignment, 2.27.83.61, 2.27.83.62	object, 2.27.81.1
conservation, 2.28.113.5	view, 2.27.81.3
contact area matrix, 2.28.82.7	rotation, 2.27.23.5
areas, 2.28.7.1	angle, 2.28.17
field, 2.27.83.30	rounding a real, 2.28.147
gap, 2.21.5.6, 2.21.5.7	output, 2.27.84.43
label, 2.27.3.1	rsWeight, 2.17.33
library file, 2.30.20	rs_, 2.8.7
name, 2.28.72	run script, 2.27.8
translation, 2.21.14.11	running a docking job, 3.13.2.6
number, 2.28.61.5	dock job, 3.13.2.5
table, 2.28.151.3	script from html, 5.8.2
property averaging, 2.28.137.3	s-s bond, 5.4.5
calculation, 2.28.58	s_alignment_rainbow, 2.19.1
proximity, 2.28.82.7	s_blastdbDir, 2.19.2
ranges, 2.8.11	s_editor, 2.19.3
selection, 2.18.21	s_entryDelimiter, 2.19.4
as string, 2.28.147.7	s_errorFormat, 2.19.5
function, 2.28.118	s_fieldDelimiter, 2.19.6
table, 3.14.4.1	s_helpEngine, 2.19.7
tethering, 2.27.83.61, 2.27.83.62	s_icmPrompt, 2.19.10
user field, 2.28.49.1	s_icmhome, 2.19.8, 3.1.2.1
residue_selections, 2.8.11	s_imageViewer, 2.19.11
selecting, 2.8.7	s_inxDir, 2.19.9
resizing, 2.28.63	s_javaCodeBase, 2.19.12
restraining molecules to shapes, 2.21.14.9	s_labelHeader, 2.19.13

s_logDir, 2.19.15	searchSeqDb, 2.29.73
s_out, 2.19.16	searchSeqFullPdb, 2.29.75
s_pdbDir, 2.19.17	searchSeqPdb, 2.29.74
s_pdbDirFtp, 2.19.18	searchSeqProsite, 2.29.76
s_pdbDirWeb, 2.19.19	searchSeqSwiss, 2.29.77
s_printCommand, 2.19.21	searches and alignments, 3.4
s_projectDir, 2.19.20	second moments, 2.28.154
s_prositeDat, 2.19.22	secondary structure derivation from 3D, 2.27.5.1
s_psViewer, 2.19.23	schematic, 2.21.5.37
s_reslib, 2.19.24	segMinLength, 2.16.19
s_skipMessages, 2.19.25	segment, 5.8.4
s_sysCp, 2.19.26	select, 2.27.82
s_sysLs, 2.19.27	atoms by number of bonded atoms, 2.28.128.3
s_sysMv, 2.19.28	of the fixed torsions, 2.28.128.2
s_sysRm, 2.19.29	by bfactor, 2.28.128.7
s_tempDir, 2.19.30	center of mass, 2.28.128.14
s_translateString, 2.19.31	coordinates, 2.28.128.7
s_userDir, 2.19.32	iarray, 2.28.128
s_usrlib, 2.19.33	length, 2.28.128.13
s_webEntrezLink, 2.19.34	occupancy, 2.28.128.7
s_webViewer, 2.19.35	user field, 2.28.128.7
s_xpdbDir, 2.19.36	chemical, 2.27.82.1
sa23, 3.3	lines, 2.27.78.1
sampling grid, 2.28.182.2	tether partners, 2.28.128.12
sarray, 2.27.22.6, 5.8.1	vw partners, 2.28.128.12
transformation in place, 2.27.96.1	selectMinGrad, 2.17.34
save print, 3.2.6	selectSphereRadius, 2.17.35
sdf file, 2.27.104.11	selected stack conformations, 2.27.22.16
saving graphics to album, 2.27.59.20	selecting by b-factor, 2.28.128
image, 2.27.104.35	y z, 2.28.128
scaffolds, 2.27.50	columns, 5.9.1
scoring, 3.13.1.4	from clusters, 3.14.6.4
screen X, 2.28.180	neighboring elements, 2.28.92
coordinates, 2.28.180	residues, 3.3.6
script, 2.28.90.4, 5.8.2	saving, 2.28.61.4
file name, 2.28.50	selection, 2.8, 2.28.128, 2.28.128.6
inside ICM, 5.8.2	elements, 2.8.4
name, 5.8.2	examples, 2.8.3
image generation, 2.27.23.3	functions, 2.8.10
scripting molecular movements, 3.2.4	gap patching, 2.28.128, 2.28.128.11
sdf, 2.27.104.23	level, 2.8, 2.28.172
file, 2.27.78.46, 2.27.78.47, 2.27.83.41, 2.27.104.11, 2.28.147.2, 5.7.3	levels, 2.8.2
to chem-table, 2.28.100	simplification, 2.28.128.11
search for chemical pattern, 2.28.51.3	transfer, 2.28.128, 2.28.147.7
pdb headers, 3.4.5	type, 2.8
prosite, 3.4.1	types, 2.8.1
sequence pattern, 2.27.34.8	variable, 2.22.11
searchObjSegment, 2.29.72	atoms, 2.8.8
searchPatternDb, 2.29.70	functions, 2.8.10
searchPatternPdb, 2.29.71	molecules, 2.8.6

output, 2.22.14	and formal charges, 2.27.83.6
residues, 2.8.7	cartesian, 2.27.83.7
torsions, 2.8.9	chain, 2.27.83.8
variables, 2.8.9	charge, 2.27.83.9
selections, 2.27.83.30	formal, 2.27.83.10
in molecular objects, 2.8	mmff, 2.27.83.11
selftether, 2.21.14.9, 5.9.4	chargemmff, 2.27.83.11
seq_ali_project, 2.28.147.5	chiral, 2.27.83.12
sequence, 2.28.163, 2.28.164, 5.8.3	color, 2.27.83.13
alignment, 2.28.5.1, 2.29.2	comment, 2.27.83.14, 2.27.83.15
intro, 1.4.3.3	sequence, 2.27.83.16
analysis intro, 1.4.3	comp_matrix, 2.27.83.17
assembly, 2.27.41.2	current map, 2.27.83.39
belongs to alignment, 2.28.64	object, 2.27.83.42
conservation, 2.28.127.6	directory, 2.27.83.18
distance, 2.28.128	drestraint, 2.27.83.19
matrix from alignment, 2.28.82.8	type, 2.27.83.20
dotplot, 1.4.3.2	electrostatic radii, 2.27.83.72
from pdb, 2.27.59.34	error, 2.27.83.29
identity, 2.29.8	field, 2.27.83.30
intro, 1.4.3	name, 2.27.83.31
modification, 2.28.170	font, 2.27.83.32
neighbor, 2.28.90.3	grob, 2.27.83.33
parray, 5.7.3.2	foreground, 2.27.83.34
pattern, 5.7.4	format, 2.27.83.35
position correspondence, 2.28.151.3	grob, 2.27.83.36
positional weights, 2.27.83.1	coordinates, 2.27.83.36
redundancy removal, 2.27.41.2	label, 2.27.83.36
search, 2.27.34.2	group, 2.27.83.56
selection, 2.27.22.22	column, 2.27.83.21
structure alignment, 2.29.1	hydrogen, 2.27.83.22
to alignment transfer, 2.28.113.3	key, 2.27.83.37
type, 5.8.3	label, 2.27.83.38
sequence-alignment mapping, 2.28.147.4, 2.28.147.5	3d label, 2.27.83.38.4
sequence-structure alignment, 2.28.5.1	chemical, 2.27.83.38.3
output format, 2.16.20, 2.16.21	distance, 2.27.83.38.1
sequenceBlock, 2.16.20	table, 2.27.83.38.2
sequenceColorScheme, 2.20.22	map, 2.27.83.39
sequenceLine, 2.16.21	molcart, 2.27.83.40
sequences, 3.4	molecular variables, 2.27.83.76
not in alignments, 2.27.22.22	name, 2.27.83.41
set, 2.27.83	sequence, 2.27.83.41.1
alternative atom, 2.27.83.15	object, 2.27.83.42
area, 2.27.83.1	occupancy, 2.27.83.43
atom, 2.27.83.2	plane, 2.27.83.44
background image, 2.27.83.3	pmf, 2.27.83.45
bfactor, 2.27.83.4	property, 2.27.83.46, 2.27.83.48
biological symmetry, 2.27.83.57	chemical view, 2.27.83.48
bond topology, 2.27.83.6	column, 2.27.83.47
type, 2.27.83.5	radii graphical, 2.27.83.79

randomize, 2.27.83.49	sh24, 3.4
resolution, 2.27.83.50	shadows, 2.21.5.29
selftether, 2.27.83.61	shell, 3.1, 5.8.5
site, 2.27.83.23	intro, 1.7.1
residue, 2.27.83.25	progression, 2.27.72
slide, 2.27.83.26	warning message, 2.28.181
sstructure backbone, 2.27.83.52	shineStyle, 2.20.23
sequence, 2.27.83.53	shininess, 2.17.37
to sequence, 2.27.83.53	show, 2.27.84, 2.27.84.37
stack, 2.27.83.54	alias, 2.27.84.6
energy, 2.27.83.54, 2.27.88.1	aliases, 2.27.84.6
stereo, 2.27.83.51	alignment, 2.27.84.7
swiss, 2.27.83.55	area, 2.27.84.8
name, 2.27.83.55	atom, 2.27.84.9
symmetry, 2.27.83.58	type, 2.27.84.10
bio, 2.27.83.57	atoms, 2.27.84.9
crystal, 2.27.83.56	bond, 2.27.84.11
group, 2.27.83.56	clash, 2.27.84.12
to a torsion, 2.27.83.58	color, 2.27.84.13
table, 2.27.83.59	column, 2.27.84.14
tautomer, 2.27.83.27	comp_matrix, 2.27.84.15
terms, 2.27.83.60	database, 2.27.84.16
tether, 2.27.83.62	drestraint, 2.27.84.17
append, 2.27.83.63	type, 2.27.84.18
texture, 2.27.83.28	energy, 2.27.84.19
type, 2.27.83.64	gradient, 2.27.84.20
mmff, 2.27.83.70	hbond, 2.27.84.21
molecule, 2.27.83.68	exact, 2.27.84.22
object, 2.27.83.67	hbondexact, 2.27.84.22
property, 2.27.83.66	html, 2.27.84.23
sequence, 2.27.83.69	iarray, 2.27.84.24
surface, 2.27.83.65	integer, 2.27.84.25
variable grid, 2.27.83.77	key, 2.27.84.3
variablegrid, 2.27.83.77	label, 2.27.84.26
view, 2.27.83.73	library, 2.27.84.27
vrestraint, 2.27.83.74	link, 2.27.84.28
vrestraintvs_var, 2.27.83.75	logical, 2.27.84.29
radii, 2.27.83.71	map, 2.27.84.4
vwelradii, 2.27.83.72	mol, 2.27.84.30
vwradii, 2.27.83.71	mol2, 2.27.84.31
window, 2.27.83.78	molecule, 2.27.84.32
xstick, 2.27.83.79	molecules, 2.27.84.5
radii, 2.27.83.79	object, 2.27.84.33
setResLabel, 2.29.79	pdb, 2.27.84.34
setcomp_matrix, 2.27.83.17	pharmacophore type, 2.27.84.51
seticmff, 2.29.78	pmf, 2.27.84.35
setting conf properties, 2.27.83.54	preferences, 2.27.84.36
setvs_var, 2.27.83.76	profile, 2.27.84.37
sf-term, 2.27.83.65	residue, 2.27.84.38
sfWeight, 2.17.36	type, 2.27.84.39

segment, 2.27.84.40	map, 2.28.137.5
sequence, 2.27.84.41	rarray, 2.28.137.1
shell variable, 2.27.84.2	surface, 2.29.86
site, 2.27.84.1	soap, 2.25
stack, 2.27.84.42	soft trim, 2.28.169
svariable, 2.27.84.2	solid sphere, 2.21.5.8
table, 2.27.84.43	solubility, 2.28.105
as database, 2.27.84.16	solvation, 2.20.24, 2.21.14.2
term, 2.27.84.44	energy, 2.17.36, 2.20.24
tethers, 2.27.84.45	solvent accessible area, 2.16.22
version, 2.27.84.46	surface, 2.21.5.50, 2.21.5.51, 2.27.84.8
volume, 2.27.84.49	sort, 2.27.85, 2.27.85.3
map, 2.27.84.50	array, 2.27.85.1
volumemap, 2.27.84.50	arrays, 2.27.85.1
vrestraint, 2.27.84.47	molecules, 2.27.85.4
type, 2.27.84.48	object, 2.27.85.3
vrestraints, 2.27.84.47	stack, 2.27.85.5
showcomp_matrix, 2.27.84.15	table, 2.27.85.2
showing weak hydrogen bonds, 2.21.5.20	sortSeqByLength, 2.29.80
side chain, 2.29.88	space group, 2.27.63
flexibility, 2.29.88	transformations, 2.28.167
sigma level, 2.21.7.5	sparse atoms, 2.21.14.3
signal recognition measure, 2.29.21	spawn background job, 2.27.59.1
similar chains, 2.28.128.13	special values, 2.28.159
similarity, 2.27.34.9, 2.27.34.10	specificity, 2.28.127.3
simple expressions, 2.9.1.1	split, 2.27.86
string substitution, 2.28.117.2	column values, 2.27.86.5
simplify mesh structure, 2.27.15.1	grob, 2.27.86.1
simulation duration, 2.17.44	group, 2.27.86.2
temperature, 2.17.43	object, 2.27.86.6
intro, 1.4.2	to molecules, 2.27.86.6
site, 2.27.11.2, 5.8.6	sequence, 2.27.86.4
arrows, 2.27.83.23	table, 2.27.86.3
table, 2.28.151.8	cell, 2.27.86.5
by residue selection, 2.27.22.23	to columns, 2.27.86.3
sequences, 2.28.151.8	tree, 2.27.86.7
sixthe power, 2.20.5	splitting selection, 2.8.11
skin, 5.8.7	sprintf, 2.27.87
intro, 1.4.1.2	sql, 2.27.75, 2.27.83.40, 2.28.45.1, 2.28.90.11, 2.28.93.5, 2.28.172.2
slide, 2.27.1.3, 2.28.135, 5.8.14	sqlite, 3.5.1
transition time, 2.27.23.21	sqrt, 2.28.34
slides, 2.28.180	square matrix to element pairs, 2.28.151.5
slideshow, 2.27.1.3, 2.27.23.21, 2.28.135	ssThreshold, 2.17.38
sln, 5.8.8	ssWeight, 2.17.39
smallest set of smallest rings, 2.28.121	ssbond, 5.4.5
smarts, 2.28.64.1	ssearch, 2.16.16, 2.27.89
smiles, 2.24	ssearchStep, 2.17.40
to chem-table element, 2.28.100	ssign sstructure segment, 2.27.5.2
smooth alignment, 2.28.137.4	stack, 2.16.11, 2.16.12, 2.16.14, 2.20.6, 2.27.83.54, 2.27.88, 2.27.88.1, 2.28.61.6, 2.28.151.6, 5.3.12, 5.8.9
interpolation, 2.27.88.3	bin size, 2.27.14

extension, 2.27.4.2	faq, 3.3.1
multiplication, 2.27.4.2	how to, 3.3.1
merge, 3.7.7	minimize, 2.27.92
standard chemical form, 2.27.64.4	support, 1.3
deviation, 2.28.124	suppressing view changes, 2.27.23.21
standardization, 2.27.22.11	surface, 5.8.15
chemical, 2.27.64	accessibility, 2.27.84.8
startup, 3.1.2.3	area, 2.29.3, 5.8.15
static RMSD, 2.28.146	charge, 5.7.13
and dynamic hbonds, 2.21.5.19	color, 2.27.83.13
stereo, 2.21.5.47, 2.27.29, 2.27.83.51	dot density, 2.21.5.50
reconstruction, 3.8.9	energy, 2.20.24, 2.27.83.65
stereo-specific hydrogens, 2.27.22.11	mesh, 2.28.182.2
stereoisomer, 2.27.29	point selection, 2.28.182
stereoisomers, 2.18.16	term, 2.17.36
stick, 5.8.10	surfaceAccuracy, 2.16.22
store, 2.27.88	surfaceMethod, 2.20.24
conf, 2.27.88, 2.27.88.1	surfaceTension, 2.17.41
frame, 2.27.88.3	svariable, 5.8.12
image, 2.27.59.20	swapping protein fragments, 3.8.7
stack object, 2.27.88.2	swiss, 2.27.83.55
torsion type, 2.27.88	swissFields, 2.22.9
strength of hydrogen bond, 2.27.23.14	swissprot, 2.27.83.23
string, 5.8.11	symmetrization of a matrix, 2.28.82.3
array, 2.28.126, 5.8.1	symmetry, 2.28.167
filtering, 2.28.169	faq, 3.10
inversion, 2.28.147.1	group, 2.16.2
label, 2.27.23.12	problem, 2.27.63
matching, 2.9, 2.28.81	syntax highlighting, 5.8.2
variables, 2.19	sys, 2.27.93
strings, 2.19	system, 5.10.2
strip, 2.27.90	command, 2.27.93
struct, 2.28.90.2	copy, 2.19.26
structural alignment, 2.27.3.4, 2.28.5.2	file move, 2.19.28
optimization, 2.27.34.1	list file, 2.19.27
superposition, 2.27.3.4	remove, 2.19.29
analysis, 3.3	table, 2.27.22.4, 2.27.83.46, 2.27.83.47, 2.27.83.48, 5.9.1
comparison, 2.28.22.2	actions, 5.9.2.4
factors, 3.11.1	column, 2.28.90
structure, 3.11.1	format, 2.27.83.35
sub-alignment to selection, 2.28.119	plot, 2.27.59.31
sub-matrix, 2.28.82.2	transformations, 2.28.95
subalignment, 2.28.5.3	creation, 2.27.41.3
submap, 2.28.78	display style, 5.9.1
subroutine, 2.27.58	expression, 5.9.2
subset, 2.6	from matrix, 2.28.151.4
substring, 2.28.81, 2.28.147, 2.28.147.1	grid view, 5.9.1
substructure, 2.27.34.9, 2.27.34.10	of atoms and distances, 2.28.151.9
search, 2.27.34.4	operations, 5.9.2.1
superimpose, 2.21.14, 2.27.91	plot, 5.9.2.3

print, 2.27.84.43	molecules, 2.27.96.2
row, 2.27.66.4	sarray, 2.27.96.1
label mark, 2.27.83.38.2	transformation, 5.9.7
mark, 2.28.72	vector, 5.9.7
selected row numbers, 2.28.64	and symmetry, 3.10
subset, 5.9.2.2	transforming points, 2.28.182.4
show html, 2.27.102.1	translate, 2.27.97
targa, 5.9.3	transparency, 2.27.83.36, 5.5.3
target coordinates, 5.9.4	background, 2.27.104.35
tautomer, 2.27.30	grob, 2.27.23.11
tempCycle, 2.17.43	grobs, 2.21.5.52
tempLocal, 2.17.42	tree, 2.27.59.35, 2.28.90.5
temperature, 2.17.43	cluster, 2.11
variations in optimizer, 2.17.43	delete, 2.27.22.34
template docking, 3.13.2.7	label format, 2.28.90.5
tensor product of two vectors, 2.28.82	representatives, 2.11.1
terminal font, 2.30.14	trim string array, 2.27.96.1
window, 2.27.42	trimming grid map values, 2.28.169
terms, 2.15	true positives, 2.28.127.3
hydrogen bonding, 2.17.18	truncate alignment, 2.27.59.33
test, 2.27.94	values, 2.28.169
binary, 2.27.94.1	tsShapeData, 2.21.14.9
testing if argument exists, 2.28.54	table format, 2.27.78.42
tether, 2.21.14.9, 2.27.104.9, 5.9.4, 5.9.5	two alignments, 2.28.40.11
text, 2.28.81	dimensional plot, 2.28.137.2
search in tables, 2.28.51.2	txdoc browser, 2.27.78.3
to script, 5.8.2	type, 2.28.172.1
texture, 5.5.3	tzMethod, 2.20.25
tga, 5.9.3	tzWeight, 2.17.47
then, 2.27.95	uncharge functional groups, 2.27.64.2
thread to template, 2.27.60.4	unclip, 2.27.23.2
threading, 2.28.5.1	underline, 2.27.83.32.1
letter code, 2.28.163, 2.28.164	undisplay, 2.27.98
thumbnails, 2.28.63	graphics, 2.27.99
tif, 5.9.6	window, 2.27.99
time, 2.28.35	unfix, 2.27.100
timeLimit, 2.17.44	unique, 2.27.13.1, 5.10.1
tolFunc, 2.17.46	atomic order, 2.27.59.36
tolGrad, 2.17.45	column values, 2.27.41.4
topological psa, 5.7.12	names, 2.28.90
torsion rmsd comparison, 2.27.14.2	new object name, 2.28.90
torsions, 2.28.93.3	smiles, 2.27.59.36
tpsa, 5.7.12	unix, 2.27.93, 5.10.2
trajectory, 2.27.57.2, 2.27.88, 2.27.88.3, 5.6.14	grep, 2.27.78.1
file, 2.30.17	unlink alignments, 2.27.22.20
frame writing, 2.27.23.17	sequences, 2.27.22.20
smoothing, 2.27.23.17	variables, 2.27.22.20
transform, 2.27.96, 2.27.96.2	update database, 2.27.64.5
general, 2.27.96	speadsheet, 2.27.1.1.1
grob coordinates, 2.27.96.2	updates, 1.1

url string parsing, 2.28.151	vrestraint, 5.10.5
user atom display, 2.21.5.2	file, 2.30.23
environment, 3.1.2.2	type, 5.10.6
menu, 2.21.10.1	file, 2.30.22
user-defined properties, 2.27.83.30	vs_, 2.8.9
solvation parameters, 2.28.7	vs_out, 2.22.14
user_startup, 3.1.2.4	vwCutoff, 2.17.49
icm, 3.1.2	vwExpand, 2.17.50
guide, 3	vwExpandDisplay, 2.17.51
v_, 2.8.1	vwMethod, 2.20.28
van der Waals surface, 2.21.5.51	vwSoftMaxEnergy, 2.17.52
varLabelStyle, 2.20.26	wait, 2.27.101
variable restraint, 2.27.83.74	warning, 2.21.14.3
selection, 2.8.9	message, 2.28.181
vector, 2.28.93.6	suppression, 2.18.28
dot product, 2.28.177.1	water.dielectric constant, 2.17.12
length, 2.28.94	waterRadius, 2.17.53
product, 2.28.177.1	wavefront format, 2.27.59.11
transformation, 2.28.95	web, 2.27.102
vertex, 2.27.13.4.2	table, 2.27.102.1
connectivity, 2.28.82.12	webEntrezOption, 2.20.29
vertexes, 2.27.13.4.2	weighted rmsd, 2.21.14
vertical alignment block, 2.27.59.33	while, 2.27.103
workspace, 2.21.8.5	whole string, 2.28.117.1
vertices, 2.27.13.4.2	window averaging, 2.28.137.1
vicinity, 2.17.48	layout, 2.28.147.8
video, 2.27.104.30	width and height, 2.28.180
view point, 2.28.180	windowSize, 2.16.23
restoration, 2.28.67	movie, 2.27.104.30
transition, 2.27.83.73	wire, 5.10.7
views, 5.8.14	wireBondSeparation, 2.17.54
virtual, 5.10.3	wireStyle, 2.20.30
arrays, 2.27.1.1.1	workspace, 2.27.99
chemistry, 2.27.64, 2.28.93.4	write, 2.27.104
field, 2.27.7.2	album, 2.27.104.21
ligand screening, 3.13, 3.13.1, 3.13.2, 3.13.3	alignment, 2.27.104.1
intro, 1.4.2.7	array, 2.27.104.8
visitsAction, 2.20.27	table, 2.27.104.8
vls, 3.13, 3.13.1, 3.13.2, 3.13.3	binary, 2.27.104.2
cluster, 3.13.3.6	blast, 2.27.104.24
faq, 3.13.3	column, 2.27.104.12
intro, 1.4.2.7	database, 2.27.104.13
job queueing, 3.13.3.6	drestraint, 2.27.104.14
overview, 3.13.1	type, 2.27.104.15
parallelization, 3.13.3.5	factor, 2.27.104.16
results, 3.13.3.8	gamess, 2.27.104.17
scores storage, 3.13.3.7	grob, 2.27.104.18
threshold, 3.13.3.2	html, 2.27.104.19
vls_intro, 3.13.3.1	iarray, 2.27.104.3
volume, 5.10.4	image, 2.27.104.20

parray, 2.27.104.21
index, 2.27.104.23
blast, 2.27.104.24
library, 2.27.104.25
map, 2.27.104.26
matrix, 2.27.104.6
model, 2.27.104.27
mol, 2.27.104.28
mol2, 2.27.104.29
molcart, 2.27.104.7
movie, 2.27.104.30
object, 2.27.104.31
parray, 2.27.104.33
simple, 2.27.104.32
pdb, 2.21.14.11, 2.27.104.34
png, 2.27.104.35
postscript, 2.27.104.36
pov, 2.27.104.37
povray, 2.27.104.37
project, 2.27.104.2
rarray, 2.27.104.4
sarray, 2.27.104.5
sequence, 2.27.104.38
session, 2.27.104.39
several array, 2.27.104.8
simple object, 2.27.104.32
stack, 2.27.104.40
table, 2.27.104.10
mol, 2.27.104.11
with links, 2.27.104.19
tether, 2.27.104.9
tethers, 2.27.104.9
trajectory, 2.27.23.17
vs_var, 2.27.104.41
writevs_var, 2.27.104.41
xml, 2.27.78.53, 2.28.81, 5.1.6
drugbank example, 2.10
xpdb, 2.27.78.2
xplor format, 2.27.78.26
xrMethod, 2.20.31
xrWeight, 2.17.55
xray density to rectangular energy map, 2.27.59.30
xstick, 5.10.8
xyz morphing, 3.8.8
zega, 5.10.9
intro, 1.4.3.6
\|, 2.12.3

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