Jul 1 2004
Contents
 
Introduction
Reference Guide
User's guide
References
Glossary
 
Index

Index

&, 2.9.3Disgeo, 2.21.36, 2.21.36, 2.21.36
3D plots intro, 1.4.3.7Distance, 2.21.37, 2.21.37, 2.21.37
     smoothing, 2.21.121.2     Dayhoff, 2.21.37.9
=, 2.9.1     alignment, 2.21.37.10
A, 5.1, 5.1     as_, 2.21.37.3
Abs, 2.21.1, 2.21.1, 2.21.1          rarray, 2.21.37.4
Acc, 2.21.2, 2.21.2, 2.21.2     chemical, 2.21.37.6
Acos, 2.21.3, 2.21.3, 2.21.3     iarray, 2.21.37.1
Acosh, 2.21.4, 2.21.4, 2.21.4     matrix, 2.21.37.5, 2.21.37.7
Align, 2.21.5     rarray, 2.21.37.2
Angle, 2.21.6, 2.21.6, 2.21.6     tether, 2.21.37.8
Area, 2.21.7, 2.21.7, 2.21.7     two alignments, 2.21.37.11
Areacontactmatrix, 2.21.8, 2.21.8DistanceTanimoto, 2.21.37.6, 2.21.37.6
Asin, 2.21.9, 2.21.9, 2.21.9Distancealignment, 2.21.37.10, 2.21.37.10
Asinh, 2.21.10, 2.21.10, 2.21.10Distanceas_, 2.21.37.3, 2.21.37.3
Ask, 2.21.11, 2.21.11, 2.21.11Distanceas_rarray, 2.21.37.4, 2.21.37.4
Atan, 2.21.12, 2.21.12, 2.21.12Distancedayhofffunction, 2.21.37.9, 2.21.37.9
Atan2, 2.21.13, 2.21.13, 2.21.13Distanceiarray, 2.21.37.1, 2.21.37.1
Atanh, 2.21.14, 2.21.14, 2.21.14Distancematrix, 2.21.37.5, 2.21.37.5
Atom, 2.21.15, 2.21.15, 2.21.15Distancematrixtwosets, 2.21.37.7, 2.21.37.7
Augment, 2.21.16, 2.21.16, 2.21.16Distancerarray, 2.21.37.2, 2.21.37.2
Axis, 2.21.17, 2.21.17, 2.21.17Distancetether, 2.21.37.8, 2.21.37.8
B, 5.2, 5.2Distancetwoalignments, 2.21.37.11, 2.21.37.11
Bfactor, 2.21.18, 2.21.18, 2.21.18E, 5.5, 5.5
Boltzmann, 2.21.19, 2.21.19, 2.21.19EST-alignment, 2.20.3.3
Box, 2.21.20, 2.21.20, 2.21.20Eigen, 2.21.38, 2.21.38, 2.21.38
Bracket, 2.21.21, 2.21.21, 2.21.21Energy, 2.21.39, 2.21.39, 2.21.39
C, 5.3, 5.3Error, 2.21.40, 2.21.40, 2.21.40
CONSENSUS, 2.18.1, 2.18.1Exist, 2.21.41, 2.21.41, 2.21.41
CONSENSUSCOLOR, 2.18.2, 2.18.2Existenv, 2.21.42, 2.21.42, 2.21.42
CONSENSUS_strength, 2.14.9, 2.14.9, 2.14.9Exp, 2.21.44, 2.21.44, 2.21.44
Cad, 2.21.22, 2.21.22, 2.21.22, 2.21.22.1, 2.21.22.2Extension, 2.21.43, 2.21.43, 2.21.43
Cad1, 2.21.22.1, 2.21.22.1FILTER, 2.18.3, 2.18.3, 2.18.3
Cadalign, 2.21.22.2, 2.21.22.2FTP, 2.18.4, 2.18.4, 2.18.4
Ceil, 2.21.23, 2.21.23, 2.21.23Field, 2.21.45, 2.21.45, 2.21.45, 2.21.46
Cell, 2.21.24, 2.21.24, 2.21.24Fielduser, 2.21.46, 2.21.46
Charge, 2.21.25, 2.21.25, 2.21.25File, 2.21.47, 2.21.47, 2.21.47
Cluster, 2.21.26, 2.21.26, 2.21.26Find, 2.21.48
Color, 2.21.27Floor, 2.21.49, 2.21.49, 2.21.49
Consensus, 2.21.28, 2.21.28, 2.21.28GRAPHICS, 2.18.5
Corr, 2.21.29, 2.21.29, 2.21.29GRID, 2.18.6, 2.18.6, 2.18.6
Cos, 2.21.30, 2.21.30, 2.21.30GROB, 2.18.7, 2.18.7, 2.18.7
Cosh, 2.21.31, 2.21.31, 2.21.31GUI, 2.18.8, 2.18.8, 2.18.8
Count, 2.21.32, 2.21.32, 2.21.32Getenv, 2.21.50, 2.21.50, 2.21.50
D, 5.4, 5.4Gradient, 2.21.51, 2.21.51, 2.21.51
DNA Representation, 1.4.1.3Graphics, 1.4.1, 1.4.1
     alignment, 2.20.3.3Grob, 2.21.52
Date, 2.21.33, 2.21.33, 2.21.33Group, 2.21.53, 2.21.53, 2.21.53
Deletion, 2.21.34, 2.21.34, 2.21.34H, 5.5, 5.5
Det, 2.21.35, 2.21.35, 2.21.35Histogram, 2.21.54, 2.21.54, 2.21.54
ICM-shell, 3.1Profile, 2.21.96, 2.21.96, 2.21.96
     intro, 1.7.1Putenv, 2.21.97, 2.21.97, 2.21.97
IMAGE, 2.18.9, 2.18.9, 2.18.9REBEL, 3.5.2
I_out, 2.19.4R_out, 2.19.6
Iarray, 2.21.55, 2.21.55, 2.21.55, 2.21.56Radius, 2.21.98, 2.21.98, 2.21.98
Iarrayatoms, 2.21.56, 2.21.56Random, 2.21.99, 2.21.99, 2.21.99
IcmSequence, 2.21.58, 2.21.58, 2.21.58Rarray, 2.21.100, 2.21.100, 2.21.100
Index, 2.21.59, 2.21.59, 2.21.59     sequence projection, 2.21.100.1
Indexx, 2.21.60     alignment projection, 2.21.100.2
Info, 2.21.62, 2.21.62, 2.21.62          strength, 2.21.100.4
Insertion, 2.21.61, 2.21.61, 2.21.61     property assignment, 2.21.100.3
Integer, 2.21.63, 2.21.63, 2.21.63RarrayAlignment, 2.21.100.4, 2.21.100.4
Integral, 2.21.64, 2.21.64, 2.21.64Real, 2.21.101, 2.21.101, 2.21.101
Interrupt, 2.21.65, 2.21.65, 2.21.65Reference Guide, 2
Introduction, 1Remainder, 2.21.102, 2.21.102, 2.21.102
LIBRARY, 2.18.10, 2.18.10, 2.18.10Replace, 2.21.103, 2.21.103, 2.21.103
Label, 2.21.66, 2.21.66, 2.21.66Res, 2.21.104, 2.21.104, 2.21.104, 2.21.105
Length, 2.21.67, 2.21.67, 2.21.67Resali, 2.21.105, 2.21.105
LinearFit, 2.21.68, 2.21.68, 2.21.68Resolution, 2.21.106, 2.21.106, 2.21.106
Link, 2.21.69, 2.21.69, 2.21.69Rfactor, 2.21.107, 2.21.107, 2.21.107
Log, 2.21.70, 2.21.70, 2.21.70Rfree, 2.21.108, 2.21.108, 2.21.108
M_out, 2.19.5, 2.19.5, 2.19.5Rmsd, 2.21.109, 2.21.109, 2.21.109
Map, 2.21.71, 2.21.71, 2.21.71Rot, 2.21.110, 2.21.110, 2.21.110
Mass, 2.21.72, 2.21.72, 2.21.72S, 5.6, 5.6
Matrix, 2.21.73, 2.21.73, 2.21.73SITE, 2.18.13
Max, 2.21.74, 2.21.74, 2.21.74SLN notation, 2.21.128.2
MaxHKL, 2.21.75, 2.21.75, 2.21.75S_out, 2.19.7
Mean, 2.21.76, 2.21.76, 2.21.76Sarray, 2.21.111, 2.21.111, 2.21.111
Method, 2.17.8Score, 2.21.112, 2.21.112, 2.21.112
Min, 2.21.77, 2.21.77, 2.21.77Select, 2.21.113, 2.21.113, 2.21.113
Mod, 2.21.79, 2.21.79, 2.21.79Sequence, 2.21.114, 2.21.114, 2.21.114
Mol, 2.21.80, 2.21.80, 2.21.80Sequence(dna reverse), 2.21.115
Money, 2.21.78, 2.21.78, 2.21.78Sign, 2.21.116, 2.21.116, 2.21.116
Name, 2.21.81, 2.21.81, 2.21.81Simulations, 1.4.2, 1.4.2
Namex, 2.21.82, 2.21.82, 2.21.82Sin, 2.21.117, 2.21.117, 2.21.117
Next, 2.21.83, 2.21.83, 2.21.83, 2.21.84Sinh, 2.21.118, 2.21.118, 2.21.118
Nextcovalentneighbors, 2.21.84, 2.21.84Site, 2.21.119, 2.21.119, 2.21.119
Nof, 2.21.85, 2.21.85, 2.21.85Smiles, 2.21.120, 2.21.120, 2.21.120
Norm, 2.21.86, 2.21.86, 2.21.86Smooth, 2.13.23, 2.21.121, 2.21.121, 2.21.121, 2.21.121.1, 2.21.121.2
OBJECT, 2.18.11, 2.18.11, 2.18.11Smoothrs, 2.21.121.2, 2.21.121.2
Obj, 2.21.87, 2.21.87, 2.21.87Sphere, 2.21.125, 2.21.125, 2.21.125
Occupancy, 2.21.88, 2.21.88, 2.21.88Split, 2.21.122, 2.21.122, 2.21.122, 2.21.126
PLOT, 2.18.12, 2.18.12, 2.18.12Sql, 2.21.123, 2.21.123, 2.21.123
Parray, 2.21.90, 2.21.90, 2.21.90Sqrt, 2.21.124, 2.21.124, 2.21.124
Path, 2.21.89, 2.21.89, 2.21.89Srmsd, 2.21.127, 2.21.127, 2.21.127
Pattern, 2.21.91, 2.21.91, 2.21.91Sstructure, 2.21.129, 2.21.129, 2.21.129
Pi, 2.21.92, 2.21.92, 2.21.92String, 2.21.128, 2.21.128, 2.21.128, 2.21.128.1
Potential, 2.21.93, 2.21.93, 2.21.93     chemical formula, 2.21.128.2
Power, 2.21.94, 2.21.94, 2.21.94Stringas, 2.21.128.1, 2.21.128.1
Probability, 2.21.95, 2.21.95, 2.21.95Sum, 2.21.130, 2.21.130, 2.21.130
T, 5.7, 5.7_gui, 2.20.36, 2.20.36
Table, 2.21.132, 2.21.132, 2.21.132_macro, 2.23.1, 2.23.1
Table(alignment), 2.21.133     icm file, 2.23.1
Table(stack), 2.21.134_plot, 2.20.56, 2.20.56
Tablestack, 2.21.134, 2.21.134_startCheck, 2.23.3
Tan, 2.21.135, 2.21.135, 2.21.135_startup, 2.23.2, 2.23.2
Tanh, 2.21.136, 2.21.136, 2.21.136     icm, 2.23.2
Tanimoto distance matrix, 2.21.37.6_startupCheck, 2.23.3, 2.23.3
Temperature, 2.21.138, 2.21.138, 2.21.138a3ht, 3.3.2, 3.3.2
Tensor, 2.21.137, 2.21.137, 2.21.137abbr, 1.6, 1.6
Time, 2.21.139, 2.21.139, 2.21.139abbreviations, 1.6
Tolower, 2.21.140, 2.21.140, 2.21.140accFunction, 2.19.2, 2.19.2, 2.19.2
Torsion, 2.21.141, 2.21.141, 2.21.141accessible residues, 3.3.6
Toupper, 2.21.142, 2.21.142, 2.21.142add rows to a table, 2.20.1
Tr123, 2.21.143, 2.21.143, 2.21.143addBfactor, 2.14.1, 2.14.1, 2.14.1
Tr321, 2.21.144, 2.21.144, 2.21.144adding in place, 2.9.4
Trace, 2.21.145, 2.21.145, 2.21.145addtable, 2.20.1, 2.20.1
Trans, 2.21.146, 2.21.146, 2.21.146advanced operations, 2.9.6
Transpose, 2.21.147, 2.21.147, 2.21.147advancedoper, 2.9.6, 2.9.6
Trim, 2.21.148, 2.21.148, 2.21.148alias, 2.20.2, 2.20.2, 2.20.2
Turn, 2.21.149, 2.21.149, 2.21.149align, 2.20.3, 2.20.3, 2.20.3
Type, 2.21.150, 2.21.150, 2.21.150     3D heavy, 2.20.3.5
U, 5.8, 5.8          how to, 3.3.2
Unix, 2.21.151, 2.21.151, 2.21.151     fragments, 2.20.3.3
Value, 2.21.152, 2.21.152, 2.21.152     number, 2.20.3.1
Vector, 2.21.16, 2.21.153, 2.21.153, 2.21.153, 2.21.153.1     sequences, 2.20.3.2
     symmetry transformation, 2.21.153.2align3D, 2.20.3.4, 2.20.3.4
Vectorproduct, 2.21.153.1, 2.21.153.1align3Dheavy, 2.20.3.5, 2.20.3.5
Vectorsymmetrytransformation, 2.21.153.2, 2.21.153.2alignMethod, 2.17.2, 2.17.2, 2.17.2
Version, 2.21.154, 2.21.154, 2.21.154alignMinCoverage, 2.14.2, 2.14.2, 2.14.2
View, 2.21.156, 2.21.156, 2.21.156alignMinMethod, 2.14.2
Volume, 2.21.155, 2.21.155, 2.21.155alignOldStatWeight, 2.14.3, 2.14.3, 2.14.3
WEBAUTOLINK, 2.18.15, 2.18.15, 2.18.15aligned residues, 2.21.105
WEBLINK, 2.18.14, 2.18.14, 2.18.14alignfragments, 2.20.3.3, 2.20.3.3
Warning, 2.21.157, 2.21.157, 2.21.157alignment block length, 2.13.21
Wavefront format, 2.20.63.20     cleaning, 2.21.121.3
Xyz, 2.21.158, 2.21.158, 2.21.158     editor, 2.4
Z, 5.8, 5.8     extraction, 2.21.5
ZEGA intro, 1.4.3.6     projection, 2.21.128
_Align, 2.21.5, 2.21.5     sequence reordering, 2.21.5
_Color, 2.21.27, 2.21.27     strength, 2.21.100.4
_Find, 2.21.48, 2.21.48     structural, 2.20.3.4, 2.21.5
_GRAPHICS, 2.18.5, 2.18.5     to sequence transfer, 2.21.100.1
_Grob, 2.21.52, 2.21.52     weighted, 2.21.5
_I_out, 2.19.4, 2.19.4     gapExtension, 2.14.15
_Indexx, 2.21.60, 2.21.60     gapOpen, 2.14.16
_R_out, 2.19.6, 2.19.6alignmenteditor, 2.4, 2.4
_SITE, 2.18.13, 2.18.13alignnumber, 2.20.3.1, 2.20.3.1
_S_out, 2.19.7, 2.19.7alignsequence, 2.20.3.2, 2.20.3.2
_Split, 2.21.126, 2.21.126alitable, 2.21.133, 2.21.133
alternative flag, 2.20.68.9build, 2.20.7, 2.20.7, 2.20.7
and, 2.9.3     from sequence, 2.20.7.1
animation, 3.7          string, 2.20.7.4
ao, 2.9.2, 2.9.2     helix, 3.8.5
append tables by shared column, 2.20.4     how to, 3.6.1
appendcolumn, 2.20.4, 2.20.4     hydrogen, 2.20.7.5
appending an element, 2.9.4     loop, 2.20.7.3
arithmetic operations, 2.9.2     model, 2.20.7.2
arithmetics, 2.9, 2.9, 2.9     string, 2.20.7.4
array derivative, 2.21.121.1buildhydrogen, 2.20.7.5, 2.20.7.5
     subset, 2.6buildloop, 2.20.7.3, 2.20.7.3
as2_out, 2.19.12, 2.19.12, 2.19.12buildmodel, 2.20.7.2, 2.20.7.2
as_, 2.8.4, 2.8.4buildpep, 2.22.1, 2.22.1, 2.22.1
as_out, 2.19.11, 2.19.11, 2.19.11buildseq, 2.20.7.1, 2.20.7.1
assign, 2.20.5, 2.20.5, 2.20.5buildstring, 2.20.7.4, 2.20.7.4
     sstructure, 2.20.5.1calcBindingEnergy, 2.22.2, 2.22.2, 2.22.2
          segment, 2.13.19calcDihedral4atoms, 2.22.3, 2.22.3, 2.22.3
assignment, 2.9.1, 2.9.1, 2.9.1calcDihedralAngle, 2.22.4, 2.22.4, 2.22.4
assignsstructure, 2.20.5.1, 2.20.5.1calcEnergyStrain, 2.22.20, 2.22.20, 2.22.20
assignsstructuresegment, 2.20.5.2, 2.20.5.2calcEnsembleAver, 2.22.5, 2.22.5, 2.22.5
atom code file, 2.23.6calcMaps, 2.22.6, 2.22.6, 2.22.6
     label font, 2.23.17calcPepHelicity, 2.22.7, 2.22.7, 2.22.7
     name, 2.21.66calcProtUnfoldingEnergy, 2.22.8, 2.22.8, 2.22.8
     selection by number, 2.21.56calcRmsd, 2.22.9, 2.22.9, 2.22.9
     type, 2.21.150calcSeqContent, 2.22.10, 2.22.10, 2.22.10
     user field, 2.21.46calculate phases, 3.9.2
atomLabelStyle, 2.17.1, 2.17.1, 2.17.1call, 2.20.8, 2.20.8, 2.20.8
atomSingleStyle, 2.17.3, 2.17.3, 2.17.3     ICM script, 2.20.8
     alternative position, 2.20.68.9cavities, 2.20.71.1
     selecting, 2.8.4     analysis, 3.3.13
     translate, 2.20.68.2cavityanalysis, 3.3.13, 3.3.13
att, 3.3.11, 3.3.11cba, 3.2.11, 3.2.11
autoSavePeriod, 2.13.1, 2.13.1, 2.13.1cbb, 3.2.9, 3.2.9
axisLength, 2.14.4, 2.14.4, 2.14.4cbc, 3.2.12, 3.2.12
az27, 3.7, 3.7cbe, 3.2.7, 3.2.7
background.color, 2.20.11.2cbh, 3.2.10, 3.2.10
be, 3.5.4, 3.5.4ccp4 maps, 2.20.63.25
bh, 3.8.5, 3.8.5ccr, 1.4.1.4, 1.4.1.4
bht, 3.6.1, 3.6.1cd, 2.20.68.12
binary file table of contents, 2.20.63.2center, 2.20.9, 2.20.9, 2.20.9
     files, 2.20.87.2change atom position, 2.20.68.2
binding energy, 3.5.4     unix directory, 2.20.68.12
     pocket finding, 3.4.3changing local stick radii, 2.20.68.50
     pockets, 2.20.71.1charge.change, 2.20.68.5
bindingsiteanalysis, 3.4.3, 3.4.3chemformula, 2.21.128.2, 2.21.128.2
blast files, 2.20.87.12chemical formula, 2.21.128.2
bond angle bending, 2.23.7     keys, 2.20.49.12
     stretching, 2.23.8     matching, 2.20.28.3
bonded atoms, 2.21.84     modification, 2.20.52
break, 2.20.6, 2.20.6, 2.20.6     substructure, 2.20.28.3
chirality, 2.15.16          contact surface, 2.20.12
cl1, 2.2, 2.2          variables, 2.20.12
clashThreshold, 2.14.5, 2.14.5, 2.14.5comparison operations, 2.9.5
clear, 2.20.10, 2.20.10, 2.20.10compress, 2.20.13, 2.20.13
     graphical selection, 2.20.10     stack, 2.20.13
     screen, 2.20.10conf, 2.20.87.26, 2.21.134
cnWeight, 2.14.6, 2.14.6, 2.14.6     data, 2.21.134
co, 2.9.5, 2.9.5configuration, 2.23.16
color, 2.20.11, 2.20.11, 2.20.11, 2.20.11.1     memory usage, 2.13.6
     background, 2.20.11.2conformational generator, 2.20.50.1
          example, 3.2.7     stack, 2.20.87.26
          accessibility, 3.2.11          file, 2.23.9
          alignment, 2.20.11.3connect, 2.20.14, 2.20.14, 2.20.14
          bfactor, 3.2.9consensus, 2.14.7
          charge, 3.2.12     coloring, 2.14.9, 2.18.2
          electrostatic potential, 2.13.5     definitions, 2.18.1
          hydrophobicity, 3.2.10consensusStrength, 2.14.7, 2.14.7, 2.14.7
     cursor, 2.20.11.4conservation, 2.21.100.4
     file, 2.23.17constant, 2.5, 2.5
     grob, 2.20.11.5constants, 2.5
          by electrostatic potential, 2.20.11.5contact areas, 2.21.73
               map, 2.20.11.5continue, 2.20.15, 2.20.15, 2.20.15
          unique, 2.20.11.5convert, 2.20.16, 2.20.16, 2.20.16, 3.11.2
          vertices, 2.20.11.5     ICM object to PDB, 2.20.75
     label, 2.20.11.6     and reroot, 2.20.16.3
     map, 2.20.11.7     comparison, 2.20.16.1
          by value, 2.20.20.13     pdb, 3.6.2
     molecule, 2.20.11.8     to icm-object, 2.20.16
     ribbon, 2.20.11.9convertcomp, 2.20.16.1, 2.20.16.1
     site, 2.20.11.1converting a chemical, 2.20.16.2
     surface by conservation, 2.20.11.3          pdb-chemical, 3.11.2
     volume, 2.20.11.10     alignment to table, 2.21.133
colorbackground, 2.20.11.2, 2.20.11.2convertmol, 2.20.16.2, 2.20.16.2
colorbyalignment, 2.20.11.3, 2.20.11.3convertreroot, 2.20.16.3, 2.20.16.3
colorcursor, 2.20.11.4, 2.20.11.4cool, 2.22.35, 2.22.35, 2.22.35
colorgrob, 2.20.11.5, 2.20.11.5coordinate frame, 2.14.4, 2.20.20.4
colorlabel, 2.20.11.6, 2.20.11.6copy, 2.20.17, 2.20.17, 2.20.17
colormap, 2.20.11.7, 2.20.11.7     site, 2.20.68.16
colormolecule, 2.20.11.8, 2.20.11.8copysite, 2.20.68.16, 2.20.68.16
colormolgrob, 2.20.11.1, 2.20.11.1correlation matrix, 2.21.137
colorribbon, 2.20.11.9, 2.20.11.9covalent neighbors, 2.21.84
colorvolume, 2.20.11.10, 2.20.11.10cp, 3.9.2, 3.9.2
combine transformations, 3.8.4cp2, 3.6.2, 3.6.2
command line editing, 2.2create a covalent bond, 2.20.49.1
          help, 2.20.37credits, 4.5
          options, 2.1crypt, 2.20.18, 2.20.18, 2.20.18
     word list, 3.1.5crystal symmetry transformation, 3.8.2
comp_matrix, 2.20.68.11, 2.20.69.14crystallographic occupancy, 2.21.88
compare, 2.13.11, 2.13.14, 2.20.12, 2.20.12, 2.20.12     symmetry intro, 1.4.2.4
     by atoms, 2.20.12cst, 3.8.2, 3.8.2
csym, 1.4.2.4, 1.4.2.4deletemolecule, 2.20.19.9, 2.20.19.9
ct, 3.8.4, 3.8.4deleteobject, 2.20.19.8, 2.20.19.8
current icm-process number, 2.13.4deletepeptidebond, 2.20.19.19, 2.20.19.19
     working directory, 2.21.89deleteselection, 2.20.19.3, 2.20.19.3
customization, 3.1.2, 3.1.2, 3.1.2deletesequence, 2.20.19.15, 2.20.19.15
cz32, 4.5, 4.5deletesession, 2.20.19.6, 2.20.19.6
da, 3.8.3, 3.8.3deleteshobject, 2.20.19.1, 2.20.19.1
dac, 3.3.10, 3.3.10deletesite, 2.20.19.16, 2.20.19.16
dafltar, 1.4.2.6, 1.4.2.6deletesstructure, 2.20.19.17, 2.20.19.17
dc, 3.9.3, 3.9.3deletestack, 2.20.19.20, 2.20.19.20
dcMethod, 2.17.4, 2.17.4, 2.17.4deletetable, 2.20.19.21, 2.20.19.21
dcWeight, 2.14.8, 2.14.8, 2.14.8deleteterm, 2.20.19.22, 2.20.19.22
defCell, 2.19.1, 2.19.1, 2.19.1deletetether, 2.20.19.23, 2.20.19.23
defSymGroup, 2.13.2, 2.13.2, 2.13.2density correlation, 2.14.8, 3.9.3
define axis, 3.8.3     fitting, 2.17.4
delete, 2.20.19, 2.20.19, 2.20.19densityCutoff, 2.14.10, 2.14.10, 2.14.10
     alias, 2.20.19.2depth cueing, 2.20.11.10
     array selection, 2.20.19.1depth-cueing, 2.14.14
     atom, 2.20.19.4dielConst, 2.14.11, 2.14.11, 2.14.11
     bond, 2.20.19.10dielConstExtern, 2.14.12, 2.14.12, 2.14.12
     boundary, 2.20.19.11dielectric constant, 2.14.11
     conf, 2.20.19.12dihedral angle calculation, 3.3.10
     directory, 2.20.19.5directory, 2.20.19.5, 2.20.49.4
     disulfide bond, 2.20.19.18display, 2.20.20, 2.20.20, 2.20.20
     drestraint, 2.20.19.13     box, 2.20.20.5
     hydrogen, 2.20.19.7     clash, 2.14.5, 2.20.20.7
     label, 2.20.19.14     cursor, 2.20.20.6
     molecule, 2.20.19.9     drestraint, 2.20.20.8
     object, 2.20.19.8     from script, 2.20.20.3
     peptide bond, 2.20.19.19     gradient, 2.20.20.9
     selection, 2.20.19.3     grob, 2.20.20.10
     sequence, 2.20.19.15     hbond, 2.20.20.11
     session, 2.20.19.6     label, 2.20.20.12
     shell object, 2.20.19.1     map, 2.20.20.13
     site, 2.20.19.16     model, 2.20.20.1
     sstructure, 2.20.19.17     movie, 2.20.20.14
     stack, 2.20.19.20     new, 2.20.20.2
     table, 2.20.19.21     off-screen, 2.20.20.3
     term, 2.20.19.22     origin, 2.20.20.4
     tether, 2.20.19.23     ribbon, 2.20.20.15
deletealias, 2.20.19.2, 2.20.19.2     site, 2.20.20.16
deleteatom, 2.20.19.4, 2.20.19.4     skin, 2.20.20.17
deletebond, 2.20.19.10, 2.20.19.10     string, 2.20.20.18
deleteboundary, 2.20.19.11, 2.20.19.11     surface, 2.20.20.17
deleteconf, 2.20.19.12, 2.20.19.12     tethers, 2.20.20.19
deletedirectory, 2.20.19.5, 2.20.19.5     window, 2.3, 2.20.20.20
deletedisulfidebond, 2.20.19.18, 2.20.19.18displaybox, 2.20.20.5, 2.20.20.5
deletedrestraint, 2.20.19.13, 2.20.19.13displayclash, 2.20.20.7, 2.20.20.7
deletehydrogen, 2.20.19.7, 2.20.19.7displaycursor, 2.20.20.6, 2.20.20.6
deletelabel, 2.20.19.14, 2.20.19.14displaydrestraint, 2.20.20.8, 2.20.20.8
displaygrob, 2.20.20.10, 2.20.20.10edit, 2.20.25, 2.20.25, 2.20.25
displayhbond, 2.20.20.11, 2.20.20.11electroMethod, 2.17.5, 2.17.5, 2.17.5
displaylabel, 2.20.20.12, 2.20.20.12electrointro, 1.4.2.8, 1.4.2.8
displaymap, 2.20.20.13, 2.20.20.13     density map generation, 2.14.1
displaymodel, 2.20.20.1, 2.20.20.1electrostatic isopotential surfaces, 2.20.49.11
displaymovie, 2.20.20.14, 2.20.20.14     solvation, 3.5.2
displaynew, 2.20.20.2, 2.20.20.2     intro, 1.4.2.8
displayoffscreen, 2.20.20.3, 2.20.20.3ellipsoid, 2.21.137
displayorigin, 2.20.20.4, 2.20.20.4elseif, 2.20.21, 2.20.21, 2.20.21
displayribbon, 2.20.20.15, 2.20.20.15endfor, 2.20.22, 2.20.22, 2.20.22
displaysite, 2.20.20.16, 2.20.20.16endif, 2.20.23, 2.20.23, 2.20.23
displayskin, 2.20.20.17, 2.20.20.17endmacro, 2.20.24, 2.20.24, 2.20.24
displaystring, 2.20.20.18, 2.20.20.18endwhile, 2.20.26, 2.20.26, 2.20.26
displaytethers, 2.20.20.19, 2.20.20.19energetics, 3.5
displaywindow, 2.20.20.20, 2.20.20.20     terms, 2.12
distance contact-based, 2.21.22, 2.21.22.1ensemble average, 3.5.5
     restraint file, 2.23.11entry atom, 2.20.16.3
          type file, 2.23.10error ignoring, 2.16.22
     restraints, 2.20.68.13error/warning bits cleanup, 2.20.10
distribution and support, 1.3errorAction, 2.17.6, 2.17.6, 2.17.6
     comparison, 2.21.112es31, 3.12, 3.12
dividing mol into individual molecules, 2.21.122     vrestraint vs_var, 2.20.68.46
docking result viewing, 2.22.26evoltreeintro, 1.4.3.5, 1.4.3.5
     simple models, 3.12.3evolutionary tree intro, 1.4.3.5
dotplotintro, 1.4.3.2, 1.4.3.2example scripts, 3.12
dps, 3.12.3, 3.12.3exit, 2.20.27, 2.20.27, 2.20.27
drestraint, 2.20.69.16expressions.arithmetics, 2.9.2
     generate from structure, 2.20.49.6     assignment, 2.9.1
     global weight, 2.14.6     comparison, 2.9.5
     set, 2.20.68.13     logical, 2.9.3
drop, 2.14.13, 2.14.13, 2.14.13ez25, 3.5, 3.5
ds3D, 2.22.29, 2.22.29, 2.22.29fast Fourier transform, 2.20.49.14
dsCellBox, 2.22.12, 2.22.12, 2.22.12ffMethod, 2.17.7, 2.17.7, 2.17.7
dsCharge, 2.22.14, 2.22.14, 2.22.14file exists, 2.21.41
dsChem, 2.22.15, 2.22.15, 2.22.15     length, 2.21.47
dsCustom, 2.22.16, 2.22.16, 2.22.16     object origin, 2.21.47
dsCustomFull, 2.22.17, 2.22.17, 2.22.17     permissions, 2.21.47
dsDistance, 2.22.18, 2.22.18, 2.22.18     time modified, 2.21.47
dsPropertySkin, 2.22.19, 2.22.19, 2.22.19     type, 2.21.47
dsPrositePdb, 2.22.22, 2.22.22, 2.22.22files, 2.23, 2.23, 2.23
dsRebel, 2.13.5, 2.22.23, 2.22.23, 2.22.23find, 2.20.28, 2.20.28
dsSeqPdbOutput, 2.22.24, 2.22.24, 2.22.24     alignment, 2.20.28.1
dsSkinLabel, 2.22.25, 2.22.25, 2.22.25     database, 2.14.2, 2.20.28.2
dsSkinPocket, 2.22.26, 2.22.26, 2.22.26     family of commands, 2.20.28
dsStackConf, 2.22.27, 2.22.27, 2.22.27     molecule, 2.20.28.3
dsVarLabels, 2.22.28, 2.22.28, 2.22.28     pattern, 2.20.28.6
dsWorm, 2.22.30, 2.22.30, 2.22.30     pdb, 2.20.28.4
dsXyz, 2.22.31, 2.22.31, 2.22.31     prosite, 2.20.28.5
dtp, 1.4.2.5, 1.4.2.5     segment, 2.20.28.7
ea, 3.5.5, 3.5.5findFuncMin, 2.22.32, 2.22.32, 2.22.32
findSymNeighbors, 2.22.13, 2.22.13, 2.22.13     fogStart, 2.14.14
findalignment, 2.20.28.1, 2.20.28.1     view vector, 2.20.68.44
finddatabase, 2.20.28.2, 2.20.28.2grid potentials, 2.20.49.15
findmolecule, 2.20.28.3, 2.20.28.3grob files, 2.23.12
findpattern, 2.20.28.6, 2.20.28.6     inside-out flip, 2.20.68.20
findpdb, 2.20.28.4, 2.20.28.4     normal directions, 2.20.68.20
findprosite, 2.20.28.5, 2.20.28.5     translate, 2.20.80
findsegment, 2.20.28.7, 2.20.28.7group, 2.20.35, 2.20.35, 2.20.35
     to density, 2.17.4     by column, 2.20.35.4
fix, 2.20.29, 2.20.29, 2.20.29     replacement, 2.20.52
flattening 3D molecule, 2.22.15     sequence, 2.20.35.1
flowcontrol, 2.10, 2.10          unique, 2.20.35.2
fog, 2.20.11.10     table, 2.20.35.3
fogStart, 2.14.14, 2.14.14, 2.14.14groupcolumn, 2.20.35.4, 2.20.35.4
fold search, 2.20.28.7groupsequence, 2.20.35.1, 2.20.35.1
foldbank.db, 2.23.4, 2.23.4, 2.23.4groupsequenceunique, 2.20.35.2, 2.20.35.2
     seg, 2.23.5, 2.23.5, 2.23.5grouptable, 2.20.35.3, 2.20.35.3
folding procedure, 3.12.1gui, 2.20.36
font size, 2.23.16     exists, 2.21.41
for, 2.20.30, 2.20.30, 2.20.30     programming, 2.20.36
fork, 2.20.31, 2.20.31, 2.20.31haze, 2.14.14
formatdb, 2.20.87.12hb, 2.14.17
fp, 3.12.1, 3.12.1hbCutoff, 2.14.17, 2.14.17, 2.14.17
fprintf, 2.20.32, 2.20.32, 2.20.32hbond.show, 2.20.69.20
fullscreen, 2.20.68.49     how to, 3.3.4
funcprot, 1.4.1.1, 1.4.1.1helicity, 3.5.6, 3.5.6
functions.selecting in objects, 2.8.6     content calculation, 3.5.6
gap expansion, 2.21.121.3help, 2.20.37, 2.20.37, 2.20.37, 2.20.37.1
gapExtension, 2.14.15, 2.14.15, 2.14.15     commands, 2.20.37.2
gapFunction, 2.19.3, 2.19.3, 2.19.3     functions, 2.20.37.3
gapOpen, 2.14.16, 2.14.16, 2.14.16     getting, 3.1.1
gc2, 2.3, 2.3helpcommands, 2.20.37.2, 2.20.37.2
gcMethod, 2.17.8, 2.17.8helpfunctions, 2.20.37.3, 2.20.37.3
genomics, 1.4.3.1, 1.4.3.1helpword, 2.20.37.1, 2.20.37.1
     clustering, 2.20.35.2hg, 3.1.1, 3.1.1
     intro, 1.4.3.1hht, 3.3.4, 3.3.4
geometry optimization, 2.20.50.1hidden display, 2.20.20.3
getstarted, 1.7, 1.7highEnergyAction, 2.17.9, 2.17.9, 2.17.9
getting started, 1.7histogram 2D, 2.21.73
gl, 3.2.1, 3.2.1history, 2.20.38, 2.20.38, 2.20.38, 2.20.87.25
global, 2.20.33, 2.20.33, 2.20.33     delete, 2.20.19.6
glossary, 5, 5, 5     of ICM, 1.2
goto, 2.20.34, 2.20.34, 2.20.34hm, 3.12.4, 3.12.4
graphical box, 2.20.20.5homodel, 2.22.36, 2.22.36, 2.22.36
graphics, 3.2homology modeling, 2.20.7.2, 3.12.4
     controls, 2.3, 2.23.17          intro, 1.4.2.2
     exists, 2.21.41homomodels, 1.4.2.2, 1.4.2.2
     intro, 1.4.1, 1.4.1.4hp, 3.3.12, 3.3.12
     learning, 3.2.1htselres, 3.3.6, 3.3.6
     attributes, 2.14.4hydration parameters, 2.23.15
          cutoff, 2.14.17     seq, 2.23.30, 2.23.30, 2.23.30
hydrophobicity profile, 3.3.12     tab, 2.23.26, 2.23.26, 2.23.26
iProc, 2.13.4, 2.13.4, 2.13.4     tot, 2.23.27, 2.23.27, 2.23.27
i_out, 2.13.3, 2.13.3, 2.13.3     var, 2.23.22, 2.23.22, 2.23.22
ic, 3.2.8, 3.2.8     vwt, 2.23.28, 2.23.28, 2.23.28
     algorithms, 4.3icmCavityFinder, 2.22.11, 2.22.11, 2.22.11
     application refs, 4.4icmPmfProfile, 2.22.21, 2.22.21, 2.22.21
     archive, 2.20.63.2icmapprefs, 4.3, 4.3
     binary, 2.21.89icmapps, 4.4, 4.4
     branching, 2.10.2icmbranching, 2.10.2, 2.10.2
     commands, 2.20icmcommands, 2.20, 2.20
     controls, 2.10icmdistribution, 1.3, 1.3
     flags, 2.1icmfunctions, 2.21, 2.21
     functions, 2.21icmgraphics, 3.2, 3.2
     jumps, 2.10.3icmhistory, 1.2, 1.2
     learning, 3.1.4icmmacros, 2.22, 2.22
     loops, 2.10.1icmoptions, 2.1, 2.1
     macros, 2.22icmrefs, 4.2, 4.2
     molecules, 2.11icmshell, 3.1, 3.1
     object file, 2.23.20icmtable, 2.18, 2.18
     table, 2.18icw, 3.1.5, 3.1.5
     ali, 2.23.32, 2.23.32, 2.23.32if, 2.20.39, 2.20.39, 2.20.39
     all, 2.23.33, 2.23.33, 2.23.33ij, 2.10.3, 2.10.3
     bbt, 2.23.7, 2.23.7, 2.23.7il, 3.1.4, 3.1.4
     bst, 2.23.8, 2.23.8, 2.23.8il2, 2.10.1, 2.10.1
     cfg, 2.23.16, 2.23.16, 2.23.16im7, 2.11, 2.11
     clr, 2.23.17, 2.23.17, 2.23.17image, 3.2.6
     cmp, 2.23.34, 2.23.34, 2.23.34     annotation, 3.2.5
     cn, 2.23.11, 2.23.11, 2.23.11     center, 3.2.8
     cnf, 2.23.9, 2.23.9, 2.23.9     high quality, 3.2.2
     cnt, 2.23.10, 2.23.10, 2.23.10imageannotation, 3.2.5, 3.2.5
     cod, 2.23.6, 2.23.6, 2.23.6imagerotation, 3.2.3, 3.2.3
     col, 2.23.25, 2.23.25, 2.23.25     place, 2.9.4
     gro, 2.23.12, 2.23.12, 2.23.12increment charge, 2.20.68.5
     hbt, 2.23.14, 2.23.14, 2.23.14index expressions, 2.6
     hdt, 2.23.15, 2.23.15, 2.23.15inplaceops, 2.9.4, 2.9.4
     htm, 2.23.13, 2.23.13, 2.23.13insert rows, 2.20.1
     iar, 2.23.36, 2.23.36, 2.23.36integer shell variables, 2.13
     map, 2.23.18, 2.23.18, 2.23.18interface residues, 3.3.5
     mat, 2.23.38, 2.23.38, 2.23.38     torsions, 3.3.7
     mov, 2.23.19, 2.23.19, 2.23.19     view, 2.22.26
     ob, 2.23.20, 2.23.20, 2.23.20internal coordinate file, 2.23.22
     pdb, 2.23.29, 2.23.29     coordinates, 2.8.5
     prf, 2.23.35, 2.23.35, 2.23.35interruptAction, 2.17.10, 2.17.10, 2.17.10
     rar, 2.23.39, 2.23.39, 2.23.39intro, 1, 1
     res, 2.23.21, 2.23.21, 2.23.21ir, 3.3.5, 3.3.5
     rs, 2.23.24, 2.23.24, 2.23.24isp, 3.2.6, 3.2.6
     rst, 2.23.23, 2.23.23, 2.23.23it, 3.3.7, 3.3.7
     sar, 2.23.37, 2.23.37, 2.23.37iv9, 2.13, 2.13
     se, 2.23.31, 2.23.31, 2.23.31keep, 2.20.40, 2.20.40, 2.20.40
l_antiAlias, 2.15.1, 2.15.1, 2.15.1     binary, 2.20.45
l_autoLink, 2.15.2, 2.15.2, 2.15.2     database, 2.20.46
l_bpmc, 2.15.3, 2.15.3, 2.15.3listbinary, 2.20.45, 2.20.45
l_breakRibbon, 2.15.4, 2.15.4, 2.15.4listdatabase, 2.20.46, 2.20.46
l_bufferedOutput, 2.15.5, 2.15.5, 2.15.5literature, 4.1
l_bug, 2.15.6, 2.15.6, 2.15.6lo, 2.9.3, 2.9.3
l_caseSensitivity, 2.15.7, 2.15.7, 2.15.7load, 2.20.47, 2.20.47, 2.20.47
l_commands, 2.15.8, 2.15.8, 2.15.8     conf, 2.20.47.1
l_confirm, 2.15.9, 2.15.9, 2.15.9     frame, 2.20.47.2
l_easyRotate, 2.15.10, 2.15.10, 2.15.10     solution, 2.20.47.3
l_info, 2.15.11, 2.15.11, 2.15.11loadconf, 2.20.47.1, 2.20.47.1
l_minRedraw, 2.15.12, 2.15.12, 2.15.12loadframe, 2.20.47.2, 2.20.47.2
l_neutralAcids, 2.15.13, 2.15.13, 2.15.13loadsolution, 2.20.47.3, 2.20.47.3
l_out, 2.15.14, 2.15.14, 2.15.14logarithm, 2.21.70
l_print, 2.15.15, 2.15.15, 2.15.15logical operations, 2.9.3
l_racemicMC, 2.15.16, 2.15.16, 2.15.16     variables, 2.15
l_readMolArom, 2.15.17, 2.15.17, 2.15.17long axes, 2.21.137
l_showAccessibility, 2.15.18, 2.15.18, 2.15.18loop database rebuilding, 2.20.87.15
l_showMC, 2.15.19, 2.15.19, 2.15.19     interrupt, 2.14.41
l_showMinSteps, 2.15.20, 2.15.20, 2.15.20     modeling intro, 1.4.2.3
l_showResCodeInSelection, 2.15.21, 2.15.21, 2.15.21loopmod, 1.4.2.3, 1.4.2.3
l_showSites, 2.15.23, 2.15.23, 2.15.23lv11, 2.15, 2.15
l_showSpecialChar, 2.15.22, 2.15.22, 2.15.22ma29, 3.9, 3.9
l_showSstructure, 2.15.24, 2.15.24, 2.15.24macro, 2.20.48, 2.20.48, 2.20.48
l_showTerms, 2.15.26, 2.15.26, 2.15.26main ICM references, 4.2
l_showWater, 2.15.25, 2.15.25, 2.15.25     concepts, 3.8.1
l_warn, 2.15.27, 2.15.27, 2.15.27make, 2.20.49, 2.20.49, 2.20.49
l_wrapLine, 2.15.28, 2.15.28, 2.15.28     bond, 2.20.49.1
l_writeStartObjMC, 2.15.29, 2.15.29, 2.15.29          chain, 2.20.49.2
l_xrUseHydrogen, 2.15.30, 2.15.30, 2.15.30     boundary, 2.20.49.3
label, 2.20.20.18     directory, 2.20.49.4
     fonts, 2.23.17     disulfide bond, 2.20.49.5
learn, 2.20.41, 2.20.41, 2.20.41     drestraint, 2.20.49.6
ligand binding, 2.22.26     factor, 2.20.49.7
     docking, 3.11, 3.11.1, 3.11.2     grob image, 2.20.49.9
          intro, 1.4.2.6          map, 2.20.49.8
     setting, 3.11.2          matrix, 2.20.49.10
ligandfit, 3.11, 3.11          potential, 2.20.49.11
ligdockht, 3.11.2, 3.11.2     key, 2.20.49.12
limits, 2.23.16     map, 2.20.49.13
lineWidth, 2.14.18, 2.14.18, 2.14.18          factor, 2.20.49.14
     internal variables of molecular object, 2.20.42          potential, 2.20.49.15
     sequences to 3D objects, 2.20.43     peptide bond, 2.20.49.16
     to alignment, 2.20.43     sequence, 2.20.49.17
     variable, 2.20.42     tree, 2.20.49.18
linkalignment, 2.20.43, 2.20.43     unique, 2.20.49.19
linked alignment, 2.21.81makeIndexChemDb, 2.22.37, 2.22.37, 2.22.37
     sequence, 2.21.81makeIndexSwiss, 2.22.38, 2.22.38, 2.22.38
linkvariable, 2.20.42, 2.20.42makePdbFromStereo, 2.22.39, 2.22.39, 2.22.39
list, 2.20.44, 2.20.44, 2.20.44makeSimpleDockObj, 2.22.75, 2.22.75, 2.22.75
makebond, 2.20.49.1, 2.20.49.1     stacks, 3.5.7
makebondchain, 2.20.49.2, 2.20.49.2     tables, 2.20.4
makeboundary, 2.20.49.3, 2.20.49.3merge2, 3.6.7, 3.6.7
makedirectory, 2.20.49.4, 2.20.49.4mfMethod, 2.17.11, 2.17.11, 2.17.11
makedisulfidebond, 2.20.49.5, 2.20.49.5mfWeight, 2.14.24, 2.14.24, 2.14.24
makedrestraint, 2.20.49.6, 2.20.49.6mi, 3.6.8, 3.6.8
makefactor, 2.20.49.7, 2.20.49.7mimelDepth, 2.14.25, 2.14.25, 2.14.25
makegrobimage, 2.20.49.9, 2.20.49.9mimelMolDensity, 2.14.26, 2.14.26, 2.14.26
makegrobmap, 2.20.49.8, 2.20.49.8minTetherWindow, 2.13.7, 2.13.7, 2.13.7
makegrobmatrix, 2.20.49.10, 2.20.49.10minimize, 2.13.9, 2.20.50, 2.20.50, 2.20.50
makegrobpotential, 2.20.49.11, 2.20.49.11     cartesian, 2.20.50.1
makekey, 2.20.49.12, 2.20.49.12     loop, 2.20.50.2
makemap, 2.20.49.13, 2.20.49.13     stack, 2.20.50.3
makemapfactor, 2.20.49.14, 2.20.49.14     tether, 2.13.7, 2.20.50.4
makemappotential, 2.20.49.15, 2.20.49.15     drop, 2.14.13
makepeptidebond, 2.20.49.16, 2.20.49.16minimizeMethod, 2.17.12, 2.17.12, 2.17.12
makesequence, 2.20.49.17, 2.20.49.17minimizecartesian, 2.20.50.1, 2.20.50.1
maketree, 2.20.49.18, 2.20.49.18minimizeloop, 2.20.50.2, 2.20.50.2
makeunique, 2.20.49.19, 2.20.49.19minimizestack, 2.20.50.3, 2.20.50.3
making Swissprot index, 2.20.87.11minimizetether, 2.20.50.4, 2.20.50.4
     predictive models, 2.20.41mkUniqPdbSequences, 2.22.40, 2.22.40, 2.22.40
manual style, 1.5mm, 3.6.5, 3.6.5
     averaging, 2.21.121.4mm26, 3.6, 3.6
     calculation, 2.20.49.14mmff torsion types, 2.20.73.2
     file, 2.23.18     type, 2.21.150
     fitting, 2.17.4     show atom types, 2.20.69.10
     mean value, 2.21.76mnSolutions, 2.13.8, 2.13.8, 2.13.8
     min value, 2.21.77mncalls, 2.13.9, 2.13.9, 2.13.9
     transformations, 2.21.121.4mncallsMC, 2.13.10, 2.13.10, 2.13.10
     trimming, 2.21.21mnconf, 2.13.11, 2.13.11, 2.13.11
     value sigma, 2.21.109mnhighEnergy, 2.13.12, 2.13.12, 2.13.12
mapSigmaLevel, 2.14.19, 2.14.19, 2.14.19mnreject, 2.13.13, 2.13.13, 2.13.13
mapping properties to sequence, 2.21.100.3mnvisits, 2.13.14, 2.13.14, 2.13.14
     and factors, 3.9model reliability, 2.22.21
     map value, 2.21.74modify, 2.20.52, 2.20.52, 2.20.52
maxColorPotential, 2.13.5, 2.13.5, 2.13.5     and reroot, 2.20.16.3
maxMemory, 2.13.6, 2.13.6, 2.13.6modules, 1.4.4, 1.4.4
mc, 3.8.1, 3.8.1     to icm, 2.20.16.2
mc2, 3.6.4, 3.6.4mol-file to chem-table element, 2.21.90
mcBell, 2.14.20, 2.14.20, 2.14.20molecular manipulations, 3.6
mcJump, 2.14.21, 2.14.21, 2.14.21     modifications, 3.6.5
mcShake, 2.14.22, 2.14.22, 2.14.22     views, 1.4.1.1
mcStep, 2.14.23, 2.14.23, 2.14.23molecule, 2.7, 2.7
mcmovie, 3.7.2, 3.7.2     create, 3.6.4
memorizing positions, 3.2.4     intermediate, 3.6.8
menu, 2.20.51, 2.20.51, 2.20.51     properties, 2.20.68.18
     script, 3.1.3     rotation, 3.2.3
merge arrays to table, 2.20.35.3     translation, 3.2.3, 3.2.4
     pdb, 3.4.6     create, 1.7.2
     sarray into string, 2.21.130     intro, 2.7
     selecting, 2.8.2os_, 2.8.1, 2.8.1
molintro, 1.7.2, 1.7.2output, 2.13.3
moltranslation, 3.2.4, 3.2.4p32, 3.10.3, 3.10.3
montecarlo, 2.13.10, 2.13.12, 2.13.13, 2.13.14, 2.13.18, 2.20.53, 2.20.53p3s, 3.10.4, 3.10.4
     command, 2.20.53     shift, 3.5.3
     local, 2.13.15packing density, 3.3.8
     trajectory, 2.20.20.14parallelization, 2.13.4, 2.13.17
mouse controls, 2.3partial least squares, 2.20.41
move, 2.20.54, 2.20.54, 2.20.54pattern search, 2.20.28.2
     atoms, 2.20.68.2pause, 2.20.55, 2.20.55, 2.20.55
     ms_molecule, 2.20.54.1pca, 3.3.9, 3.3.9
movems_molecule, 2.20.54.1, 2.20.54.1pd, 3.3.8, 3.3.8
movie, 2.20.47.2     files, 2.23.29
     file, 2.23.19     merge, 3.4.6
     frame writing, 2.20.20.14     sequence generation, 3.4.5
     molecular simulation, 3.7.2pdbDirStyle, 2.17.13, 2.17.13, 2.17.13
     smoothing, 2.20.20.14pdbmerge, 3.4.6, 3.4.6
     zooming, 3.7.1pepfold, 1.4.2.1, 1.4.2.1
ms, 3.1.3, 3.1.3peptide docking, 3.10.5
ms_, 2.8.2, 2.8.2     folding intro, 1.4.2.1
msaintro, 1.4.3.4, 1.4.3.4peptidedock, 3.10.5, 3.10.5
multiple alignment, 2.20.3.2personal gui controls, 3.1.2
     object file, 2.20.63.2     setup, 3.1.2
     sequence alignment intro, 1.4.3.4ph, 3.10.2, 3.10.2
mutate residue, 2.20.52ph30, 3.10, 3.10
mutating residue, 3.6.5plot, 2.20.56
nLocalDeformVar, 2.13.15, 2.13.15, 2.13.15     3D 2Dfunction, 3.10.3
nProc, 2.13.17, 2.13.17, 2.13.17          shape, 3.10.4
nSsearchStep, 2.13.16, 2.13.16, 2.13.16     area, 2.20.57
name, 2.21.66     histogram, 3.10.2
nice, 2.22.34, 2.22.34, 2.22.34     how to, 3.10
niceimage, 3.2.2, 3.2.2     simple, 3.10.1
non-redundant, 3.4.5plot2DSeq, 2.22.41, 2.22.41, 2.22.41
normal distribution, 2.21.99plotBestEnergies, 2.22.44, 2.22.44, 2.22.44
nota, 1.5, 1.5plotCluster, 2.22.47, 2.22.47, 2.22.47
notational conventions, 1.5plotFlexibility, 2.22.46, 2.22.46, 2.22.46
nsr, 1.4.1.3, 1.4.1.3plotMatrix, 2.22.48, 2.22.48, 2.22.48
number of elements, 2.21.85plotOldEnergy, 2.22.45, 2.22.45, 2.22.45
          occurencies, 2.21.85plotRama, 2.22.49, 2.22.49, 2.22.49
nvis, 2.21.57, 2.21.57, 2.21.57plotRose, 2.22.50, 2.22.50, 2.22.50
object properties, 2.20.68.18plotSeqDotMatrix, 2.22.42, 2.22.42, 2.22.42
     assign comment, 2.20.68.8plotSeqDotMatrix2, 2.22.43, 2.22.43, 2.22.43
     source file, 2.21.47plotSeqProperty, 2.22.51, 2.22.51, 2.22.51
     translate, 2.20.80plotarea, 2.20.57, 2.20.57
     merge, 3.6.6plots3d, 1.4.3.7, 1.4.3.7
     sort/reorder, 2.20.70.2plotting van der Waals, 3.5.1
     selecting, 2.8.1pls, 2.20.41
om, 3.6.6, 3.6.6pmf, 2.17.11
on-line help, 2.20.37.1     residue profile, 2.22.21
or, 2.9.3pocket, 2.22.26
predictSeq, 2.22.52, 2.22.52, 2.22.52     csv, 2.20.63.43
prediction quality, 2.21.112     database, 2.20.63.16
     score, 2.21.112     drestraint, 2.20.63.17
preference, 2.17, 2.17, 2.17          type, 2.20.63.18
prepSwiss, 2.22.53, 2.22.53, 2.22.53     factor, 2.20.63.19
previous atom, 2.21.84     from file, 2.20.63.1
principal axes, 2.21.137          string, 2.20.63.3
     component analysis, 3.3.9     ftp, 2.20.63.7
print, 2.20.58, 2.20.58, 2.20.58     grob, 2.20.63.20
     image, 2.20.60     http, 2.20.63.8
     to string, 2.20.72     iarray, 2.20.63.21
printFast, 2.22.54, 2.22.54, 2.22.54     index, 2.20.63.22
printMatrix, 2.22.55, 2.22.55, 2.22.55          table, 2.20.63.6
printPostScript, 2.22.56, 2.22.56, 2.22.56     library, 2.20.63.23
printTorsions, 2.22.57, 2.22.57, 2.22.57          mmff, 2.20.63.24
printf, 2.20.59, 2.20.59, 2.20.59     map, 2.20.63.25
printimage, 2.20.60, 2.20.60     matrix, 2.20.63.26
prl, 3.4.5, 3.4.5     mol, 2.15.13, 2.20.63.27
program overview, 1.4     mol2, 2.20.63.28
property, 2.20.68.27     movie, 2.20.63.29
protdockgrid, 3.12.2, 3.12.2          write, 2.20.63.30
protein docking intro, 1.4.2.5     object, 2.20.63.31
     grid docking, 3.12.2     pdb, 2.20.63.32
ps, 3.10.1, 3.10.1          sequence, 2.20.63.33
ps2, 3.5.3, 3.5.3     profile, 2.20.63.34
quit, 2.20.61, 2.20.61, 2.20.61     prosite, 2.20.63.35
r_2out, 2.14.28, 2.14.28, 2.14.28     rarray, 2.20.63.36
r_out, 2.14.27, 2.14.27, 2.14.27     sarray, 2.20.63.37
radii.electrostatic, 2.21.98     segment, 2.20.63.38
     van der Waals, 2.21.98     sequence, 2.20.63.39
ramachandran how to, 3.3.3          database, 2.20.63.40
random array, 2.21.99     stack, 2.20.63.41
randomSeed, 2.13.18, 2.13.18, 2.13.18     string, 2.20.63.42
randomize, 2.13.18, 2.20.62, 2.20.62, 2.20.62     table, 2.20.63.43
     coordinates, 2.20.62     unix, 2.20.63.9
     torsions, 2.20.62          cat, 2.20.63.10
rarrayalignmentprojection, 2.21.100.2, 2.21.100.2readFILTER, 2.20.63.4, 2.20.63.4
rarrayproperties, 2.21.100.3, 2.21.100.3readMolNames, 2.19.9, 2.19.9, 2.19.9
rarraysequenceprojection, 2.21.100.1, 2.21.100.1readPdbList, 2.22.62, 2.22.62, 2.22.62
rdBlastOutput, 2.22.60, 2.22.60, 2.22.60readalignment, 2.20.63.11, 2.20.63.11
rdSeqTab, 2.22.61, 2.22.61, 2.22.61readall, 2.20.63.5, 2.20.63.5
read, 2.20.63, 2.20.63, 2.20.63readbinary, 2.20.63.2, 2.20.63.2
     FILTER, 2.20.63.4readcolor, 2.20.63.12, 2.20.63.12
     alignment, 2.20.63.11readcomp_matrix, 2.20.63.13, 2.20.63.13
     all, 2.20.63.5readconf, 2.20.63.14, 2.20.63.14
     binary, 2.20.63.2readcsd, 2.20.63.15, 2.20.63.15
     color, 2.20.63.12readdatabase, 2.20.63.16, 2.20.63.16
     comp_matrix, 2.20.63.13readdrestraint, 2.20.63.17, 2.20.63.17
     conf, 2.20.63.14readdrestrainttype, 2.20.63.18, 2.20.63.18
     csd, 2.20.63.15readfactor, 2.20.63.19, 2.20.63.19
readfromstring, 2.20.63.3, 2.20.63.3     residue, 2.20.65
readftp, 2.20.63.7, 2.20.63.7renameobject, 2.20.65, 2.20.65
readgrob, 2.20.63.20, 2.20.63.20reorder alignment sequences, 2.20.87.1
readhttp, 2.20.63.8, 2.20.63.8reproducible randomness, 2.13.18
readiarray, 2.20.63.21, 2.20.63.21reroot, 2.20.16.3
readindex, 2.20.63.22, 2.20.63.22resLabelShift, 2.14.29, 2.14.29, 2.14.29
readindextable, 2.20.63.6, 2.20.63.6resLabelStyle, 2.17.15, 2.17.15, 2.17.15
readlibrary, 2.20.63.23, 2.20.63.23reserved names, 2.19
readlibrarymmff, 2.20.63.24, 2.20.63.24residue conservation, 2.21.100.4
readmap, 2.20.63.25, 2.20.63.25     contact areas, 2.21.8
readmatrix, 2.20.63.26, 2.20.63.26     cursor, 2.20.11.4
readmol, 2.20.63.27, 2.20.63.27     field, 2.20.68.18
readmol2, 2.20.63.28, 2.20.63.28     library file, 2.23.21
readmovie, 2.20.63.29, 2.20.63.29     name, 2.21.66
readmoviewrite, 2.20.63.30, 2.20.63.30     property averaging, 2.21.121.2
readobject, 2.20.63.31, 2.20.63.31          calculation, 2.21.53
readpdb, 2.20.63.32, 2.20.63.32     ranges, 2.8.7
readpdbsequence, 2.20.63.33, 2.20.63.33     renumbering, 2.20.3.1
readprofile, 2.20.63.34, 2.20.63.34     selection, 2.15.21
readprosite, 2.20.63.35, 2.20.63.35          as string, 2.21.128.1
readrarray, 2.20.63.36, 2.20.63.36          function, 2.21.104
readsarray, 2.20.63.37, 2.20.63.37     user field, 2.21.46
readsegment, 2.20.63.38, 2.20.63.38     selecting, 2.8.3
readsequence, 2.20.63.39, 2.20.63.39restraints, 2.12
readsequencedatabase, 2.20.63.40, 2.20.63.40     torsion, 2.20.68.45
readstack, 2.20.63.41, 2.20.63.41return, 2.20.66, 2.20.66, 2.20.66
readstring, 2.20.63.42, 2.20.63.42reverse complement, 2.21.115
readtable, 2.20.63.43, 2.20.63.43reversecompdnaseq, 2.21.115, 2.21.115
readunix, 2.20.63.9, 2.20.63.9rht, 3.3.3, 3.3.3
readunixcat, 2.20.63.10, 2.20.63.10ribbonColorStyle, 2.17.16, 2.17.16, 2.17.16
     shell variables, 2.14ribbonStyle, 2.17.17, 2.17.17, 2.17.17
rebel, 2.13.5rn15, 2.19, 2.19
rebel_ht, 3.5.2, 3.5.2rotate, 2.20.67, 2.20.67, 2.20.67
references, 4     grob, 2.20.67.2
refguide, 2, 2     object, 2.20.67.1
refineModel, 2.22.58, 2.22.58, 2.22.58     view, 2.20.67.3
refresh view, 2.20.20.2rotategrob, 2.20.67.2, 2.20.67.2
refs, 4.1, 4.1rotateobject, 2.20.67.1, 2.20.67.1
regression, 2.20.41rotateview, 2.20.67.3, 2.20.67.3
regul, 2.22.59, 2.22.59, 2.22.59rotmovie, 3.7.1, 3.7.1
regularization, 2.13.7rounding a real, 2.21.128
     procedure, 3.6.3     output, 2.20.69.41
rejectAction, 2.17.14, 2.17.14, 2.17.14rp, 3.6.3, 3.6.3
relational database, 2.21.123rsWeight, 2.14.30, 2.14.30, 2.14.30
release notes, 1.1rs_, 2.8.3, 2.8.3
releasenotes, 1.1, 1.1run script, 2.20.8
remarkObj, 2.22.63, 2.22.63, 2.22.63rv10, 2.14, 2.14
rename, 2.20.64, 2.20.64, 2.20.64rz33, 4, 4
     atom, 2.20.65s_blastdbDir, 2.16.1, 2.16.1, 2.16.1
     molecule, 2.20.65s_editor, 2.16.2, 2.16.2, 2.16.2
s_errorFormat, 2.16.4, 2.16.4, 2.16.4select by iarray, 2.21.113
s_fieldDelimiter, 2.16.5, 2.16.5, 2.16.5selectMinGrad, 2.14.31, 2.14.31, 2.14.31
s_helpEngine, 2.16.6, 2.16.6, 2.16.6selectSphereRadius, 2.14.32, 2.14.32, 2.14.32
s_icmPrompt, 2.16.9, 2.16.9, 2.16.9selecting by b-factor, 2.21.113
s_icmhome, 2.16.7, 2.16.7, 2.16.7               y z, 2.21.113
s_imageViewer, 2.16.10, 2.16.10, 2.16.10     residues, 3.3.6
s_inxDir, 2.16.8, 2.16.8, 2.16.8     saving, 2.21.56
s_javaCodeBase, 2.16.11, 2.16.11, 2.16.11selection, 2.8, 2.8
s_labelHeader, 2.16.12, 2.16.12, 2.16.12     level, 2.8, 2.21.150
s_lib, 2.16.13, 2.16.13, 2.16.13     transfer, 2.21.113, 2.21.128.1
s_logDir, 2.16.14, 2.16.14, 2.16.14     type, 2.8
s_out, 2.16.15, 2.16.15, 2.16.15     variable, 2.19.10
s_pdbDir, 2.16.16, 2.16.16, 2.16.16     atoms, 2.8.4
s_printCommand, 2.16.18, 2.16.18, 2.16.18     functions, 2.8.6
s_projectDir, 2.16.17, 2.16.17, 2.16.17     molecules, 2.8.2
s_prositeDat, 2.16.19, 2.16.19, 2.16.19     objects, 2.8.1
s_psViewer, 2.16.20, 2.16.20, 2.16.20     output, 2.19.14
s_reslib, 2.16.21, 2.16.21, 2.16.21     residues, 2.8.3
s_skipMessages, 2.16.22, 2.16.22, 2.16.22     torsions, 2.8.5
s_tempDir, 2.16.23, 2.16.23, 2.16.23     variables, 2.8.5
s_translateString, 2.16.24, 2.16.24, 2.16.24     in molecular objects, 2.8
s_userDir, 2.16.25, 2.16.25, 2.16.25selfunctions, 2.8.6, 2.8.6
s_usrlib, 2.16.26, 2.16.26, 2.16.26selranges, 2.8.7, 2.8.7
s_webEntrezLink, 2.16.27, 2.16.27, 2.16.27seqalignintro, 1.4.3.3, 1.4.3.3
s_webViewer, 2.16.28, 2.16.28, 2.16.28seqanalintro, 1.4.3, 1.4.3
s_xpdbDir, 2.16.29, 2.16.29, 2.16.29sequence alignment intro, 1.4.3.3
sa23, 3.3, 3.3     analysis intro, 1.4.3
save print, 3.2.6     assembly, 2.20.35.2
script.image generation, 2.20.20.3     dotplot, 1.4.3.2
scripting molecular movements, 3.2.4     from pdb, 2.20.49.17
sdf to chem-table, 2.21.90     name, 2.21.69
sdf/mol file indexing, 2.20.87.11     positional weights, 2.20.68.1
search pdb headers, 3.4.8     redundancy removal, 2.20.35.2
     prosite, 3.4.1     search, 2.20.28.2
     protein fragment, 3.4.2     to alignment transfer, 2.21.100.2
          topology, 3.4.4     output format, 2.13.20, 2.13.21
     sstructure database, 3.4.7sequenceBlock, 2.13.20, 2.13.20, 2.13.20
     sequence pattern, 2.20.28.6sequenceColorScheme, 2.17.18, 2.17.18, 2.17.18
searchObjSegment, 2.22.66, 2.22.66, 2.22.66sequenceLine, 2.13.21, 2.13.21, 2.13.21
searchPatternDb, 2.22.64, 2.22.64, 2.22.64sequences, 3.4
searchPatternPdb, 2.22.65, 2.22.65, 2.22.65set, 2.20.68, 2.20.68, 2.20.68
searchSeqDb, 2.22.67, 2.22.67, 2.22.67     area, 2.20.68.1
searchSeqFullPdb, 2.22.69, 2.22.69, 2.22.69     atom, 2.20.68.2
searchSeqPdb, 2.22.68, 2.22.68, 2.22.68     bfactor, 2.20.68.3
searchSeqProsite, 2.22.76, 2.22.76, 2.22.76     bond type, 2.20.68.4
searchSeqSwiss, 2.22.70, 2.22.70, 2.22.70     charge, 2.20.68.5
searches and alignments, 3.4          formal, 2.20.68.6
second moments, 2.21.137          mmff, 2.20.68.7
secondary structure derivation from 3D, 2.20.5.1     comment, 2.20.68.8
segMinLength, 2.13.19, 2.13.19, 2.13.19          sequence, 2.20.68.10
     current map, 2.20.68.24setcommentsequence, 2.20.68.10, 2.20.68.10
     directory, 2.20.68.12setcomp_matrix, 2.20.68.11, 2.20.68.11
     drestraint, 2.20.68.13setdirectory, 2.20.68.12, 2.20.68.12
          type, 2.20.68.14setdrestraint, 2.20.68.13, 2.20.68.13
     electrostatic radii, 2.20.68.43setdrestrainttype, 2.20.68.14, 2.20.68.14
     field, 2.20.68.18setfield, 2.20.68.18, 2.20.68.18
     font, 2.20.68.19setfont, 2.20.68.19, 2.20.68.19
     grob coordinates, 2.20.68.20setgrobcoordinates, 2.20.68.20, 2.20.68.20
     group, 2.20.68.35setkey, 2.20.68.21, 2.20.68.21
     key, 2.20.68.21setlabel, 2.20.68.22, 2.20.68.22
     label, 2.20.68.22setlabeldistance, 2.20.68.23, 2.20.68.23
          distance, 2.20.68.23setmap, 2.20.68.24, 2.20.68.24
     molecular variables, 2.20.68.47setoccupancy, 2.20.68.25, 2.20.68.25
     occupancy, 2.20.68.25setplane, 2.20.68.26, 2.20.68.26
     plane, 2.20.68.26setproperty, 2.20.68.27, 2.20.68.27
     property, 2.20.68.27setrandomize, 2.20.68.28, 2.20.68.28
     radii graphical, 2.20.68.50setsite, 2.20.68.15, 2.20.68.15
     randomSeed, 2.20.68.28setsiteresidue, 2.20.68.17, 2.20.68.17
     randomize, 2.20.68.28setsstructurebackbone, 2.20.68.30, 2.20.68.30
     site, 2.20.68.15setsstructuresequence, 2.20.68.31, 2.20.68.31
          residue, 2.20.68.17setstackenergy, 2.20.68.32, 2.20.68.32
     sstructure backbone, 2.20.68.30setstereo, 2.20.68.29, 2.20.68.29
          to sequence, 2.20.68.31setswiss, 2.20.68.33, 2.20.68.33
     stack energy, 2.20.68.32, 2.20.73.1setsymmetry, 2.20.68.34, 2.20.68.34
     stereo, 2.20.68.29setsymmetryobject, 2.20.68.35, 2.20.68.35
     swiss name, 2.20.68.33settable, 2.20.68.36, 2.20.68.36
     symmetry group, 2.20.68.35setterms, 2.20.68.37, 2.20.68.37
          to a torsion, 2.20.68.34settether, 2.20.68.38, 2.20.68.38
     table, 2.20.68.36settype, 2.20.68.39, 2.20.68.39
     terms, 2.20.68.37settypemmff, 2.20.68.41, 2.20.68.41
     tether, 2.20.68.38settypeseq, 2.20.68.40, 2.20.68.40
     type, 2.20.68.39setvariablegrid, 2.20.68.48, 2.20.68.48
          mmff, 2.20.68.41setview, 2.20.68.44, 2.20.68.44
          sequence, 2.20.68.40setvrestraint, 2.20.68.45, 2.20.68.45
     variable grid, 2.20.68.48setvrestraintvs_var, 2.20.68.46, 2.20.68.46
     view, 2.20.68.44setvs_var, 2.20.68.47, 2.20.68.47
     vrestraint, 2.20.68.45setvwelradii, 2.20.68.43, 2.20.68.43
          radii, 2.20.68.42setvwradii, 2.20.68.42, 2.20.68.42
     window, 2.20.68.49setwindow, 2.20.68.49, 2.20.68.49
     xstick radii, 2.20.68.50setxstick, 2.20.68.50, 2.20.68.50
setResLabel, 2.22.71, 2.22.71, 2.22.71sfWeight, 2.14.33, 2.14.33, 2.14.33
setalternativeflag, 2.20.68.9, 2.20.68.9sh24, 3.4, 3.4
setarea, 2.20.68.1, 2.20.68.1shell, 3.1
setatom, 2.20.68.2, 2.20.68.2     warning message, 2.21.157
setbfactor, 2.20.68.3, 2.20.68.3shellintro, 1.7.1, 1.7.1
setbondtype, 2.20.68.4, 2.20.68.4shineStyle, 2.17.19, 2.17.19, 2.17.19
setcharge, 2.20.68.5, 2.20.68.5shininess, 2.14.34, 2.14.34, 2.14.34
setchargeformal, 2.20.68.6, 2.20.68.6show, 2.20.69, 2.20.69, 2.20.69, 2.20.69.35
setchargemmff, 2.20.68.7, 2.20.68.7     aliases, 2.20.69.6
setcomment, 2.20.68.8, 2.20.68.8     alignment, 2.20.69.7
     atom type, 2.20.69.10showcolor, 2.20.69.12, 2.20.69.12
     atoms, 2.20.69.9showcolumn, 2.20.69.13, 2.20.69.13
     clash, 2.20.69.11showcomp_matrix, 2.20.69.14, 2.20.69.14
     color, 2.20.69.12showdatabase, 2.20.69.15, 2.20.69.15
     column, 2.20.69.13showdrestraint, 2.20.69.16, 2.20.69.16
     comp_matrix, 2.20.69.14showdrestrainttype, 2.20.69.17, 2.20.69.17
     drestraint, 2.20.69.16showenergy, 2.20.69.18, 2.20.69.18
          type, 2.20.69.17showgradient, 2.20.69.19, 2.20.69.19
     energy, 2.20.69.18showhbond, 2.20.69.20, 2.20.69.20
     gradient, 2.20.69.19showhbondexact, 2.20.69.21, 2.20.69.21
     hbond, 2.20.69.20showhtml, 2.20.69.22, 2.20.69.22
          exact, 2.20.69.21showiarray, 2.20.69.23, 2.20.69.23
     html, 2.20.69.22showinteger, 2.20.69.24, 2.20.69.24
     iarray, 2.20.69.23showkey, 2.20.69.3, 2.20.69.3
     integer, 2.20.69.24showlabel, 2.20.69.25, 2.20.69.25
     key, 2.20.69.3showlibrary, 2.20.69.26, 2.20.69.26
     label, 2.20.69.25showlink, 2.20.69.27, 2.20.69.27
     library, 2.20.69.26showlogical, 2.20.69.28, 2.20.69.28
     link, 2.20.69.27showmap, 2.20.69.4, 2.20.69.4
     logical, 2.20.69.28showmol, 2.20.69.29, 2.20.69.29
     map, 2.20.69.4showmol2, 2.20.69.30, 2.20.69.30
     mol, 2.20.69.29showmolecule, 2.20.69.31, 2.20.69.31
     mol2, 2.20.69.30showmolecules, 2.20.69.5, 2.20.69.5
     molecule, 2.20.69.31showobject, 2.20.69.32, 2.20.69.32
     molecules, 2.20.69.5showpdb, 2.20.69.33, 2.20.69.33
     object, 2.20.69.32showpreferences, 2.20.69.34, 2.20.69.34
     pdb, 2.20.69.33showprofile, 2.20.69.35, 2.20.69.35
     preferences, 2.20.69.34showresidue, 2.20.69.36, 2.20.69.36
     residue, 2.20.69.36showresiduetype, 2.20.69.37, 2.20.69.37
          type, 2.20.69.37showsegment, 2.20.69.38, 2.20.69.38
     segment, 2.20.69.38showsequence, 2.20.69.39, 2.20.69.39
     sequence, 2.20.69.39showsite, 2.20.69.1, 2.20.69.1
     shell variable, 2.20.69.2showstack, 2.20.69.40, 2.20.69.40
     site, 2.20.69.1showsvariable, 2.20.69.2, 2.20.69.2
     stack, 2.20.69.40showtable, 2.20.69.41, 2.20.69.41
     table, 2.20.69.41showterm, 2.20.69.42, 2.20.69.42
          as database, 2.20.69.15showtethers, 2.20.69.43, 2.20.69.43
     term, 2.20.69.42showversion, 2.20.69.44, 2.20.69.44
     tethers, 2.20.69.43showvolume, 2.20.69.47, 2.20.69.47
     version, 2.20.69.44showvolumemap, 2.20.69.48, 2.20.69.48
     volume, 2.20.69.47showvrestraint, 2.20.69.45, 2.20.69.45
          map, 2.20.69.48showvrestrainttype, 2.20.69.46, 2.20.69.46
     vrestraint type, 2.20.69.46sht, 3.3.1, 3.3.1
     vrestraints, 2.20.69.45simulation duration, 2.14.41
showalias, 2.20.69.6, 2.20.69.6     temperature, 2.14.40
showalignment, 2.20.69.7, 2.20.69.7     intro, 1.4.2
showarea, 2.20.69.8, 2.20.69.8skin intro, 1.4.1.2
showatom, 2.20.69.9, 2.20.69.9skinintro, 1.4.1.2, 1.4.1.2
showatomtype, 2.20.69.10, 2.20.69.10sm, 3.5.7, 3.5.7
showclash, 2.20.69.11, 2.20.69.11smiles to chem-table element, 2.21.90
smoothmap, 2.21.121.4, 2.21.121.4     superposition, 2.20.3.4
smoothr, 2.21.121.1, 2.21.121.1     analysis, 3.3
solvation energy, 2.14.33, 2.17.20     comparison, 2.21.22.2
solvent accessible area, 2.13.22     structure, 3.9.1
sort, 2.20.70, 2.20.70, 2.20.70structurefactors, 3.9.1, 3.9.1
     arrays, 2.20.70.1subalignment to selection, 2.21.105
     molecules, 2.20.70.3subset, 2.6, 2.6
     objects, 2.20.70.2substring, 2.21.128
     table, 2.20.70.4substructure search, 2.20.28.3
sortSeq, 2.22.72, 2.22.72, 2.22.72superimpose, 2.20.76, 2.20.76, 2.20.76
sortarray, 2.20.70.1, 2.20.70.1     how to, 3.3.1
sortmolecules, 2.20.70.3, 2.20.70.3surface point selection, 2.21.158
sortobjects, 2.20.70.2, 2.20.70.2     term, 2.14.33
sorttables, 2.20.70.4, 2.20.70.4surfaceAccuracy, 2.13.22, 2.13.22, 2.13.22
sp, 3.4.1, 3.4.1surfaceMethod, 2.17.20, 2.17.20, 2.17.20
spf, 3.4.2, 3.4.2surfaceTension, 2.14.38, 2.14.38, 2.14.38
sph, 3.4.8, 3.4.8sv, 2.19.10, 2.19.10
split, 2.20.71, 2.20.71, 2.20.71sv12, 2.16, 2.16
     grob, 2.20.71.1swapping protein fragments, 3.6.7
     object, 2.20.71.2swiss, 2.20.68.33
splitgrob, 2.20.71.1, 2.20.71.1swissFields, 2.19.8, 2.19.8, 2.19.8
splitobject, 2.20.71.2, 2.20.71.2swissprot name, 2.21.69
splitting selection, 2.8.7symmetry group, 2.13.2
sprintf, 2.20.72, 2.20.72, 2.20.72sys, 2.20.77, 2.20.77, 2.20.77
spt, 3.4.4, 3.4.4system command, 2.20.77
sr, 3.6.9, 3.6.9     reserved selections, 2.19.13
ssThreshold, 2.14.35, 2.14.35, 2.14.35ta28, 3.8, 3.8
ssWeight, 2.14.36, 2.14.36, 2.14.36table, 2.20.68.27
ssd, 3.4.7, 3.4.7     creation, 2.20.35.3
ssearch, 2.13.16, 2.20.74, 2.20.74, 2.20.74     pring, 2.20.69.41
ssearchStep, 2.14.37, 2.14.37, 2.14.37     selected row numbers, 2.21.59
ssign sstructure segment, 2.20.5.2     show html, 2.20.85
stack, 2.13.11, 2.13.12, 2.13.14, 2.20.73, 2.20.73.1, 2.21.57, 2.21.134tempLocal, 2.14.39, 2.14.39, 2.14.39
     bin size, 2.20.12temperature, 2.14.40, 2.14.40, 2.14.40
     merge, 3.5.7tensor product of two vectors, 2.21.73
standard deviation, 2.21.109terminal font, 2.23.16
stereo, 2.20.68.29     window, 2.20.36
     reconstruction, 3.6.9terms, 2.12, 2.12, 2.12
stereoisomers, 2.15.16     hydrogen bonding, 2.14.17
store, 2.20.73, 2.20.73then, 2.20.78, 2.20.78, 2.20.78
     conf, 2.20.73, 2.20.73.1time, 2.21.33
     torsion, 2.20.73.2timeLimit, 2.14.41, 2.14.41, 2.14.41
          type, 2.20.73tolGrad, 2.14.42, 2.14.42, 2.14.42
storeconf, 2.20.73.1, 2.20.73.1topology files, 2.23.5
storetorsion, 2.20.73.2, 2.20.73.2     search, 2.20.28.7
string filtering, 2.21.148transform, 2.20.79, 2.20.79, 2.20.79
     variables, 2.16transformations and symmetry, 3.8
strip, 2.20.75, 2.20.75, 2.20.75translate, 2.20.80, 2.20.80, 2.20.80
structural alignment, 2.20.3.4transparent grob, 2.20.20.10
          optimization, 2.20.28.1truncate values, 2.21.148
tzMethod, 2.17.21, 2.17.21, 2.17.21while, 2.20.86, 2.20.86, 2.20.86
tzWeight, 2.14.43, 2.14.43, 2.14.43window averaging, 2.21.121.1
unclip, 2.20.20.2     width and height, 2.21.156
undisplay, 2.20.81, 2.20.81, 2.20.81windowSize, 2.13.23, 2.13.23, 2.13.23
undsCharge, 2.22.73, 2.22.73, 2.22.73wireBondSeparation, 2.14.49, 2.14.49, 2.14.49
unfix, 2.20.82, 2.20.82, 2.20.82wireStyle, 2.17.26, 2.17.26, 2.17.26
unique atomic order, 2.20.49.19write, 2.20.87, 2.20.87, 2.20.87
     coloring, 2.20.11.8     alignment, 2.20.87.1
     smiles, 2.20.49.19          table, 2.20.87.4
unix, 2.20.77     binary, 2.20.87.2
updates, 1.1     blast, 2.20.87.12
url string parsing, 2.21.132     drestraint, 2.20.87.5
user-defined properties, 2.20.68.18          type, 2.20.87.6
user_startup.icm, 3.1.2     factor, 2.20.87.7
     guide, 3     grob, 2.20.87.8
usersguide, 3, 3     html, 2.20.87.9
varLabelStyle, 2.17.22, 2.17.22, 2.17.22     iarray, 2.20.87.3
variable restraint, 2.20.68.45     image, 2.20.87.10
     selection, 2.8.5     index, 2.20.87.11
vector product, 2.21.153.1          blast, 2.20.87.12
vicinity, 2.14.44, 2.14.44, 2.14.44     library, 2.20.87.13
view restoration, 2.21.62     map, 2.20.87.14
virtual ligand screening, 3.11, 3.11.1, 3.11.2, 3.11.3     model, 2.20.87.15
               intro, 1.4.2.7     mol, 2.20.87.16
visitsAction, 2.17.23, 2.17.23, 2.17.23     mol2, 2.20.87.17
vls, 3.11, 3.11.1, 3.11.2, 3.11.3     movie, 2.20.20.14
vlsht, 3.11.3, 3.11.3     object, 2.20.87.18
vlsintro, 1.4.2.7, 1.4.2.7          simple, 2.20.87.19
vlsoverview, 3.11.1, 3.11.1     pdb, 2.20.87.20
vrestraint file, 2.23.24     postscript, 2.20.87.21
     type file, 2.23.23     pov, 2.20.87.22
vs_, 2.8.5, 2.8.5     povray, 2.20.87.22
vs_out, 2.19.14, 2.19.14, 2.19.14     project, 2.20.87.2
vv, 2.19.13, 2.19.13     segment, 2.20.87.23
vwCutoff, 2.14.45, 2.14.45, 2.14.45     sequence, 2.20.87.24
vwExpand, 2.14.46, 2.14.46, 2.14.46     session, 2.20.87.25
vwMethod, 2.17.24, 2.17.24, 2.17.24     several array, 2.20.87.4
vwSoftMaxEnergy, 2.14.47, 2.14.47, 2.14.47     stack, 2.20.87.26
vwplot_ht, 3.5.1, 3.5.1     vs_var, 2.20.87.27
wait, 2.20.83, 2.20.83, 2.20.83writealignment, 2.20.87.1, 2.20.87.1
warning message, 2.21.157writearray, 2.20.87.4, 2.20.87.4
     suppression, 2.15.27writebinary, 2.20.87.2, 2.20.87.2
water.dielectric constant, 2.14.12writedrestraint, 2.20.87.5, 2.20.87.5
waterRadius, 2.14.48, 2.14.48, 2.14.48writedrestrainttype, 2.20.87.6, 2.20.87.6
wavefront format, 2.20.49.9writefactor, 2.20.87.7, 2.20.87.7
web, 2.20.84, 2.20.84, 2.20.84writegrob, 2.20.87.8, 2.20.87.8
     table, 2.20.85writehtml, 2.20.87.9, 2.20.87.9
webEntrezOption, 2.17.25, 2.17.25, 2.17.25writeiarray, 2.20.87.3, 2.20.87.3
webtable, 2.20.85, 2.20.85writeimage, 2.20.87.10, 2.20.87.10
wha, 1.4, 1.4writeindex, 2.20.87.11, 2.20.87.11
writelibrary, 2.20.87.13, 2.20.87.13 
writemap, 2.20.87.14, 2.20.87.14 
writemodel, 2.20.87.15, 2.20.87.15 
writemol, 2.20.87.16, 2.20.87.16 
writemol2, 2.20.87.17, 2.20.87.17 
writeobject, 2.20.87.18, 2.20.87.18 
writeobjectsimple, 2.20.87.19, 2.20.87.19 
writepdb, 2.20.87.20, 2.20.87.20 
writepostscript, 2.20.87.21, 2.20.87.21 
writepov, 2.20.87.22, 2.20.87.22 
writesegment, 2.20.87.23, 2.20.87.23 
writesequence, 2.20.87.24, 2.20.87.24 
writesession, 2.20.87.25, 2.20.87.25 
writestack, 2.20.87.26, 2.20.87.26 
writevs_var, 2.20.87.27, 2.20.87.27 
xplor format, 2.20.63.25 
xrMethod, 2.17.27, 2.17.27, 2.17.27 
xrWeight, 2.14.50, 2.14.50, 2.14.50 
zegaintro, 1.4.3.6, 1.4.3.6 
|, 2.9.3 

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