ICM Manual v.3.9
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2020, Molsoft LLC
Jun 5 2024

Contents
 
Introduction
Reference Guide
Command Line User's Guide
References
Glossary
 
Index

Index

&, 2.14.3Box, 2.34.21
2D chemicals, 2.23.9.16Bracket, 2.34.22
     labels, 2.33.58.1C, 5.3
     to 3D, 3.17CCP4, 5.6.6
     trees, 2.33.65.38CGI, 2.11
     smooth, 2.34.146.2COLOR.bg, 2.19.9
3D chemical builder, 1.4.2.8     distanceAtom, 2.19.10
     font size, 2.33.23.12     label, 2.19.11
     label, 2.33.23.12, 2.33.89.39CONSENSUS, 2.23.1
     labels, 2.33.58.1CONSENSUSCOLOR, 2.23.2
     mol file, 2.36.86CONSENSUS_strength, 2.19.12
     plots intro, 1.4.3.7Cad, 2.34.23, 2.34.23.1, 2.34.23.2
     smoothing, 2.34.146.3Cad1, 2.34.23.1
     superposition, 2.36.22Cadalign, 2.34.23.2
     transformations, 2.33.102.2Ceil, 2.34.24
     tree, 2.33.65.38Cell, 2.34.25
     chemical similarity, 2.34.136Charge, 2.34.26
     pharmacophore comparison, 2.34.136.3Chemical, 2.34.27
3dxml, 5.5.3     Functions, 2.27
=, 2.14.1     Synthetic Accessibility, 2.30
A, 5.1Cluster, 2.34.28
ANN, 2.33.53Collada, 5.5.3
APF distance, 2.34.136Collection, 2.34.28.1
Abs, 2.34.1Color, 2.34.29
Acc, 2.34.2     from gradient, 2.34.29.1
Acos, 2.34.3     image, 2.34.29.2
Acosh, 2.34.4     protein, 2.34.29.3
Adobe, 2.21.23Compare, 2.34.30
Align, 2.34.5Connolly surface, 5.8.7
     sequence, 2.34.5.1Consensus, 2.34.31
AlignSS, 2.35.1Contour, 2.34.32
Angle, 2.34.6Corr, 2.34.33
Apple, 3.14.6.2Cos, 2.34.34
Area, 2.34.7Cosh, 2.34.35
     residue contacts, 2.34.7.1Count, 2.34.36
Asin, 2.34.8CubicRoot, 2.34.37
Asinh, 2.34.9D, 5.4
Ask, 2.34.10DAE, 5.5.3
Askg, 2.34.11DE, 2.33.35.2
Atan, 2.34.12DNA Representation, 1.4.1.3
Atan2, 2.34.13     alignment, 2.33.3.4
Atanh, 2.34.14     melting temperature, 2.34.164
Atom, 2.34.15     views, 1.4.1.3
Augment, 2.34.16Date, 2.34.38
Axis, 2.34.17Deletion, 2.34.39
B, 5.2Descriptor, 2.34.40, 2.34.41
BPMC, 5.2.6     numeric, 2.34.40
Bfactor, 2.34.19Det, 2.34.42
Blob, 2.34.18Disgeo, 2.34.43
Boltzmann, 2.34.20Distance, 2.34.44, 2.34.44.6

          matrices, 2.34.44.9     in array, 2.34.56.1
     Dayhoff, 2.34.44.11          table, 2.34.56.2
     Tanimoto, 2.34.44.7FlexLM license info, 2.34.188
     alignment, 2.34.44.12Floor, 2.34.57
     as_, 2.34.44.3Formula, 2.34.58
          rarray, 2.34.44.4GCNN, 3.13.1.24
     atoms, 2.34.44.3GINGER, 3.13.1.20
     chemical, 2.34.44.7, 2.34.44.15GPU, 3.13.1.20, 3.18
     chemset, 2.34.44.8GRAPHICS, 2.23.5
     dayhoff, 2.34.44.11     alignmentRainbow, 2.23.5.1
     hierarchical, 2.34.44.6     atomLabelShift, 2.23.5.2
     iarray, 2.34.44.1     atomValueCircles, 2.23.5.3
          alignment, 2.34.44.12     ballRadius, 2.23.5.4, 2.23.5.31
     matrix, 2.34.44.5, 2.34.44.9     ballStickRatio, 2.23.5.5
     multiple atomic, 2.34.44.4     chainBreakLabelDisplay, 2.23.5.8
     rarray, 2.34.44.2     chainBreakStyle, 2.23.5.7
     tether, 2.34.44.10     clashWidth, 2.23.5.6
     tree, 2.34.44.14     clipStatic, 2.23.5.10
          cluster, 2.34.44.14     clippingPlane, 2.23.5.9
Docking, 3.18     cpkClipCaps, 2.23.5.11
     H, 5.5     displayLineLabels, 2.23.5.12
     Ligase protacModel.icm, 3.16     displayMapBox, 2.23.5.13
     number, 2.34.44.6     dnaBallRadius, 2.23.5.14
EDS server, 2.36.42     dnaRibbonRatio, 2.23.5.15
EST-alignment, 2.33.3.4     dnaRibbonStyle, 2.23.5.16
Eigen, 2.34.45     dnaRibbonWidth, 2.23.5.17
Enamine, 3.13.1.23     dnaRibbonWorm, 2.23.5.18
Energy, 2.34.46     dnaStickRadius, 2.23.5.19
Entropy, 2.34.47     formalChargeDisplay, 2.23.5.20
Error, 2.34.48     grobDotSize, 2.23.5.21
     soap, 2.34.49     grobLineWidth, 2.23.5.22
Exist, 2.34.50     hbondAngleSharpness, 2.23.5.26
     molcart, 2.34.50.1     hbondBallPeriod, 2.23.5.27
Existenv, 2.34.51     hbondBallStyle, 2.23.5.28
Exp, 2.34.53     hbondMinStrength, 2.23.5.25
Extension, 2.34.52     hbondRebuild, 2.23.5.24
FILTER, 2.23.3     hbondStyle, 2.23.5.23
     Z, 2.23.3.1     hbondWidth, 2.23.5.29
     gz, 2.23.3.2     hetatmZoom, 2.23.5.31
     uue, 2.23.3.3     hydrogenDisplay, 2.23.5.32
FTP, 2.23.4     light, 2.23.5.33
     createFile, 2.23.4.1     lightPosition, 2.23.5.34
     keepFile, 2.23.4.2     mapLineWidth, 2.23.5.35
     proxy, 2.23.4.3     occupancyDisplay, 2.23.5.36
Field, 2.34.54, 2.34.54.1     occupancyRadiusRatio, 2.23.5.37
     user, 2.34.54.1     quality, 2.23.5.38, 2.34.91.1
File, 2.34.55     rainbowBarStyle, 2.23.5.39
Find, 2.34.56     resLabelDrag, 2.23.5.40
     chemical, 2.34.56.3     resLabelYShift, 2.23.5.41
          pattern, 2.34.56.3     ribbonCylinderRadius, 2.23.5.42

     ribbonRatio, 2.23.5.44Header, 2.34.64
     ribbonWidth, 2.23.5.45Histogram, 2.34.65
     ribbonWorm, 2.23.5.46     N, 5.6
     rocking, 2.23.5.47ICM desktop, 2.23.8.6
     rockingRange, 2.23.5.48     documents, 2.33.84.4
     rockingSpeed, 2.23.5.49     modules, 1.4.4
     selectionLevel, 2.23.5.50     object, 2.36.13
     selectionStyle, 2.23.5.51     residue library, 2.21.24
     sketchAccents, 2.23.5.30ICM-shell, 3.1, 5.8.5
     stereoMode, 2.23.5.52     intro, 1.7.1
     stickRadius, 2.23.5.31, 2.23.5.53     script, 2.33.8
     surfaceDotDensity, 2.23.5.55ICMFF force field, 2.36.79
     surfaceDotSize, 2.23.5.54ICMHOME, 3.1.2.1
     surfaceProbeRadius, 2.23.5.56     shell variable, 3.1.2.1
     transparency, 2.23.5.57IMAGE, 2.23.9
     wormRadius, 2.23.5.58     bondLength2D, 2.23.9.15
GRID, 2.23.6     color, 2.23.9.8
     gcghExteriorPenalty, 2.23.6.1     compress, 2.23.9.9
     gpGaussianRadius, 2.23.6.6     font, 2.23.9.16
     margin, 2.23.6.2     gammaCorrection, 2.23.9.7
     maxEl, 2.23.6.3     generateAlpha, 2.23.9.10
     maxVw, 2.23.6.5     lineWidth, 2.23.9.3
     minEl, 2.23.6.4     lineWidth2D, 2.23.9.14
GROB, 2.23.7     orientation, 2.23.9.17
     arrowRadius, 2.23.7.3     paperSize, 2.23.9.18
     atomSphereRadius, 2.23.7.1     previewResolution, 2.23.9.13
     contourSigmaIncrement, 2.23.7.5     previewer, 2.23.9.12
     relArrowHead, 2.23.7.4     printerDPI, 2.23.9.2
     relArrowSize, 2.23.7.2     quality, 2.23.9.1
GUI, 2.23.8     rgb2bw, 2.23.9.19
     defaults, 3.14.6.2     scale, 2.23.9.4
     dialog, 2.32     stereoAngle, 2.23.9.6
     plot, 2.33.65.32     stereoBase, 2.23.9.5
     preferences, 2.33.85.4     stereoText, 2.23.9.11
     tableRowMarkColors, 2.23.8.5     writeScale, 2.23.9.20
     windowLayout, 2.23.8.6I_out, 2.24.4
     workspaceFolderStyle, 2.23.8.9Iarray, 2.34.66, 2.34.66.4, 2.34.66.5
     workspaceStyle, 2.23.8.7     atom numbers, 2.34.66.4
     workspaceTabStyle, 2.23.8.8     bits to integers, 2.34.66.3
GaussFit, 2.34.82     inverse, 2.34.66.2
Getarg, 2.34.59     residue numbers, 2.34.66.5
Getenv, 2.34.60     reverse, 2.34.66.2
GigaScreen, 3.13.1.24     stack, 2.34.66.6
Gradient, 2.34.61Icm Options, 2.1
Graphics, 1.4.1IcmSequence, 2.34.67
Grob, 2.34.62Image, 2.34.68
Group, 2.34.63     collection, 3.9.2.1
HTTP.ignoreProxyDomains, 2.23.4.5     frame by frame, 3.9.2.2
     proxy, 2.23.4.4InChI, 2.34.69
Hartree-Fock, 2.33.84.21, 2.33.110.17InChi, 2.34.69

Index, 2.34.70     stack, 2.34.90.11
     chemical, 2.34.70.2     sub, 2.34.90.2
     compare, 2.34.70.10     symmetric, 2.34.90.3
     element in array, 2.34.70.8     table, 2.34.90.6
     fork, 2.34.70.1     tensor, 2.34.90.7
     regexp, 2.34.70.4Max, 2.34.91
     string, 2.34.70.3     image graphic, 2.34.91.1
     table label, 2.34.70.6MaxHKL, 2.34.92
          selection, 2.34.70.5Mean, 2.34.94
     tree, 2.34.70.9Median, 2.34.93
     unique elements, 2.34.70.7Method, 2.22.13
Indexx, 2.34.71Min, 2.34.95
Info, 2.34.73Mod, 2.34.97
     image, 2.34.74Mol, 2.34.98
     model, 2.34.75MolLogP, 2.28
Insertion, 2.34.72MolLogS, 2.29
Integer, 2.34.76MolPSA, 5.7.12
Integral, 2.34.77MolSynth, 2.30
Interrupt, 2.34.78Moment, 2.34.88
Introduction, 1     of Inertia, 2.34.88
JSON, 2.33.84.57Money, 2.34.96
LIBRARY, 2.23.10N-terminus, 2.23.14.4
     men, 2.23.10.1NMR, 2.33.63.1
     res, 2.23.10.2NOE averaging, 2.22.6
Label, 2.34.79Name, 2.34.99
Laplacian, 2.34.80     chemical, 2.34.99.6
Latent, 2.34.187.3          property, 2.34.99.1
LatentVector, 2.34.187.3     close sequence, 2.34.99.3
Length, 2.34.81     conf, 2.34.99.7
LinearFit, 2.34.83     image, 2.34.99.11
LinearModel, 2.34.84     molcart, 2.34.99.12
Log, 2.34.85     object parray, 2.34.99.10
LogP, 2.28, 2.34.114     sequence, 2.34.99.8
LogS, 2.29, 2.34.114     soap, 2.34.99.2
M_out, 2.24.5     string, 2.34.99.4
Mac, 3.14.6.2     tree, 2.34.99.5
Map, 2.34.86Namex, 2.34.100
Markush structures, 2.33.55     image, 2.34.100.2
Mass, 2.34.87     sequence, 2.34.100.1
Match, 2.34.89Newick tree format, 2.34.156.4
Mathews, 2.34.136.4Next, 2.34.101, 2.34.101.1
Matrix, 2.34.90     covalent neighbors, 2.34.101.1
     alignment, 2.34.90.9Nof, 2.34.102
     boundary, 2.34.90.10     chemical, 2.34.102.2
     color, 2.34.90.4     distance, 2.34.102.3
     grob connectivity, 2.34.90.13     latent, 2.34.102.6
     histogram, 2.34.90.12     library, 2.34.102.4
     new, 2.34.90.1     molcart, 2.34.102.5
     residue areas, 2.34.90.8     soap, 2.34.102.7
          comparison, 2.34.90.5     tree, 2.34.102.1

Normalize, 2.34.104RIDGE, 3.13.1.21, 3.13.1.24, 3.18
NotInList, 2.34.105RNA topology, 2.23.5.16
     R, 5.7RTCNN, 3.13.1.24
OBJECT, 2.23.11R_2out, 2.24.7
Obj, 2.34.106R_out, 2.24.6
Occupancy, 2.34.107Radius, 2.34.120
PBS, 3.13.1.15, 3.13.1.19Random, 2.34.121
PCA, 3.3.9     string, 2.34.121.1
PLOT, 2.23.12Rarray, 2.34.122
     Yratio, 2.23.12.9     reverse, 2.34.122.2
     box, 2.23.12.1     sequence projection, 2.34.122.1
     color, 2.23.12.2     alignment projection, 2.34.122.3
     font, 2.23.12.3          strength, 2.34.122.5
     fontSize, 2.23.12.4     property assignment, 2.34.122.4
     gridLineWidth, 2.23.12.5RarrayAlignment, 2.34.122.5
     labelFont, 2.23.12.13Rarrayinverse, 2.34.122.2
     lineWidth, 2.23.12.6Real, 2.34.123
     logo, 2.23.12.10Reference, 2.34.125
     markSize, 2.23.12.7     Guide, 2
     numberOffset, 2.23.12.8Remainder, 2.34.124
     orientation, 2.23.12.11Replace, 2.34.126
     rainbowStyle, 2.23.12.14     chemical, 2.34.126.4
     seriesLabels, 2.23.12.12     exact, 2.34.126.1
PLS, 2.34.102.6     regexp, 2.34.126.3
     error, 2.34.136.4     simple, 2.34.126.2
     models, 2.34.136.4Res, 2.34.127, 2.34.128
PROTAC, 3.16Resali, 2.34.128
Parray, 2.34.109Resolution, 2.34.129
Parray-object, 2.34.109Rfactor, 2.34.131
Path, 2.34.108Rfree, 2.34.132
Pattern, 2.34.110Ride, 3.19
Pi, 2.34.111Ring, 2.34.130
Polar Surface Area, 5.7.12Rmsd, 2.34.133
Potential, 2.34.112     of subset, 2.23.14
Power, 2.34.113Rot, 2.34.134
Predict, 2.34.114S, 5.8
Probability, 2.34.115SAR analysis, 2.33.65.27, 2.33.65.28, 2.33.92.2, 2.33.92.3
Profile, 2.34.116SC, 2.33.35.2
Property, 2.34.117SEQUENCE.restoreOrigNames, 2.23.12.15
Protac, 3.16SGE, 3.13.1.19
Protonation state, 2.34.160.11SITE, 2.23.13
Putarg, 2.34.118     defSelect, 2.23.13.2
Putenv, 2.34.119     labelOffset, 2.23.13.3
QSAR, 2.33.53     labelStyle, 2.23.13.4
R-groups, 2.33.55     labelWrap, 2.23.13.5
REAL, 3.13.1.23     showSeqSkip, 2.23.13.6
REBEL, 3.7.2     wrapComment, 2.23.13.7
     faq, 3.7.2SLN notation, 2.34.156.10
     file, 2.33.55SLURM, 3.13.1.19
RIDE, 3.19SMARTS, 2.26, 2.33.10, 2.34.102.2

     request message, 2.34.152Sort, 2.34.153
SSSR, 2.34.130Sphere, 2.23.14.3, 2.34.151
S_out, 2.24.8Split, 2.34.154
S_proteinTags, 2.24.9     chemical, 2.34.154.4
Sarray, 2.34.135     multisep, 2.34.154.3
     index, 2.34.135.1     regexp, 2.34.154.2
Score, 2.34.136     tree, 2.34.154.1
     alignment, 2.34.136.8Sql, 2.34.149
     apf, 2.34.136.3Sqrt, 2.34.150
     chemset, 2.34.136.2Srmsd, 2.34.155
     conservation, 2.34.136.7Sstructure, 2.34.157
     model, 2.34.136.4String, 2.34.156, 2.34.156.8
     overlap, 2.34.136.1     alternative, 2.34.156.7
     predictions, 2.34.136.5     date, 2.34.156.2
     sequence, 2.34.136.6     mol, 2.34.156.3
Scripting Tutorials, 1.8     selection, 2.34.156.8
Select, 2.34.137     slide gui, 2.34.156.9
     break, 2.34.137.1     substring, 2.34.156.1
          alignment, 2.34.137.14     chemical formula, 2.34.156.10
          atom property, 2.34.137.7Sum, 2.34.158
          nmembers, 2.34.137.4     chemical, 2.34.158.1
          string, 2.34.137.9     image, 2.34.158.2
     expand, 2.34.137.6Swissprot, 2.33.110.24
     fix, 2.34.137.2Symgroup, 2.34.159
     graphical, 2.34.137.5T, 5.9
     neighbors, 2.34.137.3TOOLS, 2.23.14
Select_by atom numbers, 2.34.137.10     edsDir, 2.23.14.1
Select_by_sequence, 2.34.137.13     membrane, 2.23.14.2
Select_by_text, 2.34.137.9     minSphereCubeSize, 2.23.14.3
Select_lists, 2.34.137.12     pdbChargeNterm, 2.23.14.4
Select_patching, 2.34.137.11     pdbReadNmrModels, 2.23.14.5
Select_projection, 2.34.137.8     rebelPatchSize, 2.18.5, 2.23.14.6
Sequence, 2.34.138     smilesXyzSeparator, 2.23.14.7
     array, 2.34.138.2     superimposeMaxDeviation, 2.23.14.10
Sequence(dna reverse), 2.34.138.1     superimposeMaxIterations, 2.23.14.8
Shannon, 2.34.47     superimposeMinAtomFraction, 2.23.14.9
Shuffle, 2.34.139     tsShape, 2.23.14.12
Sign, 2.34.140     tsWeight, 2.23.14.13
Simulations, 1.4.2     writePdbRenameRes, 2.23.14.14
Sin, 2.34.141Table, 2.34.160
Sinh, 2.34.142     alignment numbers, 2.34.160.3
Site, 2.34.143     distance, 2.34.160.10
Slide, 2.34.144     matrix, 2.34.160.4
Smiles, 2.34.145     model, 2.34.160.8
Smooth, 2.18.24, 2.34.146, 2.34.146.1, 2.34.146.3          chem, 2.34.160.9
     matrix, 2.34.146.2     pairs, 2.34.160.5
Smoothrs, 2.34.146.3     plot, 2.34.160.7
SoapMessage, 2.34.152     stack, 2.34.160.6
SolveQuadratic, 2.34.147     url_decoder, 2.34.160.1
SolveQubic, 2.34.148Table(alignment), 2.34.160.2

Tan, 2.34.161Xyz, 2.34.192
Tanh, 2.34.162     axes, 2.34.192.8
Tanimoto, 2.34.66.3     chemical match, 2.34.192.6
     distance, 2.33.65.37     fract, 2.34.192.4
          matrix, 2.34.44.7     mesh, 2.34.192.3
Temperature, 2.34.164     points, 2.34.192.1
Tensor, 2.34.163     rings, 2.34.192.2
Time, 2.34.165     transformed xyz, 2.34.192.5
Tointeger, 2.34.166     vector2matrix, 2.34.192.7
Tolower, 2.34.167Z-shift, 2.19.35
Toreal, 2.34.168ZEGA, 5.10.9
Torsion, 2.34.169     intro, 1.4.3.6
Tostring, 2.34.170_NAME, 2.33.89.47
Toupper, 2.34.171_chemBatch, 3.1.2.5
ToxScore, 2.35.2_chemSuper, 3.15
Tr123, 2.34.172_confGen, 3.17
Tr321, 2.34.173_dockBatch, 3.13.1.7
Trace, 2.34.174_dockScan, 3.13.1.18
Trans, 2.34.175_macro, 2.37.1
Transform, 2.34.176     file, 2.37.1
Transpose, 2.34.177_startup, 3.1.2.3
Trim, 2.34.178     file, 2.37.2
     chemical, 2.34.179     icm, 2.37.2
     sequence, 2.34.180a_, 2.8.1
Turn, 2.34.181abbr, 1.6
Type, 2.34.182abbreviations, 1.6
     molcart, 2.34.182.2absolute to cell x y z, 2.34.192.4
     soap, 2.34.182.1accFunction, 2.24.2
     Z, 5.10acceptor, 3.6.1
Unique, 2.34.183access large sdf file, 2.33.84.24
Unix, 2.34.184accessMethod, 2.22.2
Uppsala, 2.36.42accessible residues, 3.3.6
     server, 2.36.43     surface, 2.33.65.14, 5.8.15
     SYNTHES, 3.13.1.23accessing sections, 2.33.110.24
VLS, 3.18accuracy, 2.34.136.4
V_, 2.8.1acidity constant, 2.33.89.11, 2.33.89.12
Value, 2.34.185activate fog, 2.33.23.24
     soap, 2.34.186     alignment, 2.33.89.40
Vector, 2.34.16, 2.34.187, 2.34.187.1, 2.34.187.3     document, 2.33.89.40
     symmetry transformation, 2.34.187.2     tab, 2.33.89.40
Vectorproduct, 2.34.187.1     table, 5.9.2.4
Vectorsymmetrytransformation, 2.34.187.2add, 2.33.1
Version, 2.34.188     column, 2.33.1.1
View, 2.34.190          function, 2.33.1.1.1
Volume, 2.34.189     matrix, 2.33.1.2
WEBAUTOLINK, 2.23.16     slide, 2.33.1.3
WEBLINK, 2.23.15     table, 2.33.1.4
Warning, 2.34.191          row, 2.33.1.4
Wavefront format, 2.33.84.22addBfactor, 2.19.1
XML, 2.12adding atoms to non-ICM objects, 2.33.7.1

     hydrogens, 2.36.13     gapExtension, 2.19.18
     in place, 2.14.4     gapOpen, 2.19.19
     to slideshow, 2.33.1.3alignment_as_text, 2.34.156.4
admet selection, 3.13.1.13aliphatic amines, 2.33.70.2
advanced chemical search, 3.6all, 5.1.2
     operations, 2.14.6     torsions table, 3.3.11
     ops, 2.14.6alpha, 2.23.5.57, 2.33.89.42, 5.1.3
ahfs, 2.34.44.6     channel, 2.23.9.10
ali_seq_project, 2.34.156.5alternative flag, 2.33.89.18
alias, 2.33.2amber, 5.1.4
align, 2.33.3amino acid, 2.21.24, 2.34.172, 2.34.173
     3D, 2.33.3.5          colors, 2.34.29.3
          faq, 3.3.2          labels, 2.33.3.2
          heavy, 2.33.3.6and, 2.14.3
          how to, 3.3.2angle rotation, 2.36.84
     chemical, 2.33.88.1angles, 2.34.102.3
     fragments, 2.33.3.4angular hbond dependence, 2.23.5.26
     intro, 1.4.3.3animated story, 5.8.14
     number, 2.33.3.2animation, 2.33.23.5, 2.33.23.6, 3.9
          chemical, 2.33.3.1annotation, 2.33.22.26, 2.33.89.26, 2.33.89.27
     res numbers, 2.33.3.2apf, 3.15, 3.19
     sequence, 2.33.3.3append, 5.1.5
     sequences, 2.33.3.3     a tables, 2.33.1.4
alignMethod, 2.22.3     column, 2.33.4.3
alignMinCoverage, 2.19.2     command, 2.33.4
alignMinMethod, 2.19.2     sequence, 2.33.4.1
alignOldStatWeight, 2.19.3          to group, 2.33.4.1
alignTwoSequences, 2.36.1     stack, 2.33.4.2
aligned residues, 2.34.128     tables, 2.33.50
alignment, 2.33.22.26, 2.33.89.27, 2.33.89.35, 2.33.89.55, 5.1.1          by shared column, 2.33.4.3
     as table, 2.34.160.2appending, 2.33.1.1
     block length, 2.18.22     an element, 2.14.4
          secondary structure, 2.35.1     menu items, 2.23.10.1
     cleaning, 2.34.146.4     representations to a slide, 2.33.23.21
     color by property, 2.33.89.34     rows to matrix, 2.33.1.2
     coloring, 2.21.1area under curve, 2.36.21
     conservation, 2.36.8arguments, 2.33.64
     distance, 2.34.137.13arithmetic operations, 2.14.2
     editor, 2.4arithmetics, 2.14
     extraction, 2.34.5aromatic planes, 2.36.4
     gap format, 5.1.1.1array, 2.33.72.4, 5.1.6, 5.7.3.1
     intro, 1.4.3.4     assignment, 2.14.1
     projection, 2.34.156, 2.34.156.5, 2.34.156.6     derivative, 2.34.146.1
     score, 2.34.136.7     overlap, 2.34.136.1
     sequence reordering, 2.34.5     parray, 2.33.22.31
     strength, 2.34.122.5     size, 2.34.102
     structural, 2.33.3.5, 2.34.5     subset, 2.6
     to sequence transfer, 2.34.122.1arrow from selection, 2.36.36
          text conversion, 2.34.156.4     length, 2.33.89.26
     weighted, 2.34.5as2_out, 2.24.14

as_graph, 2.23.5.50, 2.23.5.51, 2.34.137.5bfactor circles, 2.23.5.3
as_out, 2.24.13biased probability monte carlo, 2.33.71
assign, 2.33.5binary file table of contents, 2.33.84.2
     residue, 2.33.6.1     files, 2.33.110.2
     ring conformation to template, 2.33.66.4     string, 5.2.4
     sstructure, 2.33.5.1     key, 2.33.89.43
          segment, 2.18.20, 2.33.5.2binding energy, 3.7.4
assignment, 2.14.1     pocket finding, 3.4.2
atc code, 2.34.44.6     pockets, 2.33.92.1
atom, 2.33.13.1, 5.1.7     side comparison, 2.36.8
     centers within, 2.34.151     site analysis, 3.4.2
     code file, 2.37.4biological symmetry, 2.33.89.9
     coordinates, 2.34.192.1     vector, 2.34.66.3
     flickering, 2.33.89.3     to integers compression, 2.34.66.3
     label font, 2.37.15blast, 2.33.110.25
     labels, 2.33.89.2     files, 2.33.110.25
     name, 2.33.3.1, 2.34.79blast-formatted database, 2.33.35.3, 2.33.110.25
     pairs, 2.33.89.68, 2.33.89.69, 2.34.160.10blending, 2.33.110.31
     proximity to surface, 2.33.90.9     images, 2.34.158.2
     selection by number, 2.34.66.4blob, 5.2.4
     type, 2.34.182bold, 2.33.89.38.1
     user field, 2.34.54.1bond angle bending, 2.37.5
atomLabelStyle, 2.22.4     errors, 2.33.90.12
atomSingleStyle, 2.22.5     stretching, 2.37.6
atomic contributions, 2.33.90.20, 2.33.90.21     to protein, 2.33.72.3
     coordinate transfer, 2.33.89.3     width, 2.23.9.14
     property fieds, 3.19bonded atoms, 2.34.101.1
          fields, 3.15born radii, 2.33.90.9
     solvation contributions, 2.34.7boundary element, 5.2.5
     in residue, 2.34.63          matrix, 2.34.90.10
     alternative position, 2.33.89.18box, 2.34.21
     selecting, 2.8.8break, 2.33.6
     translate, 2.33.89.3brightness, 2.23.5.33
attenuation by occupancy, 2.33.65.25build, 2.33.7
auc enrichment, 2.36.21     atom, 2.33.7.1
auto saving log, 2.22.11     column, 2.33.7.2
autoSavePeriod, 2.18.1     conf, 2.33.7.3
automated setup, 3.13.1.7     faq, 3.8.1
avi, 2.33.110.31     from string, 2.33.7.9
axis, 5.1.8     helix, 3.10.5
axisLength, 2.19.4     how to, 3.8.1
background, 2.34.29.2     hydrogen, 2.33.7.10
     color, 2.19.9     loop, 2.33.7.7
ball, 2.33.89.2, 5.2.2     model, 2.33.7.6, 2.33.110.9
base, 5.2.1     molcart, 2.33.7.11
     pair diagram, 2.23.5.16     sequence, 2.33.7.4
basis set, 2.33.84.21, 2.33.110.17     smiles, 2.33.7.8
batch chemical processing, 3.1.2.5     string, 2.33.7.9
     docking, 3.13.1.18     tautomer, 2.33.7.5
beta, 5.2.3built-in functions, 5.5.5

     atoms, 2.33.14     2D drawings, 2.33.65.9
     contact surface, 2.33.14     SMARTS search, 2.33.35.5
     molecule, 2.33.13.1     atom annotation, 2.33.22.20
     number of bonds, 2.34.137.3     database, 3.5
     variables, 2.33.14     decomposition, 2.33.65.27, 2.33.92.2, 2.33.92.3
cage, 2.36.4     descriptors, 2.34.41, 5.7.12
calcArea, 2.36.2     distance, 2.34.44.8, 2.34.136.2, 2.34.136.3
calcBindingEnergy, 2.36.3     diversity, 3.14.6.4
calcDihedralAngle, 2.36.4     drawing, 2.23.9.14, 2.23.9.16
calcEnergyStrain, 2.36.20          quality, 2.23.9.15
calcEnsembleAver, 2.36.5     fingerprints, 2.9
calcMaps, 2.36.6     formula, 2.34.156.10
calcPairSeqIdsFromAli, 2.36.7     fragment counting, 2.34.102.2
calcPepHelicity, 2.36.9     functions, 2.27
calcProtUnfoldingEnergy, 2.36.10     keys, 2.33.65.21
calcRmsd, 2.36.11     match coordinates, 2.34.192.6
calcRoc, 2.36.21     matching, 2.33.35.4, 2.33.84.49, 2.33.84.50, 2.34.133, 2.34.155
calcSeqContent, 2.36.12     models, 2.34.99.1
calcSeqSimilarity, 2.36.8     modification, 2.33.68, 2.33.70, 2.36.37
calculate phases, 3.11.2     name, 2.34.99.6
call, 2.33.8     normalization, 2.33.70
canonical form, 2.34.45          rules, 2.33.70.4
carboxylic acid, 2.33.70.2     pattern, 2.26, 2.33.88.1
cartesian cooridnates, 2.34.192          search, 2.34.56.3
cartridge, 3.5     reaction product generation, 2.33.65.33
cavities, 2.33.92.1     search, 2.33.35.10, 2.33.88.1, 2.34.102.2
cavity, 5.3.1     similarity, 3.5
     analysis, 3.3.13     simplification, 2.34.178
ccp4 maps, 2.33.84.27     spreadsheet, 2.33.12, 2.33.84.48, 2.33.84.49, 2.33.84.50, 2.33.89.47, 2.33.110.11
cd, 2.33.89.21     structure, 2.33.110.22
cell axis vectors, 2.34.192.8          from smiles, 2.33.89.7
     specific icm commands, 5.9.2.4     substructure, 2.33.35.4
center, 2.13.1, 2.33.9          mask, 2.33.65.21
cgi programming with icm, 2.11     superposition, 2.22.7, 2.34.133, 3.15
chain breaks, 2.23.5.7, 2.23.5.8, 2.34.137.1     table, 2.25
     symbol, 2.33.89.9     text format, 5.6.11
change atom position, 2.33.89.3     topological descriptors, 2.34.40
     sequence position in multiple alignment, 2.33.72.7     view, 2.33.89.54
     unix directory, 2.33.89.21chemistry, 2.25, 2.34.27
changing local stick radii, 2.33.89.86chiral isomer generation, 2.33.30
     surface dot size, 2.23.5.54chirality, 2.20.16, 2.33.30
channel, 2.23.14.2choosing ligands, 3.13.1.2
charge, 2.23.14.4, 5.3.2chroma, 2.34.90.4
     compounds, 2.33.70.2cif, 2.33.84.48
     prediction, 2.33.89.11, 2.33.89.12circular permutation of coordinates, 2.33.69
     state, 2.33.29clamp values to range, 2.34.178
     change, 2.33.89.10clashThreshold, 2.19.5
chem formula, 2.34.156.10clashes, 2.33.65.16
chemSuper3D, 2.36.22     labels, 2.34.166
chemical, 2.23.14.7, 2.25, 2.33.35.9, 2.34.69classification, 2.34.44.6

     graphical selection, 2.33.10     preference, 2.19.10
     screen, 2.33.10     specification, 2.33.11.1
click and lock, 5.9.2.4     surface by conservation, 2.33.13.3
clipping plane, 2.23.5.9, 2.23.5.10, 2.23.5.11, 2.33.72.6, 5.3.3     table, 2.34.29.3
closer than threshold, 2.34.44.9     volume, 2.33.13.7
closest sequence, 2.34.99.3column, 5.3.5
     value, 2.34.56.1     correlation, 2.33.91.3
cluster, 2.34.154.1     function, 2.33.7.2
     center, 2.34.70.9     names, 2.33.85.1, 2.33.88.2
     centers, 2.13.1     of grobs, 2.34.109
     selection, 2.34.70.9     selection, 2.34.99
     tree, 2.34.99.5combinatorial compounds, 2.34.27
          size, 2.34.102.1     libraries, 2.33.65.33, 2.34.102.4
clustering, 2.13, 2.33.65.37, 2.33.65.38, 2.33.92.7     PDB, 2.36.92
clusters, 2.13, 2.13.1     transformations, 3.10.4
cnMethodAverage, 2.22.6combining plots, 2.33.65.32
cnWeight, 2.19.6     receptor and ligand stacks, 2.33.4.2
code, 2.34.44.6command, 2.34.99.4, 5.3.10
coil, 5.3.4     line editing, 2.2
collection, 2.12, 5.3.6          help, 2.33.45
color, 2.23.5.33, 2.33.11          options, 2.1
     accessibility, 2.33.13     word list, 3.1.5
     background, 2.33.13.2commands, 2.22.11, 5.1.1
          example, 3.2.7communication protocols, 2.31
          accessibility, 3.2.11comp, 2.34.105
          alignment, 2.33.13.3comp_matrix, 2.33.89.20, 2.33.90.16, 5.3.11
          atom contributions, 2.33.12compare, 2.18.12, 2.18.15, 2.33.14
          bfactor, 3.2.9     angles, 2.33.14.2
          charge, 3.2.12     atom, 2.33.14.1
          electrostatic potential, 2.18.5     by rmsd without superposition, 2.33.14.1
          hydrophobicity, 3.2.10     chemical tables, 2.33.35.10
          pharmacophore, 2.33.12     patch only, 2.33.14.3
          potential, 2.36.25     rmsd, 2.33.14.1
          shape depth, 2.33.13     surface, 2.33.14.3
     chemical, 2.33.12, 2.33.88.1     variables, 2.33.14.2
     choice, 2.19.9compareMethod, 2.22.7
     file, 2.37.15comparing two sarrays, 2.34.105
     grob, 2.33.13.4comparison, 2.34.70.10
          by atom selection, 2.33.13.4.3     operations, 2.14.5
               atoms, 2.23.7.1complete view, 2.34.144
          map, 2.33.13.4.4compound accessibilities, 3.14.4.1
          matrix, 2.33.13.4.2     array, 2.25
          potential, 2.33.13.4.5     property prediction, 2.33.51.2
          unique, 2.33.13.4.1compress, 2.33.15
     label, 2.33.13.5     alignment, 2.33.15.1
     map, 2.33.13.6     binary, 2.33.15.4
          by value, 2.33.23.16     conf, 2.33.15.3
     molecule, 2.33.13.1     grob, 2.33.15.2
     names, 2.34.29     in place, 2.33.15.4
     object, 2.33.11.2     objects, 2.33.15

compressed table view, 2.33.89.24          macro, 2.36.13
conditional buttons, 5.5.5     pdb, 3.8.2
     string, 2.34.156.7     to 3D, 2.33.89.8
conf, 2.33.89.61, 2.33.110.41, 2.34.160.6, 5.3.12, 5.8.9          ICM object, 2.36.86
     data, 2.34.160.6          iarray, 2.34.166
confgen, 3.17          icm-object, 2.33.18
configuration, 2.37.14          integer, 2.34.166
     file, 2.33.110.42convert2Dto3D, 2.36.85
     memory usage, 2.18.7convert3Dto3D, 2.36.86
conformation comparison, 2.22.7convertObject, 2.36.13
conformational ensemble, 2.33.7.6.2converting a chemical, 2.33.18.3
     generator, 2.33.66.1, 3.17     alignment to table, 2.34.160.2
     interpolation, 2.33.23.6     chemicals, 3.13.1.8
     stack, 2.33.110.41, 5.3.12, 5.8.9     table columns into matrix, 2.34.90.6
          compression, 2.33.15.3     to, 2.34.123
          file, 2.37.7cool, 2.36.40
     transition, 2.36.38     pictures, 2.23.5.30
conformer, 3.13.1.20cooling schedule, 2.19.46
     storage, 2.33.63.5, 2.33.94.2coordinate frame, 2.19.4, 2.33.23.4
conformers, 3.17coordinates, 2.23.14.7
connect, 2.33.16, 2.33.54copy, 2.33.19
     chains with alignments, 2.33.57     chemical image, 2.23.9.15
     molcart, 2.33.16.1     file, 2.21.26
consensus, 2.19.7     site, 2.33.89.28
     coloring, 2.19.12, 2.23.2correlation matrix, 2.34.163
     definitions, 2.23.1covalent bound count, 2.34.137.3
consensusStrength, 2.19.7     neighbors, 2.34.101.1
conservation, 2.34.122.5, 2.34.136.7covalently attached molecule, 2.34.101.1
constant, 2.5cpk, 2.19.35, 5.3.13
constants, 2.5create a covalent bond, 2.33.65.2
contact areas, 2.34.90     pharmacophore, 2.36.87
continue, 2.33.17creating a local patch object, 2.33.18.2
contour lines, 2.34.32credits, 4.5
     surfaces, 2.23.7.5crypt, 2.33.20
contouring density, 2.33.65.14crystal axis vectors, 2.34.16
contrast, 2.23.5.33     symmetry transformation, 3.10.2
conversion, 5.1.6          transformations, 2.34.176
     to real array, 2.34.168crystallographic cell, 2.33.69
convert, 2.33.18, 2.33.18.2     occupancy, 2.34.107
     3D to chemical, 2.34.27     symmetry intro, 1.4.2.4
     3D/0D to 2D, 2.33.65.9crystallography, 2.34.129
     ICM object to PDB, 2.33.96csv format, 2.33.84.44
     and reroot, 2.33.18.4csym, 1.4.2.4
     chemical 3D, 2.36.82cube, 2.23.14.2
               and optmimize geometry, 2.36.83current, 5.3.9
     comp, 2.33.18.1     map, 5.3.7
     comparison, 2.33.18.1     object, 5.3.8
     fragments, 2.33.18.2     working directory, 2.34.108
     mol, 2.33.18.3cursor action, 5.9.2.4
     object 3D and optmimize geometry, 2.36.85custom alignment color, 2.23.5.1

     interaction, 2.33.90.37     from array, 2.33.22.6
     menu, 2.32, 2.33.84.3     hydrogen, 2.33.22.11
customization, 3.1.2     label, 2.33.22.19, 2.33.22.20
     environment, 2.32          chemical, 2.33.22.20
     and paste chemicals, 2.23.9.14, 2.23.9.15     link, 2.33.22.21
cyclic temperature protocol, 2.19.46     map, 2.33.22.22
cylinder, 2.23.14.2     molcart, 2.33.22.3
cz32, 4.5     molecule, 2.33.22.13
data visualization, 2.33.65.38     object, 2.33.22.12
database, 5.4.1     parray, 2.33.22.36
     browser, 2.33.63.3          element, 2.33.22.36
     connection, 2.33.16.1     peptide bond, 2.33.22.28
     file, 3.5.1     plot, 2.33.22.4
     import, 2.33.65.26     salts, 2.33.70.3
date, 2.33.21, 2.34.156.2     selection, 2.33.22.5
     array, 2.33.21     selftether, 2.33.22.34
dcMethod, 2.22.8     sequence, 2.33.22.23
dcWeight, 2.19.8     session, 2.33.22.10
decomposition, 2.33.65.27, 2.33.92.2, 2.33.92.3     shell object, 2.33.22.1
deep learning, 2.33.53     site, 2.33.22.24
defCell, 2.24.1          alignment, 2.33.22.26
defSymGroup, 2.18.2     sstructure, 2.33.22.25
default atom colors, 2.33.89.16     stack, 2.33.22.29
     color of label, 2.19.11          object, 2.33.22.30
     parameters, 2.22.1     system, 2.33.22.9
     value, 5.8.2     table, 2.33.22.32
define axis, 3.10.3          rows, 2.33.22.32
defining space box, 2.34.21     term, 2.33.22.33
dehtml, 2.34.126.3     tether, 2.33.22.35
del, 2.33.22.9     tree, 2.33.22.36
delete, 2.33.22     variable, 2.33.22.6
     3D graphics panel, 2.33.105     views, 2.33.22
     alias, 2.33.22.2     backbone, 2.34.137.1
     array element, 2.33.22.6     restraint, 2.33.22.18
          index, 2.33.22.6deleting, 2.33.22.26
          selection, 2.33.22.1     sites by number, 2.33.22.24
     atom, 2.33.22.7delphi, 2.36.25
     bond, 2.33.22.14density correlation, 2.19.8, 3.11.3
     boundary, 2.33.22.15     fitting, 2.22.8
     chemical, 2.33.22.37     in unit cell, 2.33.65.23
          fragment, 2.33.22.37densityCutoff, 2.19.13
          selection, 2.33.22.37dependent columns, 2.33.1.1.1
     class, 2.33.22depth cueing, 2.33.13.7, 5.4.2
     column table, 2.33.22.16depth-cueing, 2.19.17
     conf, 2.33.22.17desolvation, 2.22.25
     directory, 2.33.22.8detecting bad covalent geometry, 2.33.90.12
     disulfide bond, 2.33.22.27     proximity, 2.34.44.9
     drestraint, 2.33.22.18dialog generation, 2.34.11
     element, 2.33.22.31     in html documents, 2.33.44
     file, 2.33.22.9          tables, 2.33.44

dielConst, 2.19.14     restraints, 2.33.89.22
dielConstExtern, 2.19.15distances, 2.34.102.3
dielectric constant, 2.19.14distribution, 1.3
diff, 2.34.105     comparison, 2.34.136
dihedral, 2.36.4disulfide bond, 5.4.5
     angle, 2.33.65.19diverse subset, 3.14.6.4
          calculation, 3.3.10dividing chemical into individual molecules, 2.34.154.4
directory, 2.33.22.8, 2.33.65.5, 2.34.135dna to protein sequence translation, 2.34.175.1
display, 2.33.23     translate, 2.34.175.1
     GUI window, 2.33.23.26dockBatch, 3.13.1.7
     box, 2.33.23.7dockScan, 3.13.1.18
     clash, 2.19.5, 2.33.23.8docking, 2.36.89
     contact, 2.33.65.16     intro, 3.13.1.5
     drestraint, 2.33.23.9     result viewing, 2.36.28
     field, 2.23.5.3     simple models, 3.14.3
     from script, 2.33.23.3     timing, 3.13.1.3
     gradient, 2.33.23.10     with template, 3.13.1.22
     grob, 2.33.23.11docksub, 3.13.1.19
          label, 2.33.23.12docksyb.icm, 3.13.1.19
     gui, 2.33.23.26documents, 5.5.8
     hbond, 2.33.23.13dollar separated file, 2.33.84.44
     label, 2.33.23.15dominant color, 2.34.29.2
     map, 2.23.5.13, 2.33.23.16donor, 3.6.1
     model, 2.33.23.1     plot intro, 1.4.3.2
     new, 2.33.23.2dots, 2.33.78
     off-screen, 2.33.23.3dotted surface, 2.23.5.56
     offscreen, 2.33.23.3double click action, 5.9.2.4
     origin, 2.33.23.4drestraint, 2.33.90.18, 5.4.6
     ribbon, 2.33.23.18     generate from structure, 2.33.65.7
     rotate, 2.33.23.5     global weight, 2.19.6
     site, 2.33.23.19     set, 2.33.89.22
     skin, 2.33.23.20     type, 5.4.7
     slide, 2.33.23.21drop, 2.19.16
     stack, 2.33.23.6drug, 2.12
     string, 2.33.23.22ds3D, 2.36.31
     surface, 2.33.23.20dsCellBox, 2.36.15
          area, 2.23.5.3dsChem, 2.36.17
     tethers, 2.33.23.23dsCustom, 2.36.18
     trajectory, 2.33.23.17dsPocket, 2.36.28
     volume, 2.33.23.24dsPropertySkin, 2.36.19
     window, 2.3, 2.33.23.25dsPrositePdb, 2.36.24
distance, 2.23.5.24, 2.34.41, 5.4.3dsRebel, 2.18.5, 2.23.14.6, 2.36.25
     averaging, 2.22.6dsSeqPdbOutput, 2.36.26
     contact-based, 2.34.23, 2.34.23.1dsSkinLabel, 2.36.27
     geometry, 5.4.4dsStackConf, 2.36.29
     matrix, 2.34.160.5, 2.36.7dsVarLabels, 2.36.30
          between stack conformations, 2.34.90.11dsXyz, 2.36.32
     restraint, 5.4.6dump database, 2.33.110.7
          file, 2.37.9dynamic gui, 5.5.5
          type file, 2.37.8ecepp, 5.5.1

     files, 2.23.14.1evalSidechainFlex, 2.36.90
eigen value factorization, 2.34.45evol tree intro, 1.4.3.5
eigendecomposition of a matrix, 2.34.45evolutionary tree intro, 1.4.3.5
eigenvalues, 2.34.45exact, 2.33.35.9, 2.33.35.10
eigenvectors, 2.34.45     match, 2.34.126.1
electro intro, 1.4.2.9example scripts, 3.14
electroMethod, 2.22.9excel, 2.33.84.44, 2.33.110.10
     density, 2.23.7.5, 2.33.89.36, 2.33.90.21, 2.36.42, 2.36.43exit, 2.33.34
          around selection, 2.19.25exitSeslogStyle, 2.22.11
          map generation, 2.19.1expanding substructure match, 2.33.89.70
          maps, 2.23.14.1export, 2.33.110.7
electrostatic boundary matrix, 2.34.90.10     animation, 2.33.110.31
     coloring, 2.23.14.6     pdb, 2.23.14.14
     isopotential surfaces, 2.33.65.13exporting sdf, 2.33.110.11
     potential, 2.33.13.4.5expression shortcuts, 2.10.1.2
     solvation, 3.7.2     tags, 2.24.9
     surface, 2.36.25     comparison, 2.14.5
     troubleshooting, 5.7.13     arithmetics, 2.14.2
electrostatics, 2.23.14.6     assignment, 2.14.1
     intro, 1.4.2.9     comparison, 2.14.5
elements, 2.23.9.16     logical, 2.14.3
ellipsoid, 2.34.163extending to bonded hydrogens, 2.34.137.6
elseif, 2.33.25               terminal atoms, 2.34.137.6
empty model, 2.34.109external process, 2.33.65.1
enamine, 3.19extracting from Markush, 2.33.55
endfor, 2.33.26     icm script arguments, 2.34.59
endif, 2.33.27     stack from object, 2.33.63.5
endmacro, 2.33.28ez25, 3.7
endwhile, 2.33.33factor, 5.8.13
energetics, 3.7false negatives, 2.34.136.4
     function, 2.23.14.3family, 2.33.89.38.1
     profile, 2.36.84faq, 1.3
     terms, 2.17     cheminformatics, 3.14.6
ensemble, 2.33.63.1, 2.33.94.1     chemsuper, 3.14.5
     average, 3.7.5     mac gui preferences, 3.14.6.2
entropy of alignment, 2.34.136.7     molcart dump, 3.14.6.3
     atom, 2.33.18.4          query, 3.14.6.1
enumerate, 2.33.29, 2.33.30, 2.33.31, 2.33.32     multiple chem overlay, 3.14.5.1
     charge, 2.33.29     residue table, 3.14.4.1
     chiral, 2.33.30fast Fourier transform, 2.33.65.24
     library, 2.33.32     sequence search, 2.33.35.3
     tautomer, 2.33.31fasta, 2.23.12.15, 5.5.2
enumeration, 2.34.27     format, 2.33.110.1
eps files, 2.21.23feature table, 5.8.6.1
equipotential surface, 2.34.32     in sequences, 2.33.89.26
error SOAP services, 2.34.49ffMethod, 2.22.12
     ignoring, 2.21.25field, 2.33.89.35
error/warning bits cleanup, 2.33.10     name, 2.34.99.2
errorAction, 2.22.10file, 2.33.110.24
     vrestraint vs_var, 2.33.89.82     exists, 2.34.50

     length, 2.34.55     size, 2.33.89.38.1, 2.37.14
     object origin, 2.34.55     sizes, 3.14.6.2
     permissions, 2.34.55     specification, 2.33.89.38.1
     time modified, 2.34.55for, 2.33.37
     type, 2.34.55fork, 2.33.38, 2.34.70.1
files, 2.37formal charge, 2.23.5.20, 2.33.89.12, 5.3.2
filling volume, 2.23.5.11formatdb, 2.33.110.25
filter, 2.33.35.10, 2.33.63.3fprintf, 2.33.39
     functions, 5.5.4fractional coordinates, 2.34.192.4
filtering table rows, 5.5.4     to abs coordinates, 2.34.16
find, 2.33.35fragment, 3.13.1.23
     alignment, 2.33.35.1fragmented molecule, 2.33.18.2
     and replace a chemical pattern, 2.33.70.1frame, 2.33.94, 2.33.110.31
               chemical fragment, 2.33.70fullscreen, 2.33.89.85
     chemical, 2.33.35.5function, 2.33.40, 2.33.64
          pattern, 2.33.70     columns, 2.33.1.1.1
          substructure, 2.34.70.2functions, 5.1.1
     database, 2.19.2, 2.33.35.2     selecting in objects, 2.8.10
          fast, 2.33.35.3gamess, 5.5.6
     family of commands, 2.33.35     expansion, 2.34.146.4
     in sarray, 2.34.70.8gapExtension, 2.19.18
     molcart, 2.33.35.9, 3.5gapFunction, 2.24.3
     molecule, 2.33.35.4gapOpen, 2.19.19
     motifs, 2.24.9gaussian averaging, 2.34.146.2
     pattern, 2.33.35.8gcMethod, 2.22.13
     pdb, 2.33.35.6genbank, 2.23.12.15
     pharmacophore, 2.33.35.11generalized arrays, 5.1.6
     prosite, 2.33.35.7generate intermediate conformers, 2.36.38
     scaffold, 2.34.179generating movie images, 3.9.2.1
     table, 2.33.35.10genomics, 1.4.3.1
findFuncMin, 2.36.33, 2.36.34     clustering, 2.33.43.2
findFuncZero, 2.36.35     intro, 1.4.3.1
findSymNeighbors, 2.36.16geometry optimization, 2.33.66.1
find_related_sequences, 2.36.33     started, 1.7
finding long covalent bonds, 2.34.137.1getting data from outside, 2.31
fingerprint, 2.34.41     started, 1.7
fingerprints, 2.9giga, 3.18, 3.19
     to density, 2.22.8     sized, 3.18, 3.19
fix, 2.33.36giga-sized, 3.18, 3.19
fixed branches, 2.34.137.2ginger, 3.13.1.20
flattening 3D molecule, 2.36.17global, 2.33.41
flexible superimpose, 2.36.50glossary, 5
flow control, 2.15go, 2.34.44.6
fog, 2.19.17, 2.33.13.7, 2.33.23.24, 5.4.2goto, 2.33.42
     color, 2.19.17     term, 2.19.20, 2.33.89.73
fogStart, 2.19.17gpWeights, 2.19.20
fold search, 5.8.4gpu, 3.13.1.21
foldbank.db, 2.37.3graph matching, 2.34.133
folding procedure, 3.14.1graphical box, 2.33.23.7
font, 2.33.58.1     row selection, 2.34.70.5

graphics, 2.19.9, 2.33.89.4, 2.34.188, 3.2, 5.3.3     how to, 3.3.4
     card, 2.23.5.52header, 2.33.1.1
     controls, 2.3, 2.37.15, 5.4.2helical axis, 2.36.36
     exists, 2.34.50     cylinders, 2.23.5.42
     intro, 1.4.1, 1.4.1.4helicity, 3.7.6
     learning, 3.2.1     content calculation, 3.7.6
     attributes, 2.19.4help, 2.33.45, 2.33.45.1, 2.33.45.2
     fogStart, 2.19.17     browser, 2.33.45.1
     view vector, 2.33.89.80     commands, 2.33.45.3
graphviz, 2.34.160.7     functions, 2.33.45.4
greedy matching, 2.10.1.4     getting, 3.1.1
grid energy, 2.33.90.21     word, 2.33.45.2
     potentials, 2.33.65.25     getting, 3.1.1
grob, 2.33.54, 5.5.3heterogenous environment, 2.23.14.2
     coloring, 2.33.13hidden blocks, 5.1.1.1
     files, 2.37.10     display, 2.33.23.3
     inside-out flip, 2.33.89.42     hydrogens, 2.23.5.32
     normal directions, 2.33.89.42     stack in object, 2.33.94.2
     vertex, 2.23.5.21hierarchical, 2.13
     translate, 2.33.103highEnergyAction, 2.22.14
group, 2.33.43his-tags, 2.34.180
     by column, 2.33.43.4histogram, 2.33.65.32
     column, 2.33.43.4     2D, 2.34.90
     rename of table columns, 2.33.85.1history, 2.33.46, 2.33.110.40
     replacement, 2.33.68     delete, 2.33.22.10
     select of table columns, 2.33.88.2     of ICM, 1.2
     sequence, 2.33.43.1hitlist, 3.13.1.17
          unique, 2.33.43.2homodel, 2.36.41
     table, 2.33.43.3homology modeling, 1.4.2.2, 2.33.7.6, 2.33.89.68, 2.33.89.69, 2.35.1, 3.14.4
grouping table by a column, 2.33.89.24          faq, 3.14.4
gui, 2.33.44, 5.9.2.4          intro, 1.4.2.2
     exists, 2.34.50     output, 2.33.7.6.3
     functions, 5.5.5     steps, 2.33.7.6.1
     panels, 2.33.105     to export a molcart table, 3.14.6.3
     programming, 2.32, 2.33.44, 2.33.89.24html, 2.11, 2.33.44, 2.34.99.4, 5.5.8
gvim text editor, 5.8.2     document order, 2.33.89.40
gzip files, 2.33.15.4     tag removal, 2.34.126.3
hash, 2.12, 5.3.6html-formatted text, 5.5.8
     table, 5.3.6html5, 2.11
haze, 2.19.17hue, 2.34.90.4
hb, 2.19.21hydration, 2.23.14.2, 2.34.7
hbCutoff, 2.19.21     parameters, 2.37.13
hbond, 2.23.5.25, 2.23.5.26, 2.33.22.6, 5.5.7hydrogen bond, 2.23.5.25, 2.23.5.26, 2.33.65.17, 5.5.7
     color, 2.33.23.14     bonding parameters, 2.37.12
     display, 2.23.5.27, 2.23.5.28          cutoff, 2.19.21
     energy, 2.33.23.14     bonds, 2.34.102.3
     list, 2.34.160.10     display, 2.23.5.32
     show, 2.33.90.23     placement, 2.33.89.25
hbondMinStrength, 2.23.5.25hydrophobicity profile, 3.3.12
     faq, 3.3.4iSee, 5.8.14

i_out, 2.18.3     iar, 2.37.35
iarray, 2.33.22.6, 2.34.56.1, 2.34.66.2, 2.34.70.8, 5.6.1     lps, 2.33.7.6.2
     making, 2.34.66.1     map, 2.37.16
icb files, 5.8.14     mat, 2.37.37
     GUI, 2.33.89.40     ob, 2.37.18
     algorithms, 4.3     pdb, 2.37.28
     application refs, 4.4     prf, 2.37.34
          literature, 4.3     rar, 2.37.38
     archive, 2.33.84.2     res, 2.37.20
     arguments, 2.34.59     rs, 2.37.23
     binary, 2.34.108     rst, 2.37.22
     branching, 2.15.2     sar, 2.37.36
     commands, 2.33     se, 2.37.30
     controls, 2.15     seq, 2.37.29
     flags, 2.1     tab, 2.37.25
     functions, 2.34     tot, 2.37.26
     graphics, 3.2     trj, 2.37.17
     history, 1.2     var, 2.37.21
     jumps, 2.15.3     vwt, 2.37.27
     learning, 3.1.4icmCavityFinder, 2.36.14
     loops, 2.15.1icmMacroShape, 2.36.88
     macros, 2.36icmPmfProfile, 2.36.23
     main refs, 4.2icmPocketFinder, 2.36.89
     menus, 2.23.10.1icmscript, 2.33.84.4
     method literature, 4.4     arguments, 2.34.59
     molecules, 2.16if, 2.33.47
     object file, 2.37.18ignoring swiss secondary structure, 2.24.10
     preferences, 2.22.1illegal smiles, 2.34.70.2
     session, 2.22.11image, 3.2.6
     shell, 3.1     annotation, 3.2.5
          functions, 2.35     center, 3.2.8
     support, 1.3     format, 5.9.3
     table, 2.23     high quality, 3.2.2
     ali, 2.37.31     parray, 5.7.3.3
     all, 2.37.32     resolution, 3.2.2
     bbt, 2.37.5     rotation, 3.2.3
     bst, 2.37.6implicit continuous solvation, 2.37.13
     cfg, 2.37.14     solvation, 2.33.89.72
     clr, 2.37.15imposing tether, 2.33.89.68, 2.33.89.69
     cmp, 2.37.33     place, 2.14.4
     cn, 2.37.9          ops, 2.14.4
     cnf, 2.37.7incidence, 2.34.90.13
     cnt, 2.37.8increasing the number of shell variables, 2.37.14
     cod, 2.37.4increment charge, 2.33.89.10
     col, 2.37.24index expressions, 2.6
     gro, 2.37.10     in array, 2.34.70.4
     gui, 2.32     substring, 2.34.70.3
     hbt, 2.37.12     table, 2.33.110.24
     hdt, 2.37.13          entry, 2.34.135.1
     htm, 2.37.11          sdf-file path, 2.34.108

          selected table rows, 2.34.70.5l_minRedraw, 2.20.12
infinity, 2.34.168l_neutralAcids, 2.20.13
info, 2.33.48l_out, 2.20.14
     molcart, 2.33.48.1l_print, 2.20.15
inner join, 2.33.50l_racemicMC, 2.20.16
insert rows, 2.33.1.4l_readMolArom, 2.20.17
integer, 5.6.2l_showAccessibility, 2.20.18
     array, 2.34.66, 5.6.1l_showMC, 2.20.19
     output, 2.18.4l_showMinSteps, 2.20.20
     shell variables, 2.18l_showResCodeInSelection, 2.20.21
intensity, 2.34.90.4l_showSites, 2.20.23
interaction cutoff, 2.20.27l_showSpecialChar, 2.20.22
     lists, 2.20.27, 2.23.14.3l_showSstructure, 2.20.24
interactive docking, 1.4.2.8l_showTerms, 2.20.26
interatomic distance, 2.19.10, 2.33.65.16, 2.34.151l_showWater, 2.20.25
     potential, 2.33.89.51, 2.33.90.37l_updateLists, 2.20.27
interface comparison, 2.33.14.3l_warn, 2.20.28
     residues, 3.3.5l_wrapLine, 2.20.29
     torsions, 3.3.7l_writeStartObjMC, 2.20.30
     view, 2.36.28l_xrUseHydrogen, 2.20.31
intermolecular bond, 2.33.72.3label, 2.33.23.22, 5.6.3
internal coordinate file, 2.37.21     fonts, 2.37.15
     coordinates, 2.8.9large text, 2.33.84.40
     positional restraints, 5.9.4latent, 2.34.102.6
interplanar angle, 2.36.4learn, 2.33.51, 2.33.53, 2.34.109
interpolate, 2.34.29.1     ann, 2.33.53
interpolation, 2.34.29.1     atom, 2.33.51.1
interruptAction, 2.22.15     chemical, 2.33.51.2
inverting array order, 2.34.66.2, 2.34.122.2left join, 2.33.50
italic, 2.33.89.38.1     triangle of a matrix, 2.34.90.3
iterative overlay, 2.33.97library to replacement groups, 2.33.65.27, 2.33.92.2, 2.33.92.3
     superposition, 2.23.14, 2.33.98ligand based screening, 3.15
javascript, 2.11     binding, 2.36.28
join, 2.33.50     docking, 3.13, 3.13.1
     tables, 2.33.50          intro, 1.4.2.6
keep, 2.33.49     editing, 1.4.2.8
kernel models quality, 2.34.136.4     editor, 2.36.37
     mapping, 2.37.15     fit, 3.13
kmz, 5.5.3     view, 2.23.5.31
l_antiAlias, 2.20.1ligand-based, 3.19
l_autoLink, 2.20.2light, 2.23.5.34
l_bpmc, 2.20.3lightness, 2.34.90.4
l_breakRibbon, 2.20.4limits, 2.37.14
l_bufferedOutput, 2.20.5line thickness, 2.23.12.5
l_bug, 2.20.6          in 2D chemicals, 2.23.9.14
l_caseSensitivity, 2.20.7lineWidth, 2.19.22
l_commands, 2.20.8linear chemical notation, 2.26
l_confirm, 2.20.9     regression, 2.34.84
l_easyRotate, 2.20.10     grob, 2.33.54
l_info, 2.20.11     group, 2.33.55

     ms2ali, 2.33.57make, 2.33.65
     sequences to 3D objects, 2.33.57     3d label, 2.33.65.15
     to alignment, 2.33.57     angle, 2.33.65.18
     variable, 2.33.56     background, 2.33.65.1
     variables, 2.33.56     blast index, 2.33.110.25
linked alignment, 2.34.99     bond, 2.33.65.2
     sequence, 2.34.99          chain, 2.33.65.3
linux shell, 2.33.99, 5.10.2          multi, 2.33.65.3
list, 2.33.58     boundary, 2.33.65.4
     binary, 2.33.59     directory, 2.33.65.5
     database, 2.33.60     distance, 2.33.65.16
     directory, 2.33.61     disulfide bond, 2.33.65.6
     font, 2.33.58.1     drestraint, 2.33.65.7
     html documents, 2.34.99     factor, 2.33.65.8
     molcart, 2.33.62     flat, 2.33.65.9
          database, 2.33.62          chem_array, 2.33.65.9
     of files, 2.34.135     grob, 2.36.36
     updates, 2.33.66          from image, 2.33.65.11
listUpdateThreshold, 2.19.23               matrix, 2.33.65.12
literature, 4.1          image, 2.33.65.11
load, 2.33.63          map, 2.33.65.10
     conf, 2.33.63.1          matrix, 2.33.65.12
     frame, 2.33.63.2          potential, 2.33.65.13
     molcart, 2.33.63.3          skin, 2.33.65.14
     object, 2.33.63.6     hbond, 2.33.65.17
     solution, 2.33.63.4     image, 2.33.65.20
     stack object, 2.33.63.5     index fasta, 2.33.84.24, 2.33.110.24
loadEDS, 2.36.42     key, 2.33.65.21
loadEDSweb, 2.36.43     map, 2.33.65.22
local, 3.5.1          cell, 2.33.65.23
logarithm, 2.34.85          factor, 2.33.65.24
logical, 5.6.4          potential, 2.33.65.25
     operations, 2.14.3          xray, 2.33.65.31
     variables, 2.20     molcart, 2.33.65.26
logical_ops, 2.14.3     molsar, 2.33.65.27
logicals, 2.20     pca, 2.33.65.29
long axes, 2.34.163     peptide bond, 2.33.65.30
loop database rebuilding, 2.33.110.28     plot, 2.33.65.32
     interrupt, 2.19.47     reaction, 2.33.65.33
     library, 2.33.7.6.2     sequence, 2.33.65.35, 2.33.65.36
     modeling, 1.4.2.3          alignment, 2.33.65.34
          intro, 1.4.2.3          from alignment, 2.33.65.34
     search, 2.33.7.6.2          random, 2.33.65.36
     resolution shape, 2.36.88     torsion, 2.33.65.19
lower case, 2.34.167     tree, 2.33.65.37
ma29, 3.11          object, 2.33.65.38
macro, 2.33.64, 5.6.5     unique, 2.33.65.39
macro_def, 5.6.5makeAxisArrow, 2.36.36
main ICM references, 4.2makeIndexChemDb, 2.36.44
     concepts, 3.10.1makeIndexSwiss, 2.36.45

makePharma, 2.36.87     arrays to table, 2.33.43.3
makeSimpleDockObj, 2.36.47     continuation lines, 2.33.84.39
makeSimpleModel, 2.36.48     objects, 2.33.72.2
making predictive models, 2.33.51     parts of molecule, 2.33.72.3
manual style, 1.5     pdb, 3.4.4
map, 2.19.25, 2.23.5.13, 2.23.6.1, 5.6.6     sarray into string, 2.34.158
     aa property to sequence, 2.34.122.1     stacks, 3.7.7
     averaging, 2.34.146.5     tables, 2.33.4.3, 2.33.50
     calculation, 2.33.65.24merge2, 3.8.7
     conversion, 2.33.65.31mergePdb, 2.36.92
     file, 2.37.16     several chemical, 2.34.158.1
     fitting, 2.22.8merging into one molecule, 2.33.72.3
     format, 5.6.6mesh, 2.34.109, 2.34.189
     mean value, 2.34.94     point radius, 2.23.5.21
     min value, 2.34.95     score, 3.13.1.12
     name, 2.34.86mfMethod, 2.22.16
     operations, 5.6.6mfWeight, 2.19.30
     transformations, 2.34.146.5mimel, 5.6.8
     trimming, 2.34.22mimelDepth, 2.19.31
     value sigma, 2.34.133mimelMolDensity, 2.19.32
          on atoms, 2.33.89.36minNumGrad, 2.33.66
     contouring, 2.33.65.14minTetherWindow, 2.18.8
mapAtomMargin, 2.19.25minimization exit criteria, 2.33.66
mapSigmaLevel, 2.19.24minimize, 2.18.10, 2.33.66
mapping chemical equivalences, 2.34.70     cartesian, 2.33.66.1
     properties to sequence, 2.34.122.4     loop, 2.33.66.2
     and factors, 3.11     stack, 2.33.66.3
margin, 2.23.6.1     tether, 2.18.8, 2.33.66.4
mass-spectrometry functions, 2.33.30, 2.33.31, 2.33.32     drop, 2.19.16
matching chemicals, 2.34.70.2minimizeMethod, 2.22.17
     hydrogens, 2.33.89.70missing bonds, 2.33.72.3
matrix, 5.6.7     loop, 2.23.5.7, 2.23.5.8
     derivatives, 2.34.80     residues, 2.34.54.1
     new, 2.34.90.1     triangles, 2.34.189
     plot, 2.34.32mkUniqPdbSequences, 2.36.49
     map value, 2.34.91mlr, 2.33.52
maxColorPotential, 2.18.5, 2.36.25mm26, 3.8
maxMemory, 2.18.7mmcif, 5.6.10
     movie, 3.9.2mmff, 5.6.9
mcBell, 2.19.26     type, 2.34.182
mcJump, 2.19.27     show atom types, 2.33.90.11
mcShake, 2.19.28mnSolutions, 2.18.9
mcStep, 2.19.29mncalls, 2.18.10
mean force, 2.33.89.51, 2.33.90.37mncallsMC, 2.18.11
median value, 2.34.93mnconf, 2.18.12
membrane, 2.23.14.2mnhighEnergy, 2.18.13
memorizing positions, 3.2.4mnreject, 2.18.14
menu, 2.33.67mnvisits, 2.18.15
     script, 3.1.3model reliability, 2.36.23
merge PDB, 2.36.92modify, 2.33.68

     chem, 2.33.70move, 2.33.72
          charge, 2.33.70.2     alignment sequence, 2.33.72.7
          delete salt, 2.33.70.3     atoms, 2.33.89.3
          normalize, 2.33.70.4     bonding, 2.33.72.3
     chemical column, 2.33.70.3     column, 2.33.72.5
          find replace, 2.33.70.1     element, 2.33.72.4
     molcart, 2.33.70.5     file, 2.21.28, 2.33.85.3
     rotate, 2.33.69     fragments together, 2.33.72.3
modifyGroupSmiles, 2.36.37     ligand out, 2.33.92.6
modules, 1.4.4     molecule, 2.33.72.1
mol, 2.33.84.49, 2.33.84.50, 2.33.110.11, 2.33.110.24, 5.6.11     ms_molecule, 2.33.72.1
     file, 2.34.156.3     multiple molecules, 2.33.72.2
     to icm, 2.33.18.3     object, 2.33.72.2
     translation, 3.2.4     plane, 2.33.72.6
mol-file to chem-table element, 2.34.109     sequence, 2.33.72.7
mol-format, 2.23.14.7     table column, 2.33.72.5
mol2, 5.6.12movie, 2.33.94.3
molcart, 2.33.16.1, 3.5     images by frame, 3.9.2.2
     connection options, 3.5.2     molecular simulation, 3.9.2
molecular, 2.34.58, 5.7.3.1     rotate view, 3.9.1
     arrays, 5.7.3     zooming, 3.9.1
     manipulations, 3.8moving grobs with molecules or objects, 2.33.54
     modifications, 3.8.5     selection to another object, 2.34.137.8
     object, 5.7.1mpeg, 2.33.110.31
     objects, 2.16ms_, 2.8.6
     surface, 2.33.90.9, 5.8.7multi center drestraint, 2.22.6
     views, 1.4.1.1multi-part molecule, 2.33.18.2
     volume, 2.34.114multicore, 2.34.70.1
molecule, 2.7, 2.33.54multiline input, 2.33.84.5
     create, 3.8.4multiple NMR models, 2.23.14.5
     properties, 2.33.89.34     alignment, 2.33.3.3
     rotation, 3.2.3          to pairwise similarities, 2.36.7
     translation, 3.2.3, 3.2.4     conformation storage, 5.8.9
     create, 1.7.2     conformations, 2.33.63.1, 2.33.94.1
     intro, 1.7.2, 2.7     linear regression, 2.33.52
     sort/reorder, 2.33.91.5     mol as text, 2.34.156.3
     selecting, 2.8.6     object file, 2.33.84.2
molt, 3.5.1     sequence alignment intro, 1.4.3.4
monte carlo, 2.33.71     smiles file format, 2.33.84.46
montecarlo, 2.18.11, 2.18.13, 2.18.14, 2.18.15, 2.18.19, 2.22.7, 2.33.71multiprocessor, 2.33.38
     local, 2.18.16mutate residue, 2.33.68
     trajectory, 2.33.23.17mutating residue, 3.8.5
moprphing, 2.36.38mute, 5.6.15
more, 5.6.13mysql, 2.33.16.1
morph, 2.33.23.6nLocalDeformVar, 2.18.16
     to tether target, 2.36.38nProc, 2.18.18
morph2tz, 2.36.38nSsearchStep, 2.18.17
morphing, 2.33.23.6, 2.33.89.68, 2.33.89.69, 2.33.94.3name, 2.34.79
mouse controls, 2.3     atom fields, 2.33.89.34
     file, 2.33.110.31naming compounds, 2.33.89.47

neato, 2.34.160.7optimal chemical superposition, 3.14.5.1
neighbor joining, 2.33.65.38optimization, 2.33.71
neighbors, 2.34.151     Hbond, 2.36.91
nested script, 5.8.2     hydrogen bond, 2.36.91
neural network, 2.33.53optimizeHbonds, 2.36.91
     real array, 2.34.122or, 2.14.3
nice, 2.36.39order, 2.33.3.1, 2.33.72.7
     image, 3.2.2original sequence names, 2.23.12.15
non-redundant, 3.4.3os_, 2.8.5
normal distribution, 2.34.121other variables, 2.24
normalize chemicals, 2.33.70.4out-of density atoms, 2.33.90.21
     defined, 2.34.168output, 2.18.3
nota, 1.5outside penalty, 2.23.6.1
notational conventions, 1.5overlap, 2.34.70.10
nproc, 2.33.38     by atom pairs, 2.33.97
nucleotides, 2.21.24          chemical substructure, 2.36.22
number, 2.18.18overview, 1.4
     of dots, 2.23.5.55pK shift, 3.7.3
          elements, 2.34.102pKa, 2.33.22.20, 2.33.89.11, 2.33.89.12
          hydrogen bonds, 2.33.90.23     model, 2.33.89.12
          molecules in objects, 2.34.137.4packing density, 3.3.8
          occurrences, 2.34.102pair-distances, 2.33.22.6
          residues in molecules, 2.34.137.4pairdistance parray, 2.23.5.24
          van der Waals contacts, 2.33.90.13pairwise interactions, 2.33.89.51
     transfer from sequence, 2.33.3.2panel layout, 2.23.8.6
nvis, 2.34.66.6paragraphs, 2.33.110.24
object, 2.33.13.1, 2.33.54, 5.7.1parallel, 2.18.18
     in table, 2.34.109     computing, 2.34.70.1
     parray, 5.7.3.1     processing, 2.33.38
     properties, 2.33.89.34parallelization, 2.34.70.1
     stack, 5.8.9parameter list file, 3.14.6.2
     to chemarray, 2.34.27parray, 2.33.22.6, 5.7.3
     user fields, 2.34.54.1parrayTo3D, 2.36.83
     assign comment, 2.33.89.17parrayToMol, 2.36.82
     source file, 2.34.55parse SOAP message, 2.34.186
     translate, 2.33.103parsing, 2.34.89
     merge, 3.8.6     web pages, 2.33.84.47
     selecting, 2.8.5partial least squares, 2.33.51
obsolete, 2.19.54     slide display, 2.33.23.21
occlusion shading, 2.33.13     sum, 2.34.77
octanol transfer, 2.34.114passing arguments, 5.8.2
off, 2.33.84.22     by reference, 2.33.64
     format, 5.5.3pattern, 5.7.4
oligonucleotide melting, 2.34.164     search, 2.33.35.2
on-line help, 2.33.45.1, 2.33.45.2pause, 2.33.73
     third, 2.34.37pdb, 5.6.10, 5.7.6
only, 5.7.2     file creation time, 2.34.38
ontology, 2.34.44.6     files, 2.37.28
openGL window, 2.33.105     format, 2.33.84.48
operating system, 2.33.22.9, 2.33.99, 2.34.188, 5.10.2     merge, 3.4.4

pdbDirStyle, 2.22.18pocket, 2.36.28, 2.36.89, 3.13.1.1
peptide, 5.7.7point coordinates, 2.34.192.1
     docking, 3.12.5     size, 2.23.5.21
     folding, 1.4.2.1pointer array, 5.7.3
          intro, 1.4.2.1polar hydrogens, 2.23.5.32
personal gui controls, 3.1.2     surface area, 2.34.114
     setup, 3.1.2polarization charge, 3.7.2, 5.7.13
ph30, 3.12positional constraint, 2.23.14.12
ph4, 5.7.8postscript, 2.21.23
     object faq, 3.6.1potential surface, 2.23.14.6
pharmacophore, 2.33.12, 3.5, 5.7.8          coloring, 5.7.13
     faq, 3.6pov-ray, 2.33.110.38
     grid type definitions, 2.33.89.73pow, 2.34.37
     object, 3.6.1precision, 2.34.136.4
     objects, 3.6predict, 2.33.76
pharmacophores, 3.6predictSeq, 2.36.61
     psi plot, 2.36.58prediction model, 2.34.84
pipe, 2.33.84.43     quality, 2.34.136
placeLigand, 2.36.50     score, 2.34.136
planar angle, 2.33.65.18predictive models, 2.33.51.2
plot, 2.33.74preference, 2.22
     3D 2Dfunction, 3.12.3     system, 2.22.1
          shape, 3.12.4preferences, 3.1.2.3
     area, 2.33.75prepSwiss, 2.36.62
     grid line width, 2.23.12.5previous atom, 2.34.101.1
     histogram, 3.12.2principal axes, 2.34.163
     how to, 3.12     component analysis, 3.3.9
     simple, 3.12.1     inertia moments, 2.34.88
plot2DSeq, 2.36.51print, 2.33.77
plotBestEnergies, 2.36.54     bar, 2.33.78
plotCluster, 2.36.56     image, 2.33.80
plotFlexibility, 2.36.55     to string, 2.33.93
plotMatrix, 2.36.57printMatrix, 2.36.63
plotRama, 2.36.58printPostScript, 2.36.64
plotRose, 2.36.59printTorsions, 2.36.65
plotSeqDotMatrix, 2.36.52printf, 2.33.79
plotSeqDotMatrix2, 2.36.53problem, 3.14.6.2
plotSeqProperty, 2.36.60processors, 2.18.18
     3d, 1.4.3.7profile, 5.7.9
plotting van der Waals, 3.7.1program overview, 1.4
          faq, 3.7.1progress bar, 2.33.78
pls, 2.33.51progression, 2.33.78
     column contributions, 2.34.160.8, 2.34.160.9project setup, 3.13.1.6
     model, 2.34.160.8, 2.34.160.9projected alignment, 2.34.99.3
     weights, 2.34.160.8, 2.34.160.9projecting surface charge, 3.7.2
pmf, 2.22.16property, 2.33.89.52, 2.33.89.53, 2.33.89.54
     residue profile, 2.36.23     grids, 2.19.20
pmf-file, 2.37.19     map, 2.33.89.73
pmffile, 2.37.19     superposition, 2.33.89.73
png, 2.33.110.22, 2.33.110.36, 5.7.5prosite, 5.7.10

protac, 3.16     conf, 2.33.84.15
protein docking, 2.34.192.3     csd, 2.33.84.16
          intro, 1.4.2.5     csv, 2.33.84.44
     engineering, 2.24.9     database, 2.33.84.17
     grid docking, 3.14.2     drestraint, 2.33.84.18
     health, 2.36.58          type, 2.33.84.19
     topology, 2.23.5.42     entries from database, 2.33.84.8
protonation states table, 2.34.160.11     factor, 2.33.84.20
psa, 5.7.12     file by chunk, 2.33.84.40
purple box, 2.34.21     from file, 2.33.84.1
qstat, 3.13.1.19          string, 2.33.84.5
qsub, 3.13.1.19     fromstring, 2.33.84.5
quadratic equation, 2.34.147     ftp http, 2.33.84.9
quantum mechanics, 2.33.84.21, 2.33.110.17     gamess, 2.33.84.21
qubic equation, 2.34.148     grob, 2.33.84.22
query, 3.14.6.1     gui, 2.33.84.3
     molcart, 2.33.81     html, 2.33.84.4
question mark operator, 2.34.156.7          file, 2.33.84.4
quit, 2.33.82     iarray, 2.33.84.23
     property transfer via alignment, 2.34.122.3     index, 2.33.84.24
r_2out, 2.19.34          table, 2.33.84.8
r_out, 2.19.33     json, 2.33.84.57
radii.electrostatic, 2.34.120     library, 2.33.84.25
     van der Waals, 2.34.120          mmff, 2.33.84.26
rainbow, 2.34.29.1     librarymmff, 2.33.84.26
ramachandran faq, 3.3.3     map, 2.33.84.27
     how to, 3.3.3     matrix, 2.33.84.28
random array, 2.34.121     menu file, 2.33.84.3
     order, 2.34.139     mol, 2.20.13, 2.33.84.8, 2.33.84.29
     sequence, 2.33.65.36     mol2, 2.33.84.8, 2.33.84.30
randomSeed, 2.18.19     object, 2.33.84.32
randomize, 2.18.19, 2.33.83          parray, 2.33.84.32.1
     angles, 2.33.83.1     pdb, 2.23.14.4, 2.23.14.5, 2.33.84.2, 2.33.84.33
     coordinates, 2.33.83          sequence, 2.33.84.34
     torsions, 2.33.83     profile, 2.33.84.35
rarray, 2.33.22.6, 2.34.56.1, 2.34.70.8, 2.34.122.2, 5.7.11     prosite, 2.33.84.36
     properties, 2.34.122.4     rarray, 2.33.84.37
rdBlastOutput, 2.36.68     sarray, 2.33.84.39, 2.33.84.40
rdSeqTab, 2.36.69     sequence, 2.33.84.8, 2.33.84.41
reaction, 2.33.65.33          database, 2.33.84.41.1
     group file, 2.33.55     smiles, 2.33.84.46
read, 2.33.84, 2.33.84.56, 2.33.84.57     stack, 2.33.84.42
     FILTER, 2.33.84.6     string, 2.33.84.43
     alignment, 2.33.84.12     table, 2.33.84.44
     all, 2.33.84.7          chunk, 2.33.84.45
     binary, 2.33.84.2          csv, 2.33.84.44
     blob, 2.33.84.38          html, 2.33.84.47
     color, 2.33.84.13          mmcif, 2.33.84.48
     column, 2.33.84.51          mol, 2.33.84.50
     comp_matrix, 2.33.84.14          mol2, 2.33.84.49

     trajectory, 2.33.84.31remove columns, 2.33.22.16
          and save a fragment, 2.33.84.31.1     expression tags, 2.34.180
          write, 2.33.84.31.1     file, 2.33.22.9
     unix, 2.33.84.10     trailing blanks, 2.34.178
          cat, 2.33.84.11removing html tags, 2.33.84.47
     variable, 2.33.84.52     outliers, 2.34.178
     view, 2.33.84.53rename, 2.33.3.1, 2.33.85
     vrestraint, 2.33.84.54     chemicals, 2.33.89.47
          type, 2.33.84.55     column table, 2.33.85.1
     with filter, 2.33.84.6     file, 2.33.85.3
     xml, 2.33.84.56     molcart, 2.33.85.2
readMolNames, 2.24.11     system, 2.33.85.3
readcomp_matrix, 2.33.84.14renaming, 2.23.12.15
reading external tool output, 2.33.65.1reorder, 2.33.72.7
     from standard input, 2.33.84.43     alignment sequences, 2.33.110.1
     pdb from ftp, 2.21.18     array, 2.34.139
               web, 2.21.19     columns by function, 2.33.91.3
     restraint, 2.33.84.54     objects, 2.33.91.4
real, 3.19, 5.7.14replace matching array element, 2.34.126.1
     array, 5.7.11     without interpretation, 2.34.126.2
     shell variables, 2.19replacing scaffold in a library, 2.33.70.1
     space refinement, 2.33.65.31reproducible randomness, 2.18.19
reals, 2.19reroot, 2.33.18.4
rebel, 2.18.5, 2.23.14.6, 5.7.13     selections, 3.3.6
rebuild molcart index, 2.33.7.11resLabelShift, 2.19.35
recalculate dependent values, 2.33.7.2resLabelStyle, 2.22.20
     values, 2.33.1.1.1reserved names, 2.24
receptor, 3.13.1.1residue, 2.33.13.1, 5.7.16
     preparation, 3.13.1.1     accumulators, 2.34.63
redefine hydrogen coordinates, 2.33.89.25     alignment, 2.33.89.68, 2.33.89.69
references, 4     conservation, 2.34.122.5
refineModel, 2.36.66     contact area matrix, 2.34.90.8
reflections, 2.23.5.33          areas, 2.34.7.1
refresh view, 2.33.23.2     field, 2.33.89.34
refs, 4.1     gap, 2.23.5.7, 2.23.5.8
regexp, 2.10, 2.34.89     label, 2.19.35, 2.33.3.2
     back references, 2.10.1.3     library file, 2.37.20
     syntax, 2.10.1     name, 2.34.79
regression, 2.33.51          translation, 2.23.14.14
regul, 2.36.67     number, 2.34.66.5
regular expression, 2.10, 2.34.70.4, 2.34.89          table, 2.34.160.3
          filter, 2.33.84.1     property averaging, 2.34.146.3
     expression, 2.34.126.3          calculation, 2.34.63
regularization, 2.18.8, 2.33.66.4, 5.7.15     proximity, 2.34.90.8
     procedure, 3.8.3     ranges, 2.8.11
rejectAction, 2.22.19     selection, 2.20.21
relational database, 2.34.149          as string, 2.34.156.8
relative accessible area of atoms, 2.22.2          function, 2.34.127
release notes, 1.1     table, 3.14.4.1
remarkObj, 2.36.70     tethering, 2.33.89.68, 2.33.89.69

residue_selections, 2.8.11     dock job, 3.13.1.9
     selecting, 2.8.7     script from html, 5.8.2
resizing, 2.34.68s-s bond, 5.4.5
resorting nodes edges, 2.34.160.7s_alignment_rainbow, 2.21.1
restore, 3.14.6.2s_blastdbDir, 2.21.2
     defaults, 2.33.85.4s_editor, 2.21.3
     preference, 2.33.85.4s_entryDelimiter, 2.21.4
restraining molecules to shapes, 2.23.14.12s_errorFormat, 2.21.5
restraints, 2.17, 2.33.89.68, 2.33.89.69s_fieldDelimiter, 2.21.6
     torsion, 2.33.89.81s_helpEngine, 2.21.7
return, 2.33.86s_icmPrompt, 2.21.10
reverse complement, 2.34.138.1s_icmhome, 2.21.8, 3.1.2.1
     lighting, 2.33.89.42s_imageViewer, 2.21.11
     normals, 2.33.89.42s_inxDir, 2.21.9
reversing order, 2.34.66.2s_javaCodeBase, 2.21.12
rgb, 2.34.90.4, 5.7.17s_labelHeader, 2.21.13
     matrix, 2.34.29s_lib, 2.21.14
ribbon, 5.7.18s_logDir, 2.21.15
     bullets, 2.23.5.7s_out, 2.21.16
     diagram, 2.23.5.42, 2.23.5.43s_pdbDir, 2.21.17
ribbonColorStyle, 2.22.21s_pdbDirFtp, 2.21.18
ribbonStyle, 2.22.22s_pdbDirWeb, 2.21.19
ride, 3.19s_printCommand, 2.21.21
ridge, 3.13.1.21s_projectDir, 2.21.20
right join, 2.33.50s_prositeDat, 2.21.22
rigid chemical superposition, 2.33.97s_psViewer, 2.21.23
ring, 2.34.130s_reslib, 2.21.24
     center coordinates, 2.34.192.2s_skipMessages, 2.21.25
     sampling, 3.17s_sysCp, 2.21.26
     templates, 2.33.89.8s_sysLs, 2.21.27
rm, 2.33.22.9s_sysMv, 2.21.28
rocking, 2.33.23.5s_sysRm, 2.21.29
root mean square deviation, 2.34.136.4s_tempDir, 2.21.30
roots, 2.34.147, 2.34.148s_translateString, 2.21.31
rotate, 2.33.87s_userDir, 2.21.32
     2D-chem in a table column, 2.33.87.4s_usrlib, 2.21.33
     chem, 2.33.87.4s_webEntrezLink, 2.21.34
     grob, 2.33.87.2s_webViewer, 2.21.35
     object, 2.33.87.1s_xpdbDir, 2.21.36
     view, 2.33.87.3sa23, 3.3
rotation, 2.33.23.5sampling grid, 2.34.192.3
     angle, 2.34.17sarray, 2.33.22.6, 5.8.1
rounding, 2.34.122     transformation in place, 2.33.102.1
     a real, 2.34.156save preferences, 2.33.110.42
     output, 2.33.90.45     print, 3.2.6
rsWeight, 2.19.36     sdf file, 2.33.110.11
rs_, 2.8.7saving graphics to album, 2.33.65.20
ruler, 2.19.10     image, 2.33.110.36
     script, 2.33.8scaffold, 2.34.178
running a docking job, 3.13.1.18scaffolds, 2.33.55

scoring, 3.13.1.4               y z, 2.34.137
screen X, 2.34.190     columns, 5.9.1
     coordinates, 2.34.190     from clusters, 3.14.6.4
script, 2.34.99.4, 5.8.2     neighboring elements, 2.34.101
     file name, 2.34.55     residues, 3.3.6
     inside ICM, 5.8.2     saving, 2.34.66.4
     name, 5.8.2selection, 2.8, 2.34.137, 2.34.137.6
     image generation, 2.33.23.3     elements, 2.8.4
scripting molecular movements, 3.2.4     examples, 2.8.3
sdf, 2.23.14.7, 2.33.110.24, 5.6.11     functions, 2.8.10
     file, 2.33.84.49, 2.33.84.50, 2.33.89.47, 2.33.110.11, 2.34.156.3, 5.7.3     gap patching, 2.34.137, 2.34.137.11
     to chem-table, 2.34.109     level, 2.8, 2.34.182
search for chemical pattern, 2.34.56.3     levels, 2.8.2
     pdb headers, 3.4.5     simplification, 2.34.137.11
     prosite, 3.4.1     transfer, 2.34.137, 2.34.156.8
     sequence pattern, 2.33.35.8     type, 2.8
searchObjSegment, 2.36.73     types, 2.8.1
searchPatternDb, 2.36.71     variable, 2.24.12
searchPatternPdb, 2.36.72     atoms, 2.8.8
searchSeqDb, 2.36.74     functions, 2.8.10
searchSeqFullPdb, 2.36.76     molecules, 2.8.6
searchSeqPdb, 2.36.75     objects, 2.8.5
searchSeqProsite, 2.36.77     output, 2.24.15
searchSeqSwiss, 2.36.78     residues, 2.8.7
searches and alignments, 3.4     torsions, 2.8.9
second moments, 2.34.163     variables, 2.8.9
secondary structure derivation from 3D, 2.33.5.1selections, 2.33.89.34
          schematic, 2.23.5.42     in molecular objects, 2.8
segMinLength, 2.18.20selftether, 2.23.14.12, 5.9.4
segment, 5.8.4seq_ali_project, 2.34.156.6
select, 2.33.88sequence, 2.34.172, 2.34.173, 5.8.3
     atoms by number of bonded atoms, 2.34.137.3     alignment, 2.34.5.1, 2.36.1
          of the fixed torsions, 2.34.137.2          intro, 1.4.3.3
     based on alignment, 2.34.137.14     analysis intro, 1.4.3
          bfactor, 2.34.137.7     assembly, 2.33.43.2
          center of mass, 2.34.137.15     belongs to alignment, 2.34.70
          coordinates, 2.34.137.7     conservation, 2.34.136.7
          iarray, 2.34.137     distance, 2.34.137
          length, 2.34.137.13          matrix from alignment, 2.34.90.9
          occupancy, 2.34.137.7     dotplot, 1.4.3.2
          user field, 2.34.137.7     from alignment, 2.33.22.23
     chemical, 2.33.88.1          pdb, 2.33.65.35
     column table, 2.33.88.2     identity, 2.36.7, 2.36.8
     lines, 2.33.84.1     intro, 1.4.3
     tether partners, 2.34.137.12     modification, 2.34.180
     vw partners, 2.34.137.12     neighbor, 2.34.99.3
selectMinGrad, 2.19.37     parray, 5.7.3.2
selectSphereRadius, 2.19.38     pattern, 5.7.4
selected stack conformations, 2.33.22.17     position correspondence, 2.34.160.3
selecting by b-factor, 2.34.137     positional weights, 2.33.89.1

     search, 2.33.35.2     foreground, 2.33.89.40
     selection, 2.33.22.23     format, 2.33.89.41
     structure alignment, 2.35.1     grob, 2.33.89.42
     to alignment transfer, 2.34.122.3          coordinates, 2.33.89.42
     type, 5.8.3          label, 2.33.89.42
sequence-alignment mapping, 2.34.156.5, 2.34.156.6     group, 2.33.89.63
sequence-structure alignment, 2.34.5.1          column, 2.33.89.24
     output format, 2.18.21, 2.18.22     hydrogen, 2.33.89.25
sequenceBlock, 2.18.21     key, 2.33.89.43
sequenceColorScheme, 2.22.23     label, 2.33.89.44
sequenceLine, 2.18.22          3d label, 2.33.89.44.4
sequences, 3.4          chemical, 2.33.89.44.3
     not in alignments, 2.33.22.23          distance, 2.33.89.44.1
set, 2.33.89          table, 2.33.89.44.2
     alternative atom, 2.33.89.18     map, 2.33.89.45
     area, 2.33.89.1     molcart, 2.33.89.46
     atom, 2.33.89.3     molecular variables, 2.33.89.83
          ball label, 2.33.89.2     name, 2.33.89.47
     background image, 2.33.89.4          sequence, 2.33.89.47.1
     bfactor, 2.33.89.5     object, 2.33.89.48
     biological symmetry, 2.33.89.64     occupancy, 2.33.89.49
     bond topology, 2.33.89.7     plane, 2.33.89.50
          type, 2.33.89.6     pmf, 2.33.89.51
          and formal charges, 2.33.89.7     property, 2.33.89.52, 2.33.89.54, 2.33.89.55
     cartesian, 2.33.89.8          alignment, 2.33.89.55
     chain, 2.33.89.9          chemical view, 2.33.89.54
     charge, 2.33.89.10          column, 2.33.89.53
          formal, 2.33.89.11     radii graphical, 2.33.89.86
               auto, 2.33.89.12     randomSeed, 2.33.89.56
          mmff, 2.33.89.13     randomize, 2.33.89.56
     chargemmff, 2.33.89.13     resolution, 2.33.89.57
     chiral, 2.33.89.14     selftether, 2.33.89.68
          chemical, 2.33.89.15     similarity, 2.34.44.8, 2.34.136.2
     color, 2.33.89.16     site, 2.33.89.26
     comment, 2.33.89.17, 2.33.89.18          alignment, 2.33.89.27
          sequence, 2.33.89.19          residue, 2.33.89.29
     comp_matrix, 2.33.89.20     slide, 2.33.89.30
     current map, 2.33.89.45     sstructure backbone, 2.33.89.59
          object, 2.33.89.48          sequence, 2.33.89.60
     directory, 2.33.89.21          to sequence, 2.33.89.60
     drestraint, 2.33.89.22     stack, 2.33.89.61
          type, 2.33.89.23          energy, 2.33.89.61, 2.33.94.1
     electrostatic radii, 2.33.89.79     stereo, 2.33.89.58
     error, 2.33.89.33     swiss, 2.33.89.62
     field, 2.33.89.34          name, 2.33.89.62
          alignment, 2.33.89.35     symmetry, 2.33.89.65
          map, 2.33.89.36          bio, 2.33.89.64
          name, 2.33.89.37          crystal, 2.33.89.63
     font, 2.33.89.38          group, 2.33.89.63
          grob, 2.33.89.39          to a torsion, 2.33.89.65

     tautomer, 2.33.89.31     column, 2.33.90.15
     terms, 2.33.89.67     comp_matrix, 2.33.90.16
     tether, 2.33.89.69     database, 2.33.90.17
          append, 2.33.89.70     drestraint, 2.33.90.18
     texture, 2.33.89.32          type, 2.33.90.19
     type, 2.33.89.71     energy, 2.33.90.20
          mmff, 2.33.89.77          atom, 2.33.90.21
          molecule, 2.33.89.75     gradient, 2.33.90.22
          object, 2.33.89.74     hbond, 2.33.90.23
          property, 2.33.89.73          exact, 2.33.90.24
          sequence, 2.33.89.76     hbondexact, 2.33.90.24
          surface, 2.33.89.72     html, 2.33.90.25
     variable grid, 2.33.89.84     iarray, 2.33.90.26
     variablegrid, 2.33.89.84     integer, 2.33.90.27
     view, 2.33.89.80     key, 2.33.90.4
     vrestraint, 2.33.89.81     label, 2.33.90.28
     vrestraintvs_var, 2.33.89.82     library, 2.33.90.29
          radii, 2.33.89.78     link, 2.33.90.30
     vwelradii, 2.33.89.79     logical, 2.33.90.31
     vwradii, 2.33.89.78     map, 2.33.90.5
     window, 2.33.89.85     mol, 2.33.90.32
     xstick, 2.33.89.86     mol2, 2.33.90.33
          radii, 2.33.89.86     molecule, 2.33.90.34
setResLabel, 2.36.80     molecules, 2.33.90.6
setcomp_matrix, 2.33.89.20     object, 2.33.90.35
seticmff, 2.36.79     pdb, 2.33.90.36
setting conf properties, 2.33.89.61     pharmacophore type, 2.33.90.54
setvs_var, 2.33.89.83     pmf, 2.33.90.37
sf-term, 2.33.89.72     preferences, 2.33.90.38
sfWeight, 2.19.39     profile, 2.33.90.39
sh24, 3.4     residue, 2.33.90.40
shadows, 2.23.5.34          type, 2.33.90.41
shell, 3.1, 5.8.5     residuetype, 2.33.90.41
     functions, 2.33.40     segment, 2.33.90.42
     intro, 1.7.1     selftether, 2.33.90.1
     progression, 2.33.78     sequence, 2.33.90.43
     warning message, 2.34.191     shell variable, 2.33.90.3
shineStyle, 2.22.24     site, 2.33.90.2
shininess, 2.19.40     stack, 2.33.90.44
show, 2.33.90, 2.33.90.39     svariable, 2.33.90.3
     alias, 2.33.90.7     table, 2.33.90.45
     aliases, 2.33.90.7          as database, 2.33.90.17
     alignment, 2.33.90.8     term, 2.33.90.46
     area, 2.33.90.9     tethers, 2.33.90.47
     atom, 2.33.90.10     uniprot, 2.33.90.48
          type, 2.33.90.11          entry, 2.33.90.48
     atoms, 2.33.90.10     version, 2.33.90.49
     bond, 2.33.90.12     volume, 2.33.90.52
     clash, 2.33.90.13          map, 2.33.90.53
     color, 2.33.90.14     volumemap, 2.33.90.53

          type, 2.33.90.51     energy, 2.19.39, 2.22.25
     vrestraints, 2.33.90.50solvent accessible area, 2.18.23
showcomp_matrix, 2.33.90.16          surface, 2.23.5.55, 2.23.5.56, 2.33.90.9
showing weak hydrogen bonds, 2.23.5.25sort, 2.33.91, 2.33.91.4
side chain, 2.36.90     array, 2.33.91.1
          flexibility, 2.36.90     arrays, 2.33.91.1
sigma function, 2.34.44.8, 2.34.136.2     column, 2.33.91.3
     level, 2.23.7.5          table, 2.33.91.3
signal recognition measure, 2.36.21     molecules, 2.33.91.5
similar chains, 2.34.137.13     object, 2.33.91.4
similarity, 2.33.35.9, 2.33.35.10     stack, 2.33.91.6
simple expressions, 2.10.1.1     table, 2.33.91.2
     string substitution, 2.34.126.2sortSeqByLength, 2.36.81
simplified representation, 2.23.5.16space group, 2.33.69
     compound, 2.34.179     transformations, 2.34.176
     mesh structure, 2.33.15.2sparse atoms, 2.23.14.3
simulation duration, 2.19.47spawn background job, 2.33.65.1
     temperature, 2.19.46special values, 2.34.168
     intro, 1.4.2specificity, 2.34.136.4
sinking number, 2.19.35spectral decomposition, 2.34.45
site, 2.33.11.2, 5.8.6split, 2.33.92
     arrows, 2.33.89.26     column values, 2.33.92.5
     table, 5.8.6.1     grob, 2.33.92.1
sites, 2.33.22.26     group, 2.33.92.2
     by residue selection, 2.33.22.24          array, 2.33.92.3
     sequences, 5.8.6.1     into chains, 2.33.92.6
sixthe power, 2.22.6     molsar, 2.33.65.28
skin, 2.19.35, 5.8.7     object, 2.33.92.6
     intro, 1.4.1.2          to molecules, 2.33.92.6
slide, 2.33.1.3, 2.34.144, 5.8.14     sequence, 2.33.92.4
     transition time, 2.33.23.21     table cell, 2.33.92.5
slides, 2.34.190     tree, 2.33.92.7
slideshow, 2.33.1.3, 2.33.23.21, 2.34.144splitting selection, 2.8.11
sln, 5.8.8spreadsheet, 2.33.84.44
slurm, 3.13.1.19sprintf, 2.33.93
smallest set of smallest rings, 2.34.130sql, 2.33.81, 2.33.89.46, 2.34.50.1, 2.34.99.12, 2.34.102.5, 2.34.182.2
smart, 2.23.14.7sqlite, 3.5.1
smarts, 2.34.70.2sqrt, 2.34.37
smiles, 2.23.14.7, 2.26square matrix to element pairs, 2.34.160.5
     to chem-table element, 2.34.109ssThreshold, 2.19.41
smooth alignment, 2.34.146.4ssWeight, 2.19.42
     interpolation, 2.33.94.3ssbond, 5.4.5
     map, 2.34.146.5ssearch, 2.18.17, 2.33.95
     rarray, 2.34.146.1ssearchStep, 2.19.43
     surface, 2.36.88ssign sstructure segment, 2.33.5.2
soap, 2.31stack, 2.18.12, 2.18.13, 2.18.15, 2.22.7, 2.33.89.61, 2.33.94, 2.33.94.1, 2.34.66.6, 2.34.160.6, 5.3.12, 5.8.9
soft trim, 2.34.178     bin size, 2.33.14
solid sphere, 2.23.5.11     cleaning, 2.33.22.17
solubility, 2.34.114     extension, 2.33.4.2
solvation, 2.22.25, 2.23.14.2     multiplication, 2.33.4.2

standard chemical form, 2.33.70.4     how to, 3.3.1
     deviation, 2.34.133     minimize, 2.33.98
standardization, 2.33.22.11support, 1.3
     chemical, 2.33.70suppressing view changes, 2.33.23.21
startup, 3.1.2.3surface, 2.19.35, 2.34.109, 5.8.15
static RMSD, 2.34.155     accessibility, 2.33.90.9
     and dynamic hbonds, 2.23.5.24     area, 2.36.2, 5.8.15
statistical thermodynamics, 2.34.47     charge, 5.7.13
stereo, 2.23.5.52, 2.33.30, 2.33.89.58     color, 2.33.89.16
     reconstruction, 3.8.9     dot density, 2.23.5.55
stereo-specific hydrogens, 2.33.22.11     energy, 2.22.25, 2.33.89.72
stereoisomer, 2.33.30     mesh, 2.34.192.3
stereoisomers, 2.20.16     point selection, 2.34.192
stick, 5.8.10     term, 2.19.39
store, 2.33.94surfaceAccuracy, 2.18.23
     conf, 2.33.94, 2.33.94.1surfaceMethod, 2.22.25
     frame, 2.33.94.3surfaceTension, 2.19.44
     image, 2.33.65.20svariable, 5.8.12
     stack object, 2.33.94.2svg, 2.33.110.22
     torsion type, 2.33.94     export, 2.23.9.14
strength of hydrogen bond, 2.33.23.14     map, 2.34.160.7
string, 5.8.11swapping protein fragments, 3.8.7
     array, 2.34.135, 5.8.1swiss, 2.33.89.62
     filtering, 2.34.178swissFields, 2.24.10
     inversion, 2.34.156.1swissprot, 2.33.89.26
     label, 2.33.23.12symmetrization of a matrix, 2.34.90.3
     matching, 2.10, 2.34.89symmetry, 2.34.176
     variables, 2.21     faq, 3.10
strings, 2.21     group, 2.18.2
strip, 2.33.96     problem, 2.33.69
struct, 2.34.99.2syntax highlighting, 5.8.2
structural alignment, 2.33.3.5, 2.34.5.2sys, 2.33.99
          optimization, 2.33.35.1system, 5.10.2
     superposition, 2.33.3.5     command, 2.33.99
     analysis, 3.3     copy, 2.21.26
     comparison, 2.34.23.2     file move, 2.21.28
     factors, 3.11.1     list file, 2.21.27
     structure, 3.11.1     remove, 2.21.29
sub-alignment to selection, 2.34.128table, 2.33.22.4, 2.33.89.52, 2.33.89.53, 2.33.89.54, 2.33.91.3, 5.9.1
sub-matrix, 2.34.90.2     actions, 5.9.2.4
subalignment, 2.34.5.3, 5.1.1     column, 2.34.99
submap, 2.34.86          format, 2.33.89.41
subroutine, 2.33.64          plot, 2.33.65.32
subset, 2.6          transformations, 2.34.104
substring, 2.34.89, 2.34.156, 2.34.156.1     creation, 2.33.43.3
substructure, 2.33.35.9, 2.33.35.10     display style, 5.9.1
     search, 2.33.35.4     expression, 5.9.2
     grid engine, 3.13.1.19     from matrix, 2.34.160.4
superimpose, 2.23.14, 2.33.97     grid view, 5.9.1
     faq, 3.3.1     of atoms and distances, 2.34.160.10

     plot, 5.9.2.3     file, 2.37.17
     principal component analysis, 2.33.65.29     frame writing, 2.33.23.17
     print, 2.33.90.45     smoothing, 2.33.23.17
     row, 2.33.72.4transform, 2.33.102, 2.33.102.2
          label mark, 2.33.89.44.2     general, 2.33.102
          mark, 2.34.79     grob coordinates, 2.33.102.2
     selected row numbers, 2.34.70     molecules, 2.33.102.2
     subset, 5.9.2.2     sarray, 2.33.102.1
     show html, 2.33.108.1transformation, 2.34.122, 5.9.7
targa, 5.9.3     vector, 5.9.7
target coordinates, 5.9.4     and symmetry, 3.10
tautomer, 2.33.31transforming points, 2.34.192.5
tempCycle, 2.19.46translate, 2.33.54, 2.33.103
tempLocal, 2.19.45transparency, 2.33.89.42, 5.5.3
temperature, 2.19.46     background, 2.33.110.36
     variations in optimizer, 2.19.46     grob, 2.33.23.11
template docking, 3.13.1.22     grobs, 2.23.5.57
tensor product of two vectors, 2.34.90tree, 2.33.65.37, 2.34.99.5
terminal font, 2.37.14     cluster, 2.13
     window, 2.33.44     delete, 2.33.22.36
terms, 2.17     label format, 2.34.99.5
     hydrogen bonding, 2.19.21     representatives, 2.13.1
test, 2.33.100trim string array, 2.33.102.1
     binary, 2.33.100.1trimming grid map values, 2.34.178
testing if argument exists, 2.34.59true positives, 2.34.136.4
tether, 2.23.14.12, 2.33.110.9, 5.9.4, 5.9.5truncate alignment, 2.33.65.34
text, 2.34.89     values, 2.34.178
     search in tables, 2.34.56.2     grob, 2.23.5.9, 2.23.5.10
     to script, 5.8.2tsShapeData, 2.23.14.12
texture, 5.5.3     table format, 2.33.84.44
tga, 5.9.3two alignments, 2.34.44.13
then, 2.33.101     dimensional plot, 2.34.146.2
thickness, 2.23.9.14     set comparison, 2.34.44.8, 2.34.136.2
thread to template, 2.33.66.4     sets, 2.34.70.10
threading, 2.34.5.1txdoc browser, 2.33.84.4
     letter code, 2.34.172, 2.34.173type, 2.34.182.1
thumbnails, 2.34.68tzMethod, 2.22.26
tif, 5.9.6tzWeight, 2.19.50
time, 2.34.38, 2.34.156.2ultra large libraries, 3.13.1.23
timeLimit, 2.19.47uncharge functional groups, 2.33.70.2
tolFunc, 2.19.49unclip, 2.33.23.2
tolGrad, 2.19.48underline, 2.33.89.38.1
topological psa, 5.7.12undisplay, 2.33.104
torScan, 2.36.84     graphics, 2.33.105
torsion rmsd comparison, 2.33.14.2     window, 2.33.105
     scan, 2.36.84unfix, 2.33.106
torsions, 2.34.102.3union, 2.34.70.10
     score, 2.35.2unique, 2.33.13.1, 5.10.1
tpsa, 5.7.12     atomic order, 2.33.65.39
trajectory, 2.33.63.2, 2.33.94, 2.33.94.3, 5.6.14     column values, 2.33.43.4

     new object name, 2.34.99     arrays, 2.33.1.1.1
     smiles, 2.33.65.39     chemistry, 2.33.70, 2.34.102.4
unix, 2.33.99, 5.10.2     field, 2.33.7.2
     grep, 2.33.84.1     ligand screening, 3.13, 3.13.1
unlink alignments, 2.33.22.21               intro, 1.4.2.7
     sequences, 2.33.22.21     screening, 3.18, 3.19
     variables, 2.33.22.21visitsAction, 2.22.28
update database, 2.33.70.5vls, 3.13, 3.13.1
     speadsheet, 2.33.1.1.1     cluster, 3.13.1.15
updates, 1.1     intro, 1.4.2.7
updating atom pairs, 2.20.27     job queueing, 3.13.1.15
upper case, 2.34.171     overview, 3.13.1
url string parsing, 2.34.160     parallelization, 3.13.1.14
user atom display, 2.23.5.3     results, 3.13.1.17
     commands, 2.33.84.3     scores storage, 3.13.1.16
     defaults, 2.33.110.42     threshold, 3.13.1.11
     environment, 3.1.2.2vls_intro, 3.13.1.10
     menu, 2.23.10.1volume, 5.10.4
     menus, 2.32vrestraint, 5.10.5
user-defined properties, 2.33.89.34     file, 2.37.23
     solvation parameters, 2.34.7     type, 5.10.6
user_startup, 3.1.2.4          file, 2.37.22
     icm, 3.1.2vs_, 2.8.9
     guide, 3vs_out, 2.24.15
v-synthes, 3.13.1.23vwCutoff, 2.19.52
v_, 2.8.1vwExpand, 2.19.53
van der Waals surface, 2.23.5.56vwExpandDisplay, 2.19.54
varLabelStyle, 2.22.27vwMethod, 2.22.29
variable restraint, 2.33.89.81vwSoftMaxEnergy, 2.19.55
     selection, 2.8.9wait, 2.33.107
vdW gap, 2.34.151warning, 2.23.14.3
vector, 2.34.102.6     message, 2.34.191
     dot product, 2.34.187.1     suppression, 2.20.28
     length, 2.34.103water.dielectric constant, 2.19.15
     product, 2.34.187.1waterRadius, 2.19.56
     transformation, 2.34.104wavefront format, 2.33.65.11
vertex, 2.33.13.4.2web, 2.11, 2.33.108
     connectivity, 2.34.90.13     table, 2.33.108.1
vertexes, 2.33.13.4.2webEntrezOption, 2.22.30
vertical alignment block, 2.33.65.34weighted rmsd, 2.23.14
     workspace, 2.23.8.6while, 2.33.109
vertices, 2.33.13.4.2whole string, 2.34.126.1
vicinity, 2.19.51window averaging, 2.34.146.1
video, 2.33.110.31     layout, 2.34.156.9
view, 2.23.5.9, 2.23.5.10, 2.33.89.55     width and height, 2.34.190
     point, 2.34.190windowSize, 2.18.24
     restoration, 2.34.73     movie, 2.33.110.31
     transition, 2.33.89.80wire, 5.10.7
views, 5.8.14wireBondSeparation, 2.19.57
virtual, 5.10.3wireStyle, 2.22.31

write, 2.33.110          with links, 2.33.110.19
     album, 2.33.110.21     tether, 2.33.110.9
     alignment, 2.33.110.1     tethers, 2.33.110.9
     array, 2.33.110.8     trajectory, 2.33.23.17
          table, 2.33.110.8     vs_var, 2.33.110.43
     binary, 2.33.110.2writevs_var, 2.33.110.43
     blast, 2.33.110.25x-ray crystallography, 2.33.90.21
     column, 2.33.110.12xlsx, 2.33.84.44, 2.33.110.10
     database, 2.33.110.13xml, 2.33.84.56, 2.34.89, 5.1.6
     drestraint, 2.33.110.14     drugbank example, 2.12
          type, 2.33.110.15xpdb, 2.33.84.2
     factor, 2.33.110.16xplor format, 2.33.84.27
     gamess, 2.33.110.17xrMethod, 2.22.32
     grob, 2.33.110.18xrWeight, 2.19.58
     html, 2.33.110.19xray density to rectangular energy map, 2.33.65.31
     iarray, 2.33.110.3xstick, 5.10.8
     image, 2.33.110.20     radii, 2.33.89.2
          alignment, 2.33.110.23xyz morphing, 3.8.8
          chemical, 2.33.110.22zega, 5.10.9
          parray, 2.33.110.21     intro, 1.4.3.6
     index, 2.33.84.24, 2.33.110.24|, 2.14.3
          blast, 2.33.110.25 
          fasta, 2.33.110.24 
     library, 2.33.110.26 
     map, 2.33.110.27 
     matrix, 2.33.110.6 
     model, 2.33.110.28 
     mol, 2.33.110.29 
     mol2, 2.33.110.30 
     molcart, 2.33.110.7 
     movie, 2.33.110.31 
     object, 2.33.110.32 
          parray, 2.33.110.34 
          simple, 2.33.110.33 
     pdb, 2.23.14.14, 2.33.110.35 
     png, 2.33.110.36 
     postscript, 2.33.110.37 
     pov, 2.33.110.38 
     povray, 2.33.110.38 
     project, 2.33.110.2 
     rarray, 2.33.110.4 
     sarray, 2.33.110.5 
     sequence, 2.33.110.39 
     session, 2.33.110.40 
     several array, 2.33.110.8 
     simple object, 2.33.110.33 
     stack, 2.33.110.41 
     system preference, 2.33.110.42 
     table, 2.33.110.10 
          mol, 2.33.110.11 

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