ICM Manual v.3.8
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2018, Molsoft LLC
Jan 4 2018

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

Index

&, 2.14.3C, 5.3
2D labels, 2.29.55.1CCP4, 5.6.6
     to 3D, 3.16CGI, 2.11
     trees, 2.29.62.38COLOR.bg, 2.19.9
     smooth, 2.30.143.2     distanceAtom, 2.19.10
3D chemical builder, 1.4.2.8     label, 2.19.11
     font size, 2.29.23.12CONSENSUS, 2.23.1
     label, 2.29.23.12, 2.29.86.39CONSENSUSCOLOR, 2.23.2
     labels, 2.29.55.1CONSENSUS_strength, 2.19.12
     mol file, 2.32.86Cad, 2.30.23, 2.30.23.1, 2.30.23.2
     plots intro, 1.4.3.7Cad1, 2.30.23.1
     smoothing, 2.30.143.3Cadalign, 2.30.23.2
     superposition, 2.32.22Ceil, 2.30.24
     transformations, 2.29.99.2Cell, 2.30.25
     tree, 2.29.62.38Charge, 2.30.26
     chemical similarity, 2.30.133Chemical, 2.30.27
     pharmacophore comparison, 2.30.133.3Cluster, 2.30.28
3dxml, 5.5.3Collada, 5.5.3
=, 2.14.1Collection, 2.30.28.1
A, 5.1Color, 2.30.29
APF distance, 2.30.133     from gradient, 2.30.29.1
Abs, 2.30.1     image, 2.30.29.2
Acc, 2.30.2     protein, 2.30.29.3
Acos, 2.30.3Compare, 2.30.30
Acosh, 2.30.4Connolly surface, 5.8.7
Adobe, 2.21.23Consensus, 2.30.31
Align, 2.30.5Contour, 2.30.32
     sequence, 2.30.5.1Corr, 2.30.33
AlignSS, 2.31.1Cos, 2.30.34
Angle, 2.30.6Cosh, 2.30.35
Apple, 3.14.6.2Count, 2.30.36
Area, 2.30.7CubicRoot, 2.30.37
     residue contacts, 2.30.7.1D, 5.4
Asin, 2.30.8DAE, 5.5.3
Asinh, 2.30.9DE, 2.29.35.2
Ask, 2.30.10DNA Representation, 1.4.1.3
Askg, 2.30.11     alignment, 2.29.3.4
Atan, 2.30.12     melting temperature, 2.30.161
Atan2, 2.30.13     views, 1.4.1.3
Atanh, 2.30.14Date, 2.30.38
Atom, 2.30.15Deletion, 2.30.39
Augment, 2.30.16Descriptor, 2.30.40
Axis, 2.30.17Det, 2.30.41
B, 5.2Disgeo, 2.30.42
BPMC, 5.2.6Distance, 2.30.43, 2.30.43.6
Bfactor, 2.30.19     2 alignments, 2.30.43.13
Blob, 2.30.18          matrices, 2.30.43.9
Boltzmann, 2.30.20     Dayhoff, 2.30.43.11
Box, 2.30.21     Tanimoto, 2.30.43.7
Bracket, 2.30.22     alignment, 2.30.43.12

          rarray, 2.30.43.4     atomValueCircles, 2.23.5.3
     atoms, 2.30.43.3     ballRadius, 2.23.5.4, 2.23.5.31
     chemical, 2.30.43.7, 2.30.43.15     ballStickRatio, 2.23.5.5
     chemset, 2.30.43.8     chainBreakLabelDisplay, 2.23.5.8
     dayhoff, 2.30.43.11     chainBreakStyle, 2.23.5.7
     hierarchical, 2.30.43.6     clashWidth, 2.23.5.6
     iarray, 2.30.43.1     clipStatic, 2.23.5.10
          alignment, 2.30.43.12     clippingPlane, 2.23.5.9
     matrix, 2.30.43.5, 2.30.43.9     cpkClipCaps, 2.23.5.11
     multiple atomic, 2.30.43.4     displayLineLabels, 2.23.5.12
     rarray, 2.30.43.2     displayMapBox, 2.23.5.13
     tether, 2.30.43.10     dnaBallRadius, 2.23.5.14
     tree, 2.30.43.14     dnaRibbonRatio, 2.23.5.15
          cluster, 2.30.43.14     dnaRibbonStyle, 2.23.5.16
     H, 5.5     dnaRibbonWidth, 2.23.5.17
     number, 2.30.43.6     dnaRibbonWorm, 2.23.5.18
EDS server, 2.32.42     dnaStickRadius, 2.23.5.19
EST-alignment, 2.29.3.4     formalChargeDisplay, 2.23.5.20
Eigen, 2.30.44     grobDotSize, 2.23.5.21
Energy, 2.30.45     grobLineWidth, 2.23.5.22
Entropy, 2.30.46     hbondAngleSharpness, 2.23.5.26
Error, 2.30.47     hbondBallPeriod, 2.23.5.27
     soap, 2.30.48     hbondBallStyle, 2.23.5.28
Exist, 2.30.49     hbondMinStrength, 2.23.5.25
     molcart, 2.30.49.1     hbondRebuild, 2.23.5.24
Existenv, 2.30.50     hbondStyle, 2.23.5.23
Exp, 2.30.52     hbondWidth, 2.23.5.29
Extension, 2.30.51     hetatmZoom, 2.23.5.31
FILTER, 2.23.3     hydrogenDisplay, 2.23.5.32
     Z, 2.23.3.1     light, 2.23.5.33
     gz, 2.23.3.2     lightPosition, 2.23.5.34
     uue, 2.23.3.3     mapLineWidth, 2.23.5.35
FTP, 2.23.4     occupancyDisplay, 2.23.5.36
     createFile, 2.23.4.1     occupancyRadiusRatio, 2.23.5.37
     keepFile, 2.23.4.2     quality, 2.23.5.38, 2.30.89.1
     proxy, 2.23.4.3     rainbowBarStyle, 2.23.5.39
Field, 2.30.53, 2.30.53.1     resLabelDrag, 2.23.5.40
     user, 2.30.53.1     resLabelYShift, 2.23.5.41
File, 2.30.54     ribbonCylinderRadius, 2.23.5.42
Find, 2.30.55     ribbonGapDistance, 2.23.5.43
     chemical, 2.30.55.3     ribbonRatio, 2.23.5.44
          pattern, 2.30.55.3     ribbonWidth, 2.23.5.45
     in array, 2.30.55.1     ribbonWorm, 2.23.5.46
          table, 2.30.55.2     rocking, 2.23.5.47
FlexLM license info, 2.30.185     rockingRange, 2.23.5.48
Floor, 2.30.56     rockingSpeed, 2.23.5.49
Formula, 2.30.57     selectionLevel, 2.23.5.50
GRAPHICS, 2.23.5     selectionStyle, 2.23.5.51
     alignmentRainbow, 2.23.5.1     sketchAccents, 2.23.5.30
     atomLabelShift, 2.23.5.2     stereoMode, 2.23.5.52

     surfaceDotDensity, 2.23.5.55     shell variable, 3.1.2.1
     surfaceDotSize, 2.23.5.54IMAGE, 2.23.9
     surfaceProbeRadius, 2.23.5.56     bondLength2D, 2.23.9.15
     transparency, 2.23.5.57     color, 2.23.9.8
     wormRadius, 2.23.5.58     compress, 2.23.9.9
GRID, 2.23.6     gammaCorrection, 2.23.9.7
     gcghExteriorPenalty, 2.23.6.1     generateAlpha, 2.23.9.10
     gpGaussianRadius, 2.23.6.6     lineWidth, 2.23.9.3
     margin, 2.23.6.2     lineWidth2D, 2.23.9.14
     maxEl, 2.23.6.3     orientation, 2.23.9.16
     maxVw, 2.23.6.5     paperSize, 2.23.9.17
     minEl, 2.23.6.4     previewResolution, 2.23.9.13
GROB, 2.23.7     previewer, 2.23.9.12
     arrowRadius, 2.23.7.3     printerDPI, 2.23.9.2
     atomSphereRadius, 2.23.7.1     quality, 2.23.9.1
     contourSigmaIncrement, 2.23.7.5     rgb2bw, 2.23.9.18
     relArrowHead, 2.23.7.4     scale, 2.23.9.4
     relArrowSize, 2.23.7.2     stereoAngle, 2.23.9.6
GUI, 2.23.8     stereoBase, 2.23.9.5
     defaults, 3.14.6.2     stereoText, 2.23.9.11
     dialog, 2.28     writeScale, 2.23.9.19
     plot, 2.29.62.32I_out, 2.24.4
     preferences, 2.29.82.4Iarray, 2.30.65, 2.30.65.4, 2.30.65.5
     tableRowMarkColors, 2.23.8.5     atom numbers, 2.30.65.4
     windowLayout, 2.23.8.6     bits to integers, 2.30.65.3
     workspaceFolderStyle, 2.23.8.9     inverse, 2.30.65.2
     workspaceStyle, 2.23.8.7     residue numbers, 2.30.65.5
     workspaceTabStyle, 2.23.8.8     reverse, 2.30.65.2
Getarg, 2.30.58     stack, 2.30.65.6
Getenv, 2.30.59Icm Options, 2.1
Gradient, 2.30.60IcmSequence, 2.30.66
Graphics, 1.4.1Image, 2.30.67
Grob, 2.30.61     collection, 3.9.2.1
Group, 2.30.62     frame by frame, 3.9.2.2
HTTP.ignoreProxyDomains, 2.23.4.5InChI, 2.30.68
     proxy, 2.23.4.4InChi, 2.30.68
Hartree-Fock, 2.29.81.21, 2.29.107.17InList, 2.30.102
Header, 2.30.63Index, 2.30.69
Histogram, 2.30.64     chemical, 2.30.69.2
     N, 5.6     compare, 2.30.69.10
ICM desktop, 2.23.8.6     element in array, 2.30.69.8
     documents, 2.29.81.4     fork, 2.30.69.1
     modules, 1.4.4     regexp, 2.30.69.4
     object, 2.32.13     string, 2.30.69.3
     residue library, 2.21.24     table label, 2.30.69.6
ICM-shell, 3.1, 5.8.5          selection, 2.30.69.5
     intro, 1.7.1     tree, 2.30.69.9
     script, 2.29.8     unique elements, 2.30.69.7
ICMFF force field, 2.32.79Indexx, 2.30.70
ICMHOME, 3.1.2.1Info, 2.30.72

     model, 2.30.74Moment, 2.30.86
Insertion, 2.30.71     of Inertia, 2.30.86
Integer, 2.30.75Money, 2.30.93
Integral, 2.30.76NMR, 2.29.60.1
Interrupt, 2.30.77NOE averaging, 2.22.6
Introduction, 1Name, 2.30.96
JSON, 2.29.81.57     chemical, 2.30.96.6
LIBRARY, 2.23.10          property, 2.30.96.1
     men, 2.23.10.1     close sequence, 2.30.96.3
     res, 2.23.10.2     conf, 2.30.96.7
Label, 2.30.78     image, 2.30.96.11
Laplacian, 2.30.79     molcart, 2.30.96.12
Latent, 2.30.184.3     object parray, 2.30.96.10
LatentVector, 2.30.184.3     sequence, 2.30.96.8
Length, 2.30.80     soap, 2.30.96.2
LinearFit, 2.30.81     string, 2.30.96.4
LinearModel, 2.30.82     tree, 2.30.96.5
Log, 2.30.83Namex, 2.30.97
LogP, 2.30.111     image, 2.30.97.2
LogS, 2.30.111     sequence, 2.30.97.1
M_out, 2.24.5Newick tree format, 2.30.153.4
Mac, 3.14.6.2Next, 2.30.98, 2.30.98.1
Map, 2.30.84     covalent neighbors, 2.30.98.1
Markush structures, 2.29.52Nof, 2.30.99
Mass, 2.30.85     chemical, 2.30.99.2
Match, 2.30.87     distance, 2.30.99.3
Mathews, 2.30.133.4     latent, 2.30.99.6
Matrix, 2.30.88     library, 2.30.99.4
     alignment, 2.30.88.9     molcart, 2.30.99.5
     boundary, 2.30.88.10     soap, 2.30.99.7
     color, 2.30.88.4     tree, 2.30.99.1
     grob connectivity, 2.30.88.13Norm, 2.30.100
     histogram, 2.30.88.12Normalize, 2.30.101
     new, 2.30.88.1NotInList, 2.30.102
     residue areas, 2.30.88.8     R, 5.7
          comparison, 2.30.88.5OBJECT, 2.23.11
     stack, 2.30.88.11Obj, 2.30.103
     sub, 2.30.88.2Occupancy, 2.30.104
     symmetric, 2.30.88.3PBS, 3.13.3.6
     table, 2.30.88.6PLOT, 2.23.12
     tensor, 2.30.88.7     Yratio, 2.23.12.9
Max, 2.30.89     box, 2.23.12.1
     image graphic, 2.30.89.1     color, 2.23.12.2
MaxHKL, 2.30.90     font, 2.23.12.3
Mean, 2.30.91     fontSize, 2.23.12.4
Method, 2.22.13     gridLineWidth, 2.23.12.5
Min, 2.30.92     labelFont, 2.23.12.13
Mod, 2.30.94     lineWidth, 2.23.12.6
Mol, 2.30.95     logo, 2.23.12.10
MolPSA, 5.7.12     markSize, 2.23.12.7

     orientation, 2.23.12.11Rfactor, 2.30.128
     rainbowStyle, 2.23.12.14Rfree, 2.30.129
     seriesLabels, 2.23.12.12Ring, 2.30.127
PLS, 2.30.99.6Rmsd, 2.30.130
     error, 2.30.133.4     of subset, 2.23.14
     models, 2.30.133.4Rot, 2.30.131
Parray, 2.30.106S, 5.8
Parray-object, 2.30.106SAR analysis, 2.29.62.27, 2.29.62.28, 2.29.89.2, 2.29.89.3
Path, 2.30.105SC, 2.29.35.2
Pattern, 2.30.107SEQUENCE.restoreOrigNames, 2.23.12.15
Pi, 2.30.108SITE, 2.23.13
Polar Surface Area, 5.7.12     defSelect, 2.23.13.2
Potential, 2.30.109     labelOffset, 2.23.13.3
Power, 2.30.110     labelStyle, 2.23.13.4
Predict, 2.30.111     labelWrap, 2.23.13.5
Probability, 2.30.112     showSeqSkip, 2.23.13.6
Profile, 2.30.113     wrapComment, 2.23.13.7
Property, 2.30.114SLN notation, 2.30.153.10
Putarg, 2.30.115SMARTS, 2.26, 2.29.10, 2.30.99.2
Putenv, 2.30.116SOAP, 2.30.96.2, 2.30.99.7, 2.30.179.1
R-groups, 2.29.52     request message, 2.30.149
REBEL, 3.7.2SSSR, 2.30.127
     faq, 3.7.2S_out, 2.24.8
     file, 2.29.52S_proteinTags, 2.24.9
RNA topology, 2.23.5.16Sarray, 2.30.132
R_2out, 2.24.7     index, 2.30.132.1
R_out, 2.24.6Score, 2.30.133
Radius, 2.30.117     alignment, 2.30.133.8
Random, 2.30.118     apf, 2.30.133.3
     string, 2.30.118.1     chemset, 2.30.133.2
Rarray, 2.30.119     conservation, 2.30.133.7
     reverse, 2.30.119.2     model, 2.30.133.4
     sequence projection, 2.30.119.1     overlap, 2.30.133.1
     alignment projection, 2.30.119.3     predictions, 2.30.133.5
          strength, 2.30.119.5     sequence, 2.30.133.6
     property assignment, 2.30.119.4Scripting Tutorials, 1.8
RarrayAlignment, 2.30.119.5Select, 2.30.134
Rarrayinverse, 2.30.119.2     break, 2.30.134.1
Real, 2.30.120          alignment, 2.30.134.14
Reference, 2.30.122          atom property, 2.30.134.7
     Guide, 2          nmembers, 2.30.134.4
Remainder, 2.30.121          string, 2.30.134.9
Replace, 2.30.123     expand, 2.30.134.6
     chemical, 2.30.123.4     fix, 2.30.134.2
     exact, 2.30.123.1     graphical, 2.30.134.5
     regexp, 2.30.123.3     neighbors, 2.30.134.3
     simple, 2.30.123.2Select_by atom numbers, 2.30.134.10
Res, 2.30.124, 2.30.125Select_by_sequence, 2.30.134.13
Resali, 2.30.125Select_by_text, 2.30.134.9
Resolution, 2.30.126Select_lists, 2.30.134.12

Select_projection, 2.30.134.8     smilesXyzSeparator, 2.23.14.6
Sequence, 2.30.135     superimposeMaxDeviation, 2.23.14.9
     array, 2.30.135.2     superimposeMaxIterations, 2.23.14.7
Sequence(dna reverse), 2.30.135.1     superimposeMinAtomFraction, 2.23.14.8
Shannon, 2.30.46     tsShape, 2.23.14.11
Shuffle, 2.30.136     tsWeight, 2.23.14.12
Sign, 2.30.137     writePdbRenameRes, 2.23.14.13
Simulations, 1.4.2Table, 2.30.157
Sin, 2.30.138     alignment numbers, 2.30.157.3
Sinh, 2.30.139     distance, 2.30.157.10
Site, 2.30.140     matrix, 2.30.157.4
Slide, 2.30.141     model, 2.30.157.8
Smiles, 2.30.142          chem, 2.30.157.9
Smooth, 2.18.24, 2.30.143, 2.30.143.1, 2.30.143.3     pairs, 2.30.157.5
     matrix, 2.30.143.2     plot, 2.30.157.7
Smoothrs, 2.30.143.3     stack, 2.30.157.6
SoapMessage, 2.30.149     url_decoder, 2.30.157.1
SolveQuadratic, 2.30.144Table(alignment), 2.30.157.2
SolveQubic, 2.30.145Table(stack), 2.30.157.6
Sort, 2.30.150Tan, 2.30.158
Sphere, 2.23.14.3, 2.30.148Tanh, 2.30.159
Split, 2.30.151Tanimoto, 2.30.65.3
     chemical, 2.30.151.4     distance, 2.29.62.37
     multisep, 2.30.151.3          matrix, 2.30.43.7
     regexp, 2.30.151.2Temperature, 2.30.161
     tree, 2.30.151.1Tensor, 2.30.160
Sql, 2.30.146Time, 2.30.162
Sqrt, 2.30.147Tointeger, 2.30.163
Srmsd, 2.30.152Tolower, 2.30.164
Sstructure, 2.30.154Toreal, 2.30.165
String, 2.30.153, 2.30.153.8Torsion, 2.30.166
     alternative, 2.30.153.7Tostring, 2.30.167
     date, 2.30.153.2Toupper, 2.30.168
     mol, 2.30.153.3ToxScore, 2.31.2
     selection, 2.30.153.8Tr123, 2.30.169
     slide gui, 2.30.153.9Tr321, 2.30.170
     substring, 2.30.153.1Trace, 2.30.171
     chemical formula, 2.30.153.10Trans, 2.30.172
Sum, 2.30.155Transform, 2.30.173
     chemical, 2.30.155.1Transpose, 2.30.174
     image, 2.30.155.2Trim, 2.30.175
Swissprot, 2.29.107.24     chemical, 2.30.176
Symgroup, 2.30.156     sequence, 2.30.177
T, 5.9Turn, 2.30.178
TOOLS, 2.23.14Type, 2.30.179
     edsDir, 2.23.14.1     molcart, 2.30.179.2
     membrane, 2.23.14.2     soap, 2.30.179.1
     minSphereCubeSize, 2.23.14.3     Z, 5.10
     pdbReadNmrModels, 2.23.14.4Unique, 2.30.180
     rebelPatchSize, 2.18.5, 2.23.14.5Unix, 2.30.181

     server, 2.32.43activate fog, 2.29.23.24
V_, 2.8.1     alignment, 2.29.86.40
Value, 2.30.182     document, 2.29.86.40
     soap, 2.30.183     tab, 2.29.86.40
Vector, 2.30.16, 2.30.184, 2.30.184.1, 2.30.184.3     table, 5.9.2.4
     symmetry transformation, 2.30.184.2add, 2.29.1
Vectorproduct, 2.30.184.1     column, 2.29.1.1
Vectorsymmetrytransformation, 2.30.184.2          function, 2.29.1.1.1
Version, 2.30.185     matrix, 2.29.1.2
View, 2.30.187     slide, 2.29.1.3
Volume, 2.30.186     table, 2.29.1.4
WEBAUTOLINK, 2.23.16          row, 2.29.1.4
WEBLINK, 2.23.15addBfactor, 2.19.1
Warning, 2.30.188adding atoms to non-ICM objects, 2.29.7.1
Wavefront format, 2.29.81.22     columns to table, 2.29.1.1
XML, 2.12     hydrogens, 2.32.13
Xyz, 2.30.189     in place, 2.14.4
     axes, 2.30.189.7     to slideshow, 2.29.1.3
     chemical match, 2.30.189.5admet selection, 3.13.3.4
     fract, 2.30.189.3advanced chemical search, 3.6
     mesh, 2.30.189.2     operations, 2.14.6
     points, 2.30.189.1     ops, 2.14.6
     transformed xyz, 2.30.189.4ahfs, 2.30.43.6
     vector2matrix, 2.30.189.6ali_seq_project, 2.30.153.5
Z-shift, 2.19.35alias, 2.29.2
ZEGA, 5.10.9align, 2.29.3
     intro, 1.4.3.6     3D, 2.29.3.5
_NAME, 2.29.86.47          faq, 3.3.2
_chemBatch, 3.1.2.5          heavy, 2.29.3.6
_chemSuper, 3.15          how to, 3.3.2
_confGen, 3.16     chemical, 2.29.85.1
_dockScan, 3.13.2.5     fragments, 2.29.3.4
_macro, 2.33.1     intro, 1.4.3.3
     file, 2.33.1     number, 2.29.3.2
_startup, 3.1.2.3          chemical, 2.29.3.1
     file, 2.33.2     res numbers, 2.29.3.2
     icm, 2.33.2     sequence, 2.29.3.3
a_, 2.8.1     sequences, 2.29.3.3
abbr, 1.6alignMethod, 2.22.3
abbreviations, 1.6alignMinCoverage, 2.19.2
absolute to cell x y z, 2.30.189.3alignMinMethod, 2.19.2
accFunction, 2.24.2alignOldStatWeight, 2.19.3
acceptor, 3.6.1alignTwoSequences, 2.32.1
access large sdf file, 2.29.81.24aligned residues, 2.30.125
accessMethod, 2.22.2alignment, 2.29.22.26, 2.29.86.27, 2.29.86.35, 2.29.86.55, 5.1.1
accessible residues, 3.3.6     as table, 2.30.157.2
     surface, 2.29.62.14, 5.8.15     block length, 2.18.22
accessing sections, 2.29.107.24          secondary structure, 2.31.1
accuracy, 2.30.133.4     cleaning, 2.30.143.4
acidity constant, 2.29.86.11, 2.29.86.12     color by property, 2.29.86.34

     conservation, 2.32.8arguments, 2.29.61
     distance, 2.30.134.13arithmetic operations, 2.14.2
     editor, 2.4arithmetics, 2.14
     extraction, 2.30.5aromatic planes, 2.32.4
     gap format, 5.1.1.1array, 2.29.69.4, 5.1.6, 5.7.3.1
     intro, 1.4.3.4     assignment, 2.14.1
     projection, 2.30.153, 2.30.153.5, 2.30.153.6     derivative, 2.30.143.1
     score, 2.30.133.7     overlap, 2.30.133.1
     sequence reordering, 2.30.5     parray, 2.29.22.31
     strength, 2.30.119.5     size, 2.30.99
     structural, 2.29.3.5, 2.30.5     subset, 2.6
     to sequence transfer, 2.30.119.1arrow from selection, 2.32.36
          text conversion, 2.30.153.4     length, 2.29.86.26
     weighted, 2.30.5as2_out, 2.24.14
     gapExtension, 2.19.18as_, 2.8.8
     gapOpen, 2.19.19as_graph, 2.23.5.50, 2.23.5.51, 2.30.134.5
alignment_as_text, 2.30.153.4as_out, 2.24.13
aliphatic amines, 2.29.67.2assign, 2.29.5
all, 5.1.2     residue, 2.29.6.1
     torsions table, 3.3.11     ring conformation to template, 2.29.63.4
alpha, 2.23.5.57, 2.29.86.42, 5.1.3     sstructure, 2.29.5.1
     channel, 2.23.9.10          segment, 2.18.20, 2.29.5.2
alternative flag, 2.29.86.18assignment, 2.14.1
amber, 5.1.4atc code, 2.30.43.6
amino acid, 2.21.24, 2.30.169, 2.30.170atom, 2.29.13.1, 5.1.7
          colors, 2.30.29.3     centers within, 2.30.148
          labels, 2.29.3.2     code file, 2.33.4
and, 2.14.3     coordinates, 2.30.189.1
angle rotation, 2.32.84     flickering, 2.29.86.3
angles, 2.30.99.3     label font, 2.33.15
angular hbond dependence, 2.23.5.26     labels, 2.29.86.2
animated story, 5.8.14     name, 2.29.3.1, 2.30.78
animation, 2.29.23.5, 2.29.23.6, 3.9     pairs, 2.29.86.68, 2.29.86.69, 2.30.157.10
annotation, 2.29.22.26, 2.29.86.26, 2.29.86.27     proximity to surface, 2.29.87.9
apf, 3.15     selection by number, 2.30.65.4
append, 5.1.5     type, 2.30.179
     a tables, 2.29.1.4     user field, 2.30.53.1
     column, 2.29.4.3atomLabelStyle, 2.22.4
     command, 2.29.4atomSingleStyle, 2.22.5
     sequence, 2.29.4.1atomic contributions, 2.29.87.20, 2.29.87.21
          to group, 2.29.4.1     coordinate transfer, 2.29.86.3
     stack, 2.29.4.2     property fields, 3.15
     tables, 2.29.50     solvation contributions, 2.30.7
          by shared column, 2.29.4.3     in residue, 2.30.62
appending, 2.29.1.1     alternative position, 2.29.86.18
     an element, 2.14.4     selecting, 2.8.8
     menu items, 2.23.10.1     translate, 2.29.86.3
     representations to a slide, 2.29.23.21attenuation by occupancy, 2.29.62.25
     rows to matrix, 2.29.1.2auc enrichment, 2.32.21
area under curve, 2.32.21auto saving log, 2.22.11

avi, 2.29.107.31     helix, 3.10.5
axis, 5.1.8     how to, 3.8.1
axisLength, 2.19.4     hydrogen, 2.29.7.9
background, 2.30.29.2     loop, 2.29.7.6
     color, 2.19.9     model, 2.29.7.5, 2.29.107.9
ball, 2.29.86.2, 5.2.2     molcart, 2.29.7.10
base, 5.2.1     sequence, 2.29.7.3
     pair diagram, 2.23.5.16     smiles, 2.29.7.7
basis set, 2.29.81.21, 2.29.107.17     string, 2.29.7.8
batch chemical processing, 3.1.2.5     tautomer, 2.29.7.4
     docking, 3.13.2.5built-in functions, 5.5.5
beta, 5.2.3     plot, 2.29.86.53
bfactor circles, 2.23.5.3     atoms, 2.29.14
biased probability monte carlo, 2.29.68     contact surface, 2.29.14
binary file table of contents, 2.29.81.2     molecule, 2.29.13.1
     files, 2.29.107.2     number of bonds, 2.30.134.3
     string, 5.2.4     variables, 2.29.14
     key, 2.29.86.43cage, 2.32.4
binding energy, 3.7.4calcArea, 2.32.2
     pocket finding, 3.4.2calcBindingEnergy, 2.32.3
     pockets, 2.29.89.1calcDihedralAngle, 2.32.4
     side comparison, 2.32.8calcEnergyStrain, 2.32.20
     site analysis, 3.4.2calcEnsembleAver, 2.32.5
biological symmetry, 2.29.86.9calcMaps, 2.32.6
     vector, 2.30.65.3calcPairSeqIdsFromAli, 2.32.7
     to integers compression, 2.30.65.3calcPepHelicity, 2.32.9
blast, 2.29.107.25calcProtUnfoldingEnergy, 2.32.10
     files, 2.29.107.25calcRmsd, 2.32.11
blast-formatted database, 2.29.35.3, 2.29.107.25calcRoc, 2.32.21
blending, 2.29.107.31calcSeqContent, 2.32.12
     images, 2.30.155.2calcSeqSimilarity, 2.32.8
blob, 5.2.4calculate phases, 3.11.2
bold, 2.29.86.38.1call, 2.29.8
bond angle bending, 2.33.5canonical form, 2.30.44
     errors, 2.29.87.12carboxylic acid, 2.29.67.2
     stretching, 2.33.6cartesian cooridnates, 2.30.189
     to protein, 2.29.69.3cartridge, 3.5
     width, 2.23.9.14cavities, 2.29.89.1
bonded atoms, 2.30.98.1cavity, 5.3.1
born radii, 2.29.87.9     analysis, 3.3.13
boundary element, 5.2.5ccp4 maps, 2.29.81.27
          matrix, 2.30.88.10cd, 2.29.86.21
box, 2.30.21cell axis vectors, 2.30.189.7
break, 2.29.6     specific icm commands, 5.9.2.4
brightness, 2.23.5.33center, 2.13.1, 2.29.9
build, 2.29.7cgi programming with icm, 2.11
     atom, 2.29.7.1chain breaks, 2.23.5.7, 2.23.5.8, 2.30.134.1
     column, 2.29.7.2     symbol, 2.29.86.9
     faq, 3.8.1change atom position, 2.29.86.3
     from string, 2.29.7.8     sequence position in multiple alignment, 2.29.69.7

changing local stick radii, 2.29.86.86chroma, 2.30.88.4
     surface dot size, 2.23.5.54cif, 2.29.81.48
channel, 2.23.14.2circular permutation of coordinates, 2.29.66
charge, 5.3.2clamp values to range, 2.30.175
     compounds, 2.29.67.2clashThreshold, 2.19.5
     prediction, 2.29.86.11, 2.29.86.12clashes, 2.29.62.16
     state, 2.29.29     labels, 2.30.163
     change, 2.29.86.10classification, 2.30.43.6
chem formula, 2.30.153.10clear, 2.29.10
chemSuper3D, 2.32.22     graphical selection, 2.29.10
chemical, 2.23.14.6, 2.25, 2.29.35.9, 2.30.68     screen, 2.29.10
     2D drawings, 2.29.62.9click and lock, 5.9.2.4
     SMARTS search, 2.29.35.5clipping plane, 2.23.5.9, 2.23.5.10, 2.23.5.11, 2.29.69.6, 5.3.3
     atom annotation, 2.29.22.20closer than threshold, 2.30.43.9
     database, 3.5closest sequence, 2.30.96.3
     decomposition, 2.29.62.27, 2.29.89.2, 2.29.89.3     value, 2.30.55.1
     descriptors, 2.30.40, 5.7.12cluster, 2.30.151.1
     distance, 2.30.43.8, 2.30.133.2, 2.30.133.3     center, 2.30.69.9
     diversity, 3.14.6.4     centers, 2.13.1
     drawing, 2.23.9.14     selection, 2.30.69.9
          quality, 2.23.9.15     tree, 2.30.96.5
     fingerprints, 2.9          size, 2.30.99.1
     formula, 2.30.153.10clustering, 2.13, 2.29.62.37, 2.29.62.38, 2.29.89.7
     fragment counting, 2.30.99.2clusters, 2.13, 2.13.1
     keys, 2.29.62.21cnMethodAverage, 2.22.6
     match coordinates, 2.30.189.5cnWeight, 2.19.6
     matching, 2.29.35.4, 2.29.81.49, 2.29.81.50, 2.30.130, 2.30.152code, 2.30.43.6
     models, 2.30.96.1coil, 5.3.4
     modification, 2.29.65, 2.29.67, 2.32.37collection, 2.12, 5.3.6
     name, 2.30.96.6color, 2.23.5.33, 2.29.11
     normalization, 2.29.67     accessibility, 2.29.13
          rules, 2.29.67.4     background, 2.29.13.2
     pattern, 2.26, 2.29.85.1          example, 3.2.7
          search, 2.30.55.3          accessibility, 3.2.11
     reaction product generation, 2.29.62.33          alignment, 2.29.13.3
     search, 2.29.35.10, 2.29.85.1, 2.30.99.2          atom contributions, 2.29.12
     similarity, 3.5          bfactor, 3.2.9
     simplification, 2.30.175          charge, 3.2.12
     spreadsheet, 2.29.12, 2.29.81.48, 2.29.81.49, 2.29.81.50, 2.29.86.47, 2.29.107.11          electrostatic potential, 2.18.5
     structure from smiles, 2.29.86.7          hydrophobicity, 3.2.10
     substructure, 2.29.35.4          pharmacophore, 2.29.12
          mask, 2.29.62.21          potential, 2.32.25
     superposition, 2.22.7, 2.30.130, 3.15          shape depth, 2.29.13
     table, 2.25     chemical, 2.29.12, 2.29.85.1
     text format, 5.6.11     choice, 2.19.9
     view, 2.29.86.54     file, 2.33.15
chemistry, 2.25, 2.30.27     grob, 2.29.13.4
chiral isomer generation, 2.29.30          by atom selection, 2.29.13.4.3
chirality, 2.20.16, 2.29.30               atoms, 2.23.7.1
choosing ligands, 3.13.1.2          map, 2.29.13.4.4

          potential, 2.29.13.4.5     property prediction, 2.29.51.2
          unique, 2.29.13.4.1compress, 2.29.15
     label, 2.29.13.5     alignment, 2.29.15.1
     map, 2.29.13.6     binary, 2.29.15.4
          by value, 2.29.23.16     conf, 2.29.15.3
     molecule, 2.29.13.1     grob, 2.29.15.2
     names, 2.30.29     in place, 2.29.15.4
     object, 2.29.11.2     objects, 2.29.15
     preference, 2.19.10     stack, 2.29.15.3
     specification, 2.29.11.1compressed table view, 2.29.86.24
     surface by conservation, 2.29.13.3conditional buttons, 5.5.5
     table, 2.30.29.3     string, 2.30.153.7
     volume, 2.29.13.7conf, 2.29.86.61, 2.29.107.41, 2.30.157.6, 5.3.12, 5.8.9
column, 5.3.5     data, 2.30.157.6
     correlation, 2.29.88.3confgen, 3.16
     function, 2.29.7.2configuration, 2.33.14
     names, 2.29.82.1, 2.29.85.2     file, 2.29.107.42
     of grobs, 2.30.106     memory usage, 2.18.7
     selection, 2.30.96conformation comparison, 2.22.7
combinatorial compounds, 2.30.27conformational ensemble, 2.29.7.5.2
     libraries, 2.29.62.33, 2.30.99.4     generator, 2.29.63.1, 3.16
     PDB, 2.32.92     interpolation, 2.29.23.6
     transformations, 3.10.4     stack, 2.29.107.41, 5.3.12, 5.8.9
combining plots, 2.29.62.32          compression, 2.29.15.3
     receptor and ligand stacks, 2.29.4.2          file, 2.33.7
command, 2.30.96.4, 5.3.10     transition, 2.32.38
     line editing, 2.2conformer storage, 2.29.60.5, 2.29.91.2
          help, 2.29.45conformers, 3.16
          options, 2.1connect, 2.29.16
     word list, 3.1.5     chains with alignments, 2.29.54
commands, 2.22.11, 5.1.1     molcart, 2.29.16.1
communication protocols, 2.27consensus, 2.19.7
comp, 2.30.102     coloring, 2.19.12, 2.23.2
comp_matrix, 2.29.86.20, 2.29.87.16, 5.3.11     definitions, 2.23.1
compare, 2.18.12, 2.18.15, 2.29.14consensusStrength, 2.19.7
     angles, 2.29.14.2conservation, 2.30.119.5, 2.30.133.7
     atom, 2.29.14.1constant, 2.5
     by rmsd without superposition, 2.29.14.1constants, 2.5
     chemical tables, 2.29.35.10contact areas, 2.30.88
     patch only, 2.29.14.3continue, 2.29.17
     rmsd, 2.29.14.1contour lines, 2.30.32
     surface, 2.29.14.3     surfaces, 2.23.7.5
     variables, 2.29.14.2contouring density, 2.29.62.14
compareMethod, 2.22.7contrast, 2.23.5.33
comparing two sarrays, 2.30.102conversion, 5.1.6
comparison, 2.30.69.10     to real array, 2.30.165
     operations, 2.14.5convert, 2.29.18, 2.29.18.2, 3.13.2
complete view, 2.30.141     3D to chemical, 2.30.27
compound accessibilities, 3.14.4.1     3D/0D to 2D, 2.29.62.9
     array, 2.25     ICM object to PDB, 2.29.93

     chemical 3D, 2.32.82csym, 1.4.2.4
               and optmimize geometry, 2.32.83cube, 2.23.14.2
     comp, 2.29.18.1current, 5.3.9
     comparison, 2.29.18.1     map, 5.3.7
     fragments, 2.29.18.2     object, 5.3.8
     mol, 2.29.18.3     working directory, 2.30.105
     object 3D and optmimize geometry, 2.32.85cursor action, 5.9.2.4
          macro, 2.32.13custom alignment color, 2.23.5.1
     pdb, 3.8.2     field, 2.29.86.51
     to 3D, 2.29.86.8     interaction, 2.29.87.37
          ICM object, 2.32.86     menu, 2.28, 2.29.81.3
          iarray, 2.30.163customization, 3.1.2
          icm-object, 2.29.18     environment, 2.28
          integer, 2.30.163     and paste chemicals, 2.23.9.14, 2.23.9.15
convert2Dto3D, 2.32.85cyclic temperature protocol, 2.19.46
convert3Dto3D, 2.32.86cylinder, 2.23.14.2
convertObject, 2.32.13cz32, 4.5
converting a chemical, 2.29.18.3data visualization, 2.29.62.38
          pdb-chemical, 3.13.2database, 5.4.1
     alignment to table, 2.30.157.2     browser, 2.29.60.3
     chemicals, 3.13.2.3     connection, 2.29.16.1
     table columns into matrix, 2.30.88.6     file, 3.5.1
     to, 2.30.120     import, 2.29.62.26
cool, 2.32.40date, 2.29.21, 2.30.153.2
     pictures, 2.23.5.30     array, 2.29.21
cooling schedule, 2.19.46dcMethod, 2.22.8
coordinate frame, 2.19.4, 2.29.23.4dcWeight, 2.19.8
coordinates, 2.23.14.6decomposition, 2.29.62.27, 2.29.89.2, 2.29.89.3
copy, 2.29.19defCell, 2.24.1
     chemical image, 2.23.9.15defSymGroup, 2.18.2
     file, 2.21.26default atom colors, 2.29.86.16
     site, 2.29.86.28     color of label, 2.19.11
correlation matrix, 2.30.160     parameters, 2.22.1
covalent bound count, 2.30.134.3     value, 5.8.2
     neighbors, 2.30.98.1define axis, 3.10.3
covalently attached molecule, 2.30.98.1defining space box, 2.30.21
cpk, 2.19.35, 5.3.13dehtml, 2.30.123.3
create a covalent bond, 2.29.62.2del, 2.29.22.9
     pharmacophore, 2.32.87delete, 2.29.22
creating a local patch object, 2.29.18.2     3D graphics panel, 2.29.102
credits, 4.5     alias, 2.29.22.2
crypt, 2.29.20     array element, 2.29.22.6
crystal axis vectors, 2.30.16          index, 2.29.22.6
     symmetry transformation, 3.10.2          selection, 2.29.22.1
          transformations, 2.30.173     atom, 2.29.22.7
crystallographic cell, 2.29.66     bond, 2.29.22.14
     occupancy, 2.30.104     boundary, 2.29.22.15
     symmetry intro, 1.4.2.4     chemical, 2.29.22.37
crystallography, 2.30.126          fragment, 2.29.22.37
csv format, 2.29.81.44          selection, 2.29.22.37

     column table, 2.29.22.16depth-cueing, 2.19.17
     conf, 2.29.22.17desolvation, 2.22.25
     directory, 2.29.22.8detecting bad covalent geometry, 2.29.87.12
     disulfide bond, 2.29.22.27     proximity, 2.30.43.9
     drestraint, 2.29.22.18dialog generation, 2.30.11
     element, 2.29.22.31     in html documents, 2.29.44
     file, 2.29.22.9          tables, 2.29.44
     from array, 2.29.22.6     scripting, 2.30.11
     hydrogen, 2.29.22.11dielConst, 2.19.14
     label, 2.29.22.19, 2.29.22.20dielConstExtern, 2.19.15
          chemical, 2.29.22.20dielectric constant, 2.19.14
     link, 2.29.22.21diff, 2.30.102
     map, 2.29.22.22dihedral, 2.32.4
     molcart, 2.29.22.3     angle, 2.29.62.19
     molecule, 2.29.22.13          calculation, 3.3.10
     object, 2.29.22.12directory, 2.29.22.8, 2.29.62.5, 2.30.132
     parray, 2.29.22.36display, 2.29.23
          element, 2.29.22.36     GUI window, 2.29.23.26
     peptide bond, 2.29.22.28     box, 2.29.23.7
     plot, 2.29.22.4     clash, 2.19.5, 2.29.23.8
     salts, 2.29.67.3     contact, 2.29.62.16
     selection, 2.29.22.5     drestraint, 2.29.23.9
     selftether, 2.29.22.34     field, 2.23.5.3
     sequence, 2.29.22.23     from script, 2.29.23.3
     session, 2.29.22.10     gradient, 2.29.23.10
     shell object, 2.29.22.1     grob, 2.29.23.11
     site, 2.29.22.24          label, 2.29.23.12
          alignment, 2.29.22.26     gui, 2.29.23.26
     sstructure, 2.29.22.25     hbond, 2.29.23.13
     stack, 2.29.22.29     label, 2.29.23.15
          object, 2.29.22.30     map, 2.23.5.13, 2.29.23.16
     system, 2.29.22.9     model, 2.29.23.1
     table, 2.29.22.32     new, 2.29.23.2
          rows, 2.29.22.32     off-screen, 2.29.23.3
     term, 2.29.22.33     offscreen, 2.29.23.3
     tether, 2.29.22.35     origin, 2.29.23.4
     tree, 2.29.22.36     ribbon, 2.29.23.18
     variable, 2.29.22.6     rotate, 2.29.23.5
     views, 2.29.22     site, 2.29.23.19
     backbone, 2.30.134.1     skin, 2.29.23.20
     restraint, 2.29.22.18     slide, 2.29.23.21
deleting, 2.29.22.26     stack, 2.29.23.6
     sites by number, 2.29.22.24     string, 2.29.23.22
delphi, 2.32.25     surface, 2.29.23.20
density correlation, 2.19.8, 3.11.3          area, 2.23.5.3
     fitting, 2.22.8     tethers, 2.29.23.23
     in unit cell, 2.29.62.23     trajectory, 2.29.23.17
densityCutoff, 2.19.13     volume, 2.29.23.24
dependent columns, 2.29.1.1.1     window, 2.3, 2.29.23.25
depth cueing, 2.29.13.7, 5.4.2distance, 2.23.5.24, 2.30.40, 5.4.3

     contact-based, 2.30.23, 2.30.23.1dsXyz, 2.32.32
     geometry, 5.4.4dump database, 2.29.107.7
     matrix, 2.30.157.5, 2.32.7dynamic gui, 5.5.5
          between stack conformations, 2.30.88.11ecepp, 5.5.1
     restraint, 5.4.6edit, 2.29.24
          file, 2.33.9     files, 2.23.14.1
          type file, 2.33.8eigen value factorization, 2.30.44
     restraints, 2.29.86.22eigendecomposition of a matrix, 2.30.44
distances, 2.30.99.3eigenvalues, 2.30.44
distribution, 1.3eigenvectors, 2.30.44
     comparison, 2.30.133electro intro, 1.4.2.9
disulfide bond, 5.4.5electroMethod, 2.22.9
diverse subset, 3.14.6.4     density, 2.23.7.5, 2.29.86.36, 2.29.87.21, 2.32.42, 2.32.43
dividing chemical into individual molecules, 2.30.151.4          around selection, 2.19.25
dna to protein sequence translation, 2.30.172.1          map generation, 2.19.1
     translate, 2.30.172.1          maps, 2.23.14.1
dockScan, 3.13.2.5electrostatic boundary matrix, 2.30.88.10
docking, 2.32.89     coloring, 2.23.14.5
     intro, 3.13.2.1     isopotential surfaces, 2.29.62.13
     result viewing, 2.32.28     potential, 2.29.13.4.5
     simple models, 3.14.3     solvation, 3.7.2
     timing, 3.13.1.3     surface, 2.32.25
     with template, 3.13.2.6     troubleshooting, 5.7.13
documents, 5.5.8electrostatics, 2.23.14.5
dollar separated file, 2.29.81.44     intro, 1.4.2.9
dominant color, 2.30.29.2ellipsoid, 2.30.160
donor, 3.6.1elseif, 2.29.25
     plot intro, 1.4.3.2empty model, 2.30.106
dots, 2.29.75endfor, 2.29.26
dotted surface, 2.23.5.56endif, 2.29.27
double click action, 5.9.2.4endmacro, 2.29.28
drestraint, 2.29.87.18, 5.4.6endwhile, 2.29.33
     generate from structure, 2.29.62.7energetics, 3.7
     global weight, 2.19.6     function, 2.23.14.3
     set, 2.29.86.22     profile, 2.32.84
     type, 5.4.7     terms, 2.17
drop, 2.19.16ensemble, 2.29.60.1, 2.29.91.1
drug, 2.12     average, 3.7.5
ds3D, 2.32.31entropy of alignment, 2.30.133.7
dsCellBox, 2.32.15     atom, 2.29.18.4
dsChem, 2.32.17enumerate, 2.29.29, 2.29.30, 2.29.31, 2.29.32
dsCustom, 2.32.18     charge, 2.29.29
dsPocket, 2.32.28     chiral, 2.29.30
dsPropertySkin, 2.32.19     library, 2.29.32
dsPrositePdb, 2.32.24     tautomer, 2.29.31
dsRebel, 2.18.5, 2.23.14.5, 2.32.25enumeration, 2.30.27
dsSeqPdbOutput, 2.32.26eps files, 2.21.23
dsSkinLabel, 2.32.27equipotential surface, 2.30.32
dsStackConf, 2.32.29error SOAP services, 2.30.48
dsVarLabels, 2.32.30     ignoring, 2.21.25

errorAction, 2.22.10file, 2.29.107.24
     vrestraint vs_var, 2.29.86.82     exists, 2.30.49
evalSidechainFlex, 2.32.90     list, 2.30.58
evol tree intro, 1.4.3.5     length, 2.30.54
evolutionary tree intro, 1.4.3.5     object origin, 2.30.54
exact, 2.29.35.9, 2.29.35.10     permissions, 2.30.54
     match, 2.30.123.1     time modified, 2.30.54
example scripts, 3.14     type, 2.30.54
excel, 2.29.81.44files, 2.33
exit, 2.29.34filling volume, 2.23.5.11
exitSeslogStyle, 2.22.11filter, 2.29.35.10, 2.29.60.3
expanding substructure match, 2.29.86.70     functions, 5.5.4
export, 2.29.107.7filtering table rows, 5.5.4
     animation, 2.29.107.31find, 2.29.35
     pdb, 2.23.14.13     alignment, 2.29.35.1
exporting sdf, 2.29.107.11     and replace a chemical pattern, 2.29.67.1
expression shortcuts, 2.10.1.2               chemical fragment, 2.29.67
     tags, 2.24.9     chemical, 2.29.35.5
     comparison, 2.14.5          pattern, 2.29.67
     arithmetics, 2.14.2          substructure, 2.30.69.2
     assignment, 2.14.1     database, 2.19.2, 2.29.35.2
     comparison, 2.14.5          fast, 2.29.35.3
     logical, 2.14.3     family of commands, 2.29.35
extending to bonded hydrogens, 2.30.134.6     in sarray, 2.30.69.8
               terminal atoms, 2.30.134.6     molcart, 2.29.35.9, 3.5
external process, 2.29.62.1     molecule, 2.29.35.4
extracting from Markush, 2.29.52     motifs, 2.24.9
     icm script arguments, 2.30.58     pattern, 2.29.35.8
     stack from object, 2.29.60.5     pdb, 2.29.35.6
ez25, 3.7     pharmacophore, 2.29.35.11
factor, 5.8.13     prosite, 2.29.35.7
false negatives, 2.30.133.4     scaffold, 2.30.176
family, 2.29.86.38.1     table, 2.29.35.10
faq, 1.3findFuncMin, 2.32.33, 2.32.34
     cheminformatics, 3.14.6findFuncZero, 2.32.35
     chemsuper, 3.14.5findSymNeighbors, 2.32.16
     mac gui preferences, 3.14.6.2find_related_sequences, 2.32.33
     molcart dump, 3.14.6.3finding long covalent bonds, 2.30.134.1
          query, 3.14.6.1fingerprint, 2.30.40
     multiple chem overlay, 3.14.5.1fingerprints, 2.9
     residue table, 3.14.4.1     to density, 2.22.8
fast Fourier transform, 2.29.62.24fix, 2.29.36
     sequence search, 2.29.35.3fixed branches, 2.30.134.2
fasta, 2.23.12.15, 5.5.2flattening 3D molecule, 2.32.17
     format, 2.29.107.1flexible superimpose, 2.32.50
feature table, 5.8.6.1flow control, 2.15
     in sequences, 2.29.86.26fog, 2.19.17, 2.29.13.7, 2.29.23.24, 5.4.2
ffMethod, 2.22.12     color, 2.19.17
field, 2.29.86.35fogStart, 2.19.17
     name, 2.30.96.2fold search, 5.8.4

folding procedure, 3.14.1     exists, 2.30.49
font, 2.29.55.1     intro, 1.4.1, 1.4.1.4
     size, 2.29.86.38.1, 2.33.14     learning, 3.2.1
     sizes, 3.14.6.2     attributes, 2.19.4
     specification, 2.29.86.38.1     fogStart, 2.19.17
for, 2.29.37     view vector, 2.29.86.80
fork, 2.29.38, 2.30.69.1graphviz, 2.30.157.7
formal charge, 2.23.5.20, 2.29.86.12, 5.3.2greedy matching, 2.10.1.4
formatdb, 2.29.107.25grid energy, 2.29.87.21
fprintf, 2.29.39     potentials, 2.29.62.25
fractional coordinates, 2.30.189.3grob, 5.5.3
     to abs coordinates, 2.30.16     coloring, 2.29.13
fragmented molecule, 2.29.18.2     files, 2.33.10
frame, 2.29.91, 2.29.107.31     inside-out flip, 2.29.86.42
fullscreen, 2.29.86.85     normal directions, 2.29.86.42
function, 2.29.40, 2.29.61     vertex, 2.23.5.21
     columns, 2.29.1.1.1     translate, 2.29.100
functions, 5.1.1group, 2.29.43
     selecting in objects, 2.8.10     by column, 2.29.43.4
gamess, 5.5.6     column, 2.29.43.4
     expansion, 2.30.143.4     rename of table columns, 2.29.82.1
gapExtension, 2.19.18     replacement, 2.29.65
gapFunction, 2.24.3     select of table columns, 2.29.85.2
gapOpen, 2.19.19     sequence, 2.29.43.1
gaussian averaging, 2.30.143.2          unique, 2.29.43.2
gcMethod, 2.22.13     table, 2.29.43.3
genbank, 2.23.12.15grouping table by a column, 2.29.86.24
generalized arrays, 5.1.6gui, 2.29.44, 5.9.2.4
generate intermediate conformers, 2.32.38     exists, 2.30.49
generating movie images, 3.9.2.1     functions, 5.5.5
genomics, 1.4.3.1     panels, 2.29.102
     clustering, 2.29.43.2     programming, 2.28, 2.29.44, 2.29.86.24
     intro, 1.4.3.1gvim text editor, 5.8.2
geometry optimization, 2.29.63.1gzip files, 2.29.15.4
     started, 1.7hash, 2.12, 5.3.6
getting data from outside, 2.27     table, 5.3.6
     started, 1.7haze, 2.19.17
global, 2.29.41hb, 2.19.21
glossary, 5hbCutoff, 2.19.21
go, 2.30.43.6hbond, 2.23.5.25, 2.23.5.26, 2.29.22.6, 5.5.7
goto, 2.29.42     color, 2.29.23.14
     term, 2.19.20, 2.29.86.73     display, 2.23.5.27, 2.23.5.28
gpWeights, 2.19.20     energy, 2.29.23.14
graph matching, 2.30.130     list, 2.30.157.10
graphical box, 2.29.23.7     show, 2.29.87.23
     row selection, 2.30.69.5hbondMinStrength, 2.23.5.25
     selection, 2.30.134.5     faq, 3.3.4
graphics, 2.19.9, 2.29.86.4, 2.30.185, 3.2, 5.3.3     how to, 3.3.4
     card, 2.23.5.52header, 2.29.1.1
     controls, 2.3, 2.33.15, 5.4.2helical axis, 2.32.36

helicity, 3.7.6     GUI, 2.29.86.40
     content calculation, 3.7.6     algorithms, 4.3
help, 2.29.45, 2.29.45.1, 2.29.45.2     application refs, 4.4
     browser, 2.29.45.1          literature, 4.3
     commands, 2.29.45.3     archive, 2.29.81.2
     functions, 2.29.45.4     arguments, 2.30.58
     getting, 3.1.1     binary, 2.30.105
     word, 2.29.45.2     branching, 2.15.2
     getting, 3.1.1     commands, 2.29
heterogenous environment, 2.23.14.2     controls, 2.15
hidden blocks, 5.1.1.1     flags, 2.1
     display, 2.29.23.3     functions, 2.30
     hydrogens, 2.23.5.32     graphics, 3.2
     stack in object, 2.29.91.2     history, 1.2
hierarchical, 2.13     jumps, 2.15.3
highEnergyAction, 2.22.14     learning, 3.1.4
his-tags, 2.30.177     loops, 2.15.1
histogram, 2.29.62.32     macros, 2.32
     2D, 2.30.88     main refs, 4.2
history, 2.29.46, 2.29.107.40     menus, 2.23.10.1
     delete, 2.29.22.10     method literature, 4.4
     of ICM, 1.2     molecules, 2.16
homodel, 2.32.41     object file, 2.33.18
homology modeling, 1.4.2.2, 2.29.7.5, 2.29.86.68, 2.29.86.69, 2.31.1, 3.14.4     preferences, 2.22.1
          faq, 3.14.4     session, 2.22.11
          intro, 1.4.2.2     shell, 3.1
     output, 2.29.7.5.3          functions, 2.31
     steps, 2.29.7.5.1     support, 1.3
     to export a molcart table, 3.14.6.3     table, 2.23
html, 2.11, 2.29.44, 2.30.96.4, 5.5.8     ali, 2.33.31
     document order, 2.29.86.40     all, 2.33.32
     tag removal, 2.30.123.3     bbt, 2.33.5
html-formatted text, 5.5.8     bst, 2.33.6
html5, 2.11     cfg, 2.33.14
hue, 2.30.88.4     clr, 2.33.15
hydration, 2.23.14.2, 2.30.7     cmp, 2.33.33
     parameters, 2.33.13     cn, 2.33.9
hydrogen bond, 2.23.5.25, 2.23.5.26, 2.29.62.17, 5.5.7     cnf, 2.33.7
     bonding parameters, 2.33.12     cnt, 2.33.8
          cutoff, 2.19.21     cod, 2.33.4
     bonds, 2.30.99.3     col, 2.33.24
     display, 2.23.5.32     gro, 2.33.10
     placement, 2.29.86.25     gui, 2.28
hydrophobicity profile, 3.3.12     hbt, 2.33.12
iSee, 5.8.14     hdt, 2.33.13
i_2out, 2.18.4     htm, 2.33.11
i_out, 2.18.3     iar, 2.33.35
iarray, 2.29.22.6, 2.30.55.1, 2.30.65.2, 2.30.69.8, 5.6.1     lps, 2.29.7.5.2
     making, 2.30.65.1     map, 2.33.16
icb files, 5.8.14     mat, 2.33.37

     pdb, 2.33.28inner join, 2.29.50
     prf, 2.33.34insert rows, 2.29.1.4
     rar, 2.33.38integer, 5.6.2
     res, 2.33.20     array, 2.30.65, 5.6.1
     rs, 2.33.23     output, 2.18.4
     rst, 2.33.22     shell variables, 2.18
     sar, 2.33.36intensity, 2.30.88.4
     se, 2.33.30interaction cutoff, 2.20.27
     seq, 2.33.29     lists, 2.20.27, 2.23.14.3
     tab, 2.33.25interactive docking, 1.4.2.8
     tot, 2.33.26interatomic distance, 2.19.10, 2.29.62.16, 2.30.148
     trj, 2.33.17     potential, 2.29.86.51, 2.29.87.37
     var, 2.33.21interface comparison, 2.29.14.3
     vwt, 2.33.27     residues, 3.3.5
icmCavityFinder, 2.32.14     torsions, 3.3.7
icmMacroShape, 2.32.88     view, 2.32.28
icmPmfProfile, 2.32.23intermolecular bond, 2.29.69.3
icmPocketFinder, 2.32.89internal coordinate file, 2.33.21
icmscript, 2.29.81.4     coordinates, 2.8.9
     arguments, 2.30.58     positional restraints, 5.9.4
if, 2.29.47interplanar angle, 2.32.4
ignoring swiss secondary structure, 2.24.10interpolate, 2.30.29.1
illegal smiles, 2.30.69.2interpolation, 2.30.29.1
image, 3.2.6interruptAction, 2.22.15
     annotation, 3.2.5inverting array order, 2.30.65.2, 2.30.119.2
     center, 3.2.8italic, 2.29.86.38.1
     format, 5.9.3iterative overlay, 2.29.94
     high quality, 3.2.2     superposition, 2.23.14, 2.29.95
     parray, 5.7.3.3javascript, 2.11
     resolution, 3.2.2join, 2.29.50
     rotation, 3.2.3     tables, 2.29.50
implicit continuous solvation, 2.33.13keep, 2.29.49
     solvation, 2.29.86.72kernel models quality, 2.30.133.4
imposing tether, 2.29.86.68, 2.29.86.69     mapping, 2.33.15
     place, 2.14.4kmz, 5.5.3
          ops, 2.14.4l_antiAlias, 2.20.1
incidence, 2.30.88.13l_autoLink, 2.20.2
increasing the number of shell variables, 2.33.14l_bpmc, 2.20.3
increment charge, 2.29.86.10l_breakRibbon, 2.20.4
index expressions, 2.6l_bufferedOutput, 2.20.5
     in array, 2.30.69.4l_bug, 2.20.6
     substring, 2.30.69.3l_caseSensitivity, 2.20.7
     table, 2.29.107.24l_commands, 2.20.8
          entry, 2.30.132.1l_confirm, 2.20.9
          sdf-file path, 2.30.105l_easyRotate, 2.20.10
indices of labeled table rows, 2.30.69.6l_info, 2.20.11
          selected table rows, 2.30.69.5l_minRedraw, 2.20.12
infinity, 2.30.165l_neutralAcids, 2.20.13
info, 2.29.48l_out, 2.20.14
     molcart, 2.29.48.1l_print, 2.20.15

l_readMolArom, 2.20.17linked alignment, 2.30.96
l_showAccessibility, 2.20.18     sequence, 2.30.96
l_showMC, 2.20.19linux shell, 2.29.96, 5.10.2
l_showMinSteps, 2.20.20list, 2.29.55
l_showResCodeInSelection, 2.20.21     binary, 2.29.56
l_showSites, 2.20.23     database, 2.29.57
l_showSpecialChar, 2.20.22     directory, 2.29.58
l_showSstructure, 2.20.24     font, 2.29.55.1
l_showTerms, 2.20.26     html documents, 2.30.96
l_showWater, 2.20.25     molcart, 2.29.59
l_updateLists, 2.20.27          database, 2.29.59
l_warn, 2.20.28     of files, 2.30.132
l_wrapLine, 2.20.29     updates, 2.29.63
l_writeStartObjMC, 2.20.30listUpdateThreshold, 2.19.23
l_xrUseHydrogen, 2.20.31literature, 4.1
label, 2.29.23.22, 5.6.3load, 2.29.60
     fonts, 2.33.15     conf, 2.29.60.1
large text, 2.29.81.40     frame, 2.29.60.2
latent, 2.30.99.6     molcart, 2.29.60.3
learn, 2.29.51, 2.30.106     object, 2.29.60.6
     atom, 2.29.51.1     solution, 2.29.60.4
     chemical, 2.29.51.2     stack object, 2.29.60.5
left join, 2.29.50loadEDS, 2.32.42
     triangle of a matrix, 2.30.88.3loadEDSweb, 2.32.43
library to replacement groups, 2.29.62.27, 2.29.89.2, 2.29.89.3local, 3.5.1
ligand based screening, 3.15logarithm, 2.30.83
     binding, 2.32.28logical, 5.6.4
     dock faq, 3.13.2     operations, 2.14.3
     docking, 3.13, 3.13.1, 3.13.2     variables, 2.20
          intro, 1.4.2.6logical_ops, 2.14.3
     editing, 1.4.2.8logicals, 2.20
     editor, 2.32.37long axes, 2.30.160
     fit, 3.13loop database rebuilding, 2.29.107.28
     setting, 3.13.2     interrupt, 2.19.47
     view, 2.23.5.31     library, 2.29.7.5.2
light, 2.23.5.34     modeling, 1.4.2.3
lightness, 2.30.88.4          intro, 1.4.2.3
limits, 2.33.14     search, 2.29.7.5.2
line thickness, 2.23.12.5     resolution shape, 2.32.88
          in 2D chemicals, 2.23.9.14lower case, 2.30.164
lineWidth, 2.19.22ma29, 3.11
linear chemical notation, 2.26macro, 2.29.61, 5.6.5
     regression, 2.30.82macro_def, 5.6.5
     group, 2.29.52main ICM references, 4.2
     internal variables of molecular object, 2.29.53     concepts, 3.10.1
     ms2ali, 2.29.54make, 2.29.62
     sequences to 3D objects, 2.29.54     3d label, 2.29.62.15
     to alignment, 2.29.54     angle, 2.29.62.18
     variable, 2.29.53     background, 2.29.62.1
     variables, 2.29.53     blast index, 2.29.107.25

          chain, 2.29.62.3map, 2.19.25, 2.23.5.13, 2.23.6.1, 5.6.6
          multi, 2.29.62.3     aa property to sequence, 2.30.119.1
     boundary, 2.29.62.4     averaging, 2.30.143.5
     directory, 2.29.62.5     calculation, 2.29.62.24
     distance, 2.29.62.16     conversion, 2.29.62.31
     disulfide bond, 2.29.62.6     file, 2.33.16
     drestraint, 2.29.62.7     fitting, 2.22.8
     factor, 2.29.62.8     format, 5.6.6
     flat, 2.29.62.9     mean value, 2.30.91
          chem_array, 2.29.62.9     min value, 2.30.92
     grob, 2.32.36     name, 2.30.84
          from image, 2.29.62.11     operations, 5.6.6
               matrix, 2.29.62.12     transformations, 2.30.143.5
          image, 2.29.62.11     trimming, 2.30.22
          map, 2.29.62.10     value sigma, 2.30.130
          matrix, 2.29.62.12          on atoms, 2.29.86.36
          potential, 2.29.62.13     contouring, 2.29.62.14
          skin, 2.29.62.14mapAtomMargin, 2.19.25
     hbond, 2.29.62.17mapSigmaLevel, 2.19.24
     image, 2.29.62.20mapping chemical equivalences, 2.30.69
     index fasta, 2.29.81.24, 2.29.107.24     properties to sequence, 2.30.119.4
     key, 2.29.62.21     and factors, 3.11
     map, 2.29.62.22margin, 2.23.6.1
          cell, 2.29.62.23mass-spectrometry functions, 2.29.30, 2.29.31, 2.29.32
          factor, 2.29.62.24matching chemicals, 2.30.69.2
          potential, 2.29.62.25     hydrogens, 2.29.86.70
          xray, 2.29.62.31matrix, 5.6.7
     molcart, 2.29.62.26     derivatives, 2.30.79
     molsar, 2.29.62.27     new, 2.30.88.1
     pca, 2.29.62.29     plot, 2.30.32
     peptide bond, 2.29.62.30     map value, 2.30.89
     plot, 2.29.62.32maxColorPotential, 2.18.5, 2.32.25
     reaction, 2.29.62.33maxMemory, 2.18.7
     sequence, 2.29.62.35, 2.29.62.36     movie, 3.9.2
          alignment, 2.29.62.34mcBell, 2.19.26
          from alignment, 2.29.62.34mcJump, 2.19.27
          random, 2.29.62.36mcShake, 2.19.28
     torsion, 2.29.62.19mcStep, 2.19.29
     tree, 2.29.62.37mean force, 2.29.86.51, 2.29.87.37
          object, 2.29.62.38membrane, 2.23.14.2
     unique, 2.29.62.39memorizing positions, 3.2.4
makeAxisArrow, 2.32.36menu, 2.29.64
makeIndexChemDb, 2.32.44     script, 3.1.3
makeIndexSwiss, 2.32.45merge PDB, 2.32.92
makePdbFromStereo, 2.32.46     arrays to table, 2.29.43.3
makePharma, 2.32.87     continuation lines, 2.29.81.39
makeSimpleDockObj, 2.32.47     objects, 2.29.69.2
makeSimpleModel, 2.32.48     parts of molecule, 2.29.69.3
making predictive models, 2.29.51     pdb, 3.4.4
manual style, 1.5     sarray into string, 2.30.155

     tables, 2.29.4.3, 2.29.50     rotate, 2.29.66
merge2, 3.8.7modifyGroupSmiles, 2.32.37
mergePdb, 2.32.92modules, 1.4.4
     several chemical, 2.30.155.1mol, 2.29.81.49, 2.29.81.50, 2.29.107.11, 2.29.107.24, 5.6.11
merging into one molecule, 2.29.69.3     file, 2.30.153.3
mesh, 2.30.106, 2.30.186     to icm, 2.29.18.3
     point radius, 2.23.5.21     translation, 3.2.4
     score, 3.13.3.3mol-file to chem-table element, 2.30.106
mfMethod, 2.22.16mol-format, 2.23.14.6
mfWeight, 2.19.30mol2, 5.6.12
mimel, 5.6.8molcart, 2.29.16.1, 3.5
mimelDepth, 2.19.31     connection options, 3.5.2
mimelMolDensity, 2.19.32molecular, 2.30.57, 5.7.3.1
minNumGrad, 2.29.63     arrays, 5.7.3
minTetherWindow, 2.18.8     manipulations, 3.8
minimization exit criteria, 2.29.63     modifications, 3.8.5
minimize, 2.18.10, 2.29.63     object, 5.7.1
     cartesian, 2.29.63.1     objects, 2.16
     loop, 2.29.63.2     surface, 2.29.87.9, 5.8.7
     stack, 2.29.63.3     views, 1.4.1.1
     tether, 2.18.8, 2.29.63.4     volume, 2.30.111
     drop, 2.19.16molecule, 2.7
minimizeMethod, 2.22.17     create, 3.8.4
missing bonds, 2.29.69.3     properties, 2.29.86.34
     loop, 2.23.5.7, 2.23.5.8     rotation, 3.2.3
     residues, 2.30.53.1     translation, 3.2.3, 3.2.4
     triangles, 2.30.186     create, 1.7.2
mkUniqPdbSequences, 2.32.49     intro, 1.7.2, 2.7
mm26, 3.8     sort/reorder, 2.29.88.5
mmcif, 5.6.10     selecting, 2.8.6
mmff, 5.6.9monte carlo, 2.29.68
     type, 2.30.179montecarlo, 2.18.11, 2.18.13, 2.18.14, 2.18.15, 2.18.19, 2.22.7, 2.29.68
     show atom types, 2.29.87.11     local, 2.18.16
mnSolutions, 2.18.9     trajectory, 2.29.23.17
mncalls, 2.18.10moprphing, 2.32.38
mncallsMC, 2.18.11more, 5.6.13
mnconf, 2.18.12morph, 2.29.23.6
mnhighEnergy, 2.18.13     to tether target, 2.32.38
mnreject, 2.18.14morph2tz, 2.32.38
mnvisits, 2.18.15morphing, 2.29.23.6, 2.29.86.68, 2.29.86.69, 2.29.91.3
model reliability, 2.32.23mouse controls, 2.3
modify, 2.29.65     file, 2.29.107.31
     and reroot, 2.29.18.4move, 2.29.69
     chem, 2.29.67     alignment sequence, 2.29.69.7
          charge, 2.29.67.2     atoms, 2.29.86.3
          delete salt, 2.29.67.3     bonding, 2.29.69.3
          normalize, 2.29.67.4     column, 2.29.69.5
     chemical column, 2.29.67.3     element, 2.29.69.4
          find replace, 2.29.67.1     file, 2.21.28, 2.29.82.3
     molcart, 2.29.67.5     fragments together, 2.29.69.3

     ms_molecule, 2.29.69.1nota, 1.5
     multiple molecules, 2.29.69.2notational conventions, 1.5
     object, 2.29.69.2nproc, 2.29.38
     plane, 2.29.69.6nucleotides, 2.21.24
     sequence, 2.29.69.7number, 2.18.18
     table column, 2.29.69.5     of dots, 2.23.5.55
movie, 2.29.91.3          elements, 2.30.99
     images by frame, 3.9.2.2          hydrogen bonds, 2.29.87.23
     molecular simulation, 3.9.2          molecules in objects, 2.30.134.4
     rotate view, 3.9.1          occurrences, 2.30.99
     zooming, 3.9.1          residues in molecules, 2.30.134.4
moving selection to another object, 2.30.134.8          van der Waals contacts, 2.29.87.13
mpeg, 2.29.107.31     transfer from sequence, 2.29.3.2
ms_, 2.8.6nvis, 2.30.65.6
multi center drestraint, 2.22.6object, 2.29.13.1, 5.7.1
multi-part molecule, 2.29.18.2     in table, 2.30.106
multicore, 2.30.69.1     parray, 5.7.3.1
multiline input, 2.29.81.5     properties, 2.29.86.34
multiple NMR models, 2.23.14.4     stack, 5.8.9
     alignment, 2.29.3.3     to chemarray, 2.30.27
          to pairwise similarities, 2.32.7     user fields, 2.30.53.1
     conformation storage, 5.8.9     assign comment, 2.29.86.17
     conformations, 2.29.60.1, 2.29.91.1     source file, 2.30.54
     mol as text, 2.30.153.3     translate, 2.29.100
     object file, 2.29.81.2     merge, 3.8.6
     sequence alignment intro, 1.4.3.4     selecting, 2.8.5
     smiles file format, 2.29.81.46obsolete, 2.19.54
multiprocessor, 2.29.38occlusion shading, 2.29.13
mutate residue, 2.29.65octanol transfer, 2.30.111
mutating residue, 3.8.5off, 2.29.81.22
mute, 5.6.15     format, 5.5.3
mysql, 2.29.16.1oligonucleotide melting, 2.30.161
nLocalDeformVar, 2.18.16on-line help, 2.29.45.1, 2.29.45.2
nProc, 2.18.18     third, 2.30.37
nSsearchStep, 2.18.17only, 5.7.2
name, 2.30.78ontology, 2.30.43.6
     atom fields, 2.29.86.34openGL window, 2.29.102
naming compounds, 2.29.86.47operating system, 2.29.22.9, 2.29.96, 2.30.185, 5.10.2
nearest sequence, 2.30.92optimal chemical superposition, 3.14.5.1
neato, 2.30.157.7optimization, 2.29.68
neighbor joining, 2.29.62.38     Hbond, 2.32.91
neighbors, 2.30.148     hydrogen bond, 2.32.91
nested script, 5.8.2optimizeHbonds, 2.32.91
     real array, 2.30.119or, 2.14.3
nice, 2.32.39order, 2.29.3.1, 2.29.69.7
     image, 3.2.2original sequence names, 2.23.12.15
non-redundant, 3.4.3os_, 2.8.5
normal distribution, 2.30.118other variables, 2.24
normalize chemicals, 2.29.67.4out-of density atoms, 2.29.87.21
     defined, 2.30.165output, 2.18.3

overlap, 2.30.69.10     grid type definitions, 2.29.86.73
     by atom pairs, 2.29.94     object, 3.6.1
          chemical substructure, 2.32.22     objects, 3.6
overview, 1.4pharmacophores, 3.6
pK shift, 3.7.3     psi plot, 2.32.58
pKa, 2.29.22.20, 2.29.86.11, 2.29.86.12pipe, 2.29.81.43
     model, 2.29.86.12placeLigand, 2.32.50
packing density, 3.3.8planar angle, 2.29.62.18
pair-distances, 2.29.22.6plot, 2.29.71
pairdistance parray, 2.23.5.24     3D 2Dfunction, 3.12.3
pairwise interactions, 2.29.86.51          shape, 3.12.4
panel layout, 2.23.8.6     area, 2.29.72
paragraphs, 2.29.107.24     grid line width, 2.23.12.5
parallel, 2.18.18     histogram, 3.12.2
     computing, 2.30.69.1     how to, 3.12
     processing, 2.29.38     simple, 3.12.1
parallelization, 2.30.69.1plot2DSeq, 2.32.51
parameter list file, 3.14.6.2plotBestEnergies, 2.32.54
parray, 2.29.22.6, 5.7.3plotCluster, 2.32.56
parrayTo3D, 2.32.83plotFlexibility, 2.32.55
parrayToMol, 2.32.82plotMatrix, 2.32.57
parse SOAP message, 2.30.183plotRama, 2.32.58
parsing, 2.30.87plotRose, 2.32.59
     web pages, 2.29.81.47plotSeqDotMatrix, 2.32.52
partial least squares, 2.29.51plotSeqDotMatrix2, 2.32.53
     slide display, 2.29.23.21plotSeqProperty, 2.32.60
     sum, 2.30.76     3d, 1.4.3.7
passing arguments, 5.8.2plotting van der Waals, 3.7.1
     by reference, 2.29.61          faq, 3.7.1
pattern, 5.7.4pls, 2.29.51
     search, 2.29.35.2     column contributions, 2.30.157.8, 2.30.157.9
pause, 2.29.70     model, 2.30.157.8, 2.30.157.9
pdb, 5.6.10, 5.7.6     weights, 2.30.157.8, 2.30.157.9
     file creation time, 2.30.38pmf, 2.22.16
     files, 2.33.28     residue profile, 2.32.23
     format, 2.29.81.48pmf-file, 2.33.19
     merge, 3.4.4pmffile, 2.33.19
     sequence generation, 3.4.3png, 2.29.107.36, 5.7.5
pdbDirStyle, 2.22.18pocket, 2.32.28, 2.32.89, 3.13.1.1
peptide, 5.7.7point coordinates, 2.30.189.1
     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, 2.30.111
     setup, 3.1.2polarization charge, 3.7.2, 5.7.13
ph30, 3.12positional constraint, 2.23.14.11
ph4, 5.7.8postscript, 2.21.23
     object faq, 3.6.1potential surface, 2.23.14.5
pharmacophore, 2.29.12, 3.5, 5.7.8          coloring, 5.7.13
     faq, 3.6pov-ray, 2.29.107.38

precision, 2.30.133.4     molcart, 2.29.78
predict, 2.29.73question mark operator, 2.30.153.7
predictSeq, 2.32.61quit, 2.29.79
prediction model, 2.30.82     property transfer via alignment, 2.30.119.3
     quality, 2.30.133r_2out, 2.19.34
     score, 2.30.133r_out, 2.19.33
predictive models, 2.29.51.2radii.electrostatic, 2.30.117
preference, 2.22     van der Waals, 2.30.117
     system, 2.22.1rainbow, 2.30.29.1
preferences, 3.1.2.3ramachandran faq, 3.3.3
prepSwiss, 2.32.62     how to, 3.3.3
previous atom, 2.30.98.1random array, 2.30.118
principal axes, 2.30.160     order, 2.30.136
     component analysis, 3.3.9     sequence, 2.29.62.36
     inertia moments, 2.30.86randomSeed, 2.18.19
print, 2.29.74randomize, 2.18.19, 2.29.80
     bar, 2.29.75     angles, 2.29.80.1
     image, 2.29.77     coordinates, 2.29.80
     to string, 2.29.90     torsions, 2.29.80
printMatrix, 2.32.63rarray, 2.29.22.6, 2.30.55.1, 2.30.119.2, 5.7.11
printPostScript, 2.32.64     properties, 2.30.119.4
printTorsions, 2.32.65rdBlastOutput, 2.32.68
printf, 2.29.76rdSeqTab, 2.32.69
problem, 3.14.6.2reaction, 2.29.62.33
processors, 2.18.18     group file, 2.29.52
profile, 5.7.9read, 2.29.81, 2.29.81.56, 2.29.81.57
program overview, 1.4     FILTER, 2.29.81.6
progress bar, 2.29.75     alignment, 2.29.81.12
progression, 2.29.75     all, 2.29.81.7
project setup, 3.13.2.2     binary, 2.29.81.2
projected alignment, 2.30.96.3     blob, 2.29.81.38
projecting surface charge, 3.7.2     color, 2.29.81.13
property, 2.29.86.52, 2.29.86.53, 2.29.86.54     column, 2.29.81.51
     grids, 2.19.20     comp_matrix, 2.29.81.14
     map, 2.29.86.73     conf, 2.29.81.15
     superposition, 2.29.86.73     csd, 2.29.81.16
prosite, 5.7.10     csv, 2.29.81.44
     pattern, 5.7.4     database, 2.29.81.17
protein docking, 2.30.189.2     drestraint, 2.29.81.18
          intro, 1.4.2.5          type, 2.29.81.19
     engineering, 2.24.9     entries from database, 2.29.81.8
     grid docking, 3.14.2     factor, 2.29.81.20
     health, 2.32.58     file by chunk, 2.29.81.40
     topology, 2.23.5.42     from file, 2.29.81.1
psa, 5.7.12          string, 2.29.81.5
purple box, 2.30.21     fromstring, 2.29.81.5
quadratic equation, 2.30.144     ftp http, 2.29.81.9
quantum mechanics, 2.29.81.21, 2.29.107.17     gamess, 2.29.81.21
qubic equation, 2.30.145     grob, 2.29.81.22
query, 3.14.6.1     gui, 2.29.81.3

          file, 2.29.81.4               web, 2.21.19
     iarray, 2.29.81.23     restraint, 2.29.81.54
     index, 2.29.81.24real, 5.7.14
          table, 2.29.81.8     array, 5.7.11
     json, 2.29.81.57     shell variables, 2.19
     library, 2.29.81.25     space refinement, 2.29.62.31
          mmff, 2.29.81.26reals, 2.19
     librarymmff, 2.29.81.26rebel, 2.18.5, 2.23.14.5, 5.7.13
     map, 2.29.81.27rebuild molcart index, 2.29.7.10
     matrix, 2.29.81.28recalculate dependent values, 2.29.7.2
     menu file, 2.29.81.3     values, 2.29.1.1.1
     mol, 2.20.13, 2.29.81.8, 2.29.81.29receptor, 3.13.1.1
     mol2, 2.29.81.8, 2.29.81.30     preparation, 3.13.1.1
     object, 2.29.81.32redefine hydrogen coordinates, 2.29.86.25
          parray, 2.29.81.32.1references, 4
     pdb, 2.23.14.4, 2.29.81.2, 2.29.81.33refineModel, 2.32.66
          sequence, 2.29.81.34reflections, 2.23.5.33
     profile, 2.29.81.35refresh view, 2.29.23.2
     prosite, 2.29.81.36refs, 4.1
     rarray, 2.29.81.37regexp, 2.10, 2.30.87
     sarray, 2.29.81.39, 2.29.81.40     back references, 2.10.1.3
     sequence, 2.29.81.8, 2.29.81.41     syntax, 2.10.1
          database, 2.29.81.41.1regression, 2.29.51
     smiles, 2.29.81.46regul, 2.32.67
     stack, 2.29.81.42regular expression, 2.10, 2.30.69.4, 2.30.87
     string, 2.29.81.43          filter, 2.29.81.1
     table, 2.29.81.44     expression, 2.30.123.3
          chunk, 2.29.81.45regularization, 2.18.8, 2.29.63.4, 5.7.15
          csv, 2.29.81.44     procedure, 3.8.3
          html, 2.29.81.47rejectAction, 2.22.19
          mmcif, 2.29.81.48relational database, 2.30.146
          mol, 2.29.81.50relative accessible area of atoms, 2.22.2
          mol2, 2.29.81.49release notes, 1.1
     text, 2.29.81.40remarkObj, 2.32.70
     trajectory, 2.29.81.31remove columns, 2.29.22.16
          and save a fragment, 2.29.81.31.1     expression tags, 2.30.177
          write, 2.29.81.31.1     file, 2.29.22.9
     unix, 2.29.81.10     trailing blanks, 2.30.175
          cat, 2.29.81.11removing html tags, 2.29.81.47
     variable, 2.29.81.52     outliers, 2.30.175
     view, 2.29.81.53rename, 2.29.3.1, 2.29.82
     vrestraint, 2.29.81.54     chemicals, 2.29.86.47
          type, 2.29.81.55     column table, 2.29.82.1
     with filter, 2.29.81.6     file, 2.29.82.3
     xml, 2.29.81.56     molcart, 2.29.82.2
readMolNames, 2.24.11     system, 2.29.82.3
readcomp_matrix, 2.29.81.14renaming, 2.23.12.15
reading external tool output, 2.29.62.1reorder, 2.29.69.7
     from standard input, 2.29.81.43     alignment sequences, 2.29.107.1
     pdb from ftp, 2.21.18     array, 2.30.136

     objects, 2.29.88.4     matrix, 2.30.29
replace matching array element, 2.30.123.1ribbon, 5.7.18
     without interpretation, 2.30.123.2     bullets, 2.23.5.7
replacing scaffold in a library, 2.29.67.1     diagram, 2.23.5.42, 2.23.5.43
reproducible randomness, 2.18.19ribbonColorStyle, 2.22.21
reroot, 2.29.18.4ribbonStyle, 2.22.22
     selections, 3.3.6right join, 2.29.50
resLabelShift, 2.19.35rigid chemical superposition, 2.29.94
resLabelStyle, 2.22.20ring, 2.30.127
reserved names, 2.24     sampling, 3.16
residue, 2.29.13.1, 5.7.16     templates, 2.29.86.8
     accumulators, 2.30.62rm, 2.29.22.9
     alignment, 2.29.86.68, 2.29.86.69rocking, 2.29.23.5
     conservation, 2.30.119.5root mean square deviation, 2.30.133.4
     contact area matrix, 2.30.88.8roots, 2.30.144, 2.30.145
          areas, 2.30.7.1rotate, 2.29.84
     field, 2.29.86.34     grob, 2.29.84.2
     gap, 2.23.5.7, 2.23.5.8     object, 2.29.84.1
     label, 2.19.35, 2.29.3.2     view, 2.29.84.3
     library file, 2.33.20rotation, 2.29.23.5
     name, 2.30.78     angle, 2.30.17
          translation, 2.23.14.13rounding, 2.30.119
     number, 2.30.65.5     a real, 2.30.153
          table, 2.30.157.3     output, 2.29.87.45
     property averaging, 2.30.143.3rsWeight, 2.19.36
          calculation, 2.30.62rs_, 2.8.7
     proximity, 2.30.88.8ruler, 2.19.10
     ranges, 2.8.11     script, 2.29.8
     selection, 2.20.21running a docking job, 3.13.2.5
          as string, 2.30.153.8     dock job, 3.13.2.4
          function, 2.30.124     script from html, 5.8.2
     table, 3.14.4.1s-s bond, 5.4.5
     tethering, 2.29.86.68, 2.29.86.69s_alignment_rainbow, 2.21.1
     user field, 2.30.53.1s_blastdbDir, 2.21.2
residue_selections, 2.8.11s_editor, 2.21.3
     selecting, 2.8.7s_entryDelimiter, 2.21.4
resizing, 2.30.67s_errorFormat, 2.21.5
resorting nodes edges, 2.30.157.7s_fieldDelimiter, 2.21.6
restore, 3.14.6.2s_helpEngine, 2.21.7
     defaults, 2.29.82.4s_icmPrompt, 2.21.10
     preference, 2.29.82.4s_icmhome, 2.21.8, 3.1.2.1
restraining molecules to shapes, 2.23.14.11s_imageViewer, 2.21.11
restraints, 2.17, 2.29.86.68, 2.29.86.69s_inxDir, 2.21.9
     torsion, 2.29.86.81s_javaCodeBase, 2.21.12
return, 2.29.83s_labelHeader, 2.21.13
reverse complement, 2.30.135.1s_lib, 2.21.14
     lighting, 2.29.86.42s_logDir, 2.21.15
     normals, 2.29.86.42s_out, 2.21.16
reversing order, 2.30.65.2s_pdbDir, 2.21.17
rgb, 2.30.88.4, 5.7.17s_pdbDirFtp, 2.21.18

s_printCommand, 2.21.21searchSeqProsite, 2.32.77
s_projectDir, 2.21.20searchSeqSwiss, 2.32.78
s_prositeDat, 2.21.22searches and alignments, 3.4
s_psViewer, 2.21.23second moments, 2.30.160
s_reslib, 2.21.24secondary structure derivation from 3D, 2.29.5.1
s_skipMessages, 2.21.25          schematic, 2.23.5.42
s_sysCp, 2.21.26segMinLength, 2.18.20
s_sysLs, 2.21.27segment, 5.8.4
s_sysMv, 2.21.28select, 2.29.85
s_sysRm, 2.21.29     atoms by number of bonded atoms, 2.30.134.3
s_tempDir, 2.21.30          of the fixed torsions, 2.30.134.2
s_translateString, 2.21.31     based on alignment, 2.30.134.14
s_userDir, 2.21.32          bfactor, 2.30.134.7
s_usrlib, 2.21.33          center of mass, 2.30.134.15
s_webEntrezLink, 2.21.34          coordinates, 2.30.134.7
s_webViewer, 2.21.35          iarray, 2.30.134
s_xpdbDir, 2.21.36          length, 2.30.134.13
sa23, 3.3          occupancy, 2.30.134.7
sampling grid, 2.30.189.2          user field, 2.30.134.7
sarray, 2.29.22.6, 5.8.1     chemical, 2.29.85.1
     transformation in place, 2.29.99.1     column table, 2.29.85.2
save preferences, 2.29.107.42     lines, 2.29.81.1
     print, 3.2.6     tether partners, 2.30.134.12
     sdf file, 2.29.107.11     vw partners, 2.30.134.12
saving graphics to album, 2.29.62.20selectMinGrad, 2.19.37
     image, 2.29.107.36selectSphereRadius, 2.19.38
scaffold, 2.30.175selected stack conformations, 2.29.22.17
scaffolds, 2.29.52selecting by b-factor, 2.30.134
scoring, 3.13.1.4               y z, 2.30.134
screen X, 2.30.187     columns, 5.9.1
     coordinates, 2.30.187     from clusters, 3.14.6.4
script, 2.30.96.4, 5.8.2     neighboring elements, 2.30.98
     file name, 2.30.54     residues, 3.3.6
     inside ICM, 5.8.2     saving, 2.30.65.4
     name, 5.8.2selection, 2.8, 2.30.134, 2.30.134.6
     image generation, 2.29.23.3     elements, 2.8.4
scripting molecular movements, 3.2.4     examples, 2.8.3
sdf, 2.23.14.6, 2.29.107.24, 5.6.11     functions, 2.8.10
     file, 2.29.81.49, 2.29.81.50, 2.29.86.47, 2.29.107.11, 2.30.153.3, 5.7.3     gap patching, 2.30.134, 2.30.134.11
     to chem-table, 2.30.106     level, 2.8, 2.30.179
search for chemical pattern, 2.30.55.3     levels, 2.8.2
     pdb headers, 3.4.5     simplification, 2.30.134.11
     prosite, 3.4.1     transfer, 2.30.134, 2.30.153.8
     sequence pattern, 2.29.35.8     type, 2.8
searchObjSegment, 2.32.73     types, 2.8.1
searchPatternDb, 2.32.71     variable, 2.24.12
searchPatternPdb, 2.32.72     atoms, 2.8.8
searchSeqDb, 2.32.74     functions, 2.8.10
searchSeqFullPdb, 2.32.76     molecules, 2.8.6
searchSeqPdb, 2.32.75     objects, 2.8.5

     residues, 2.8.7          type, 2.29.86.6
     torsions, 2.8.9          and formal charges, 2.29.86.7
     variables, 2.8.9     cartesian, 2.29.86.8
selections, 2.29.86.34     chain, 2.29.86.9
     in molecular objects, 2.8     charge, 2.29.86.10
selftether, 2.23.14.11, 5.9.4          formal, 2.29.86.11
seq_ali_project, 2.30.153.6               auto, 2.29.86.12
sequence, 2.30.169, 2.30.170, 5.8.3          mmff, 2.29.86.13
     alignment, 2.30.5.1, 2.32.1     chargemmff, 2.29.86.13
          intro, 1.4.3.3     chiral, 2.29.86.14
     analysis intro, 1.4.3          chemical, 2.29.86.15
     assembly, 2.29.43.2     color, 2.29.86.16
     belongs to alignment, 2.30.69     comment, 2.29.86.17, 2.29.86.18
     conservation, 2.30.133.7          sequence, 2.29.86.19
     distance, 2.30.134     comp_matrix, 2.29.86.20
          matrix from alignment, 2.30.88.9     current map, 2.29.86.45
     dotplot, 1.4.3.2          object, 2.29.86.48
     from alignment, 2.29.22.23     directory, 2.29.86.21
          pdb, 2.29.62.35     drestraint, 2.29.86.22
     identity, 2.32.7, 2.32.8          type, 2.29.86.23
     intro, 1.4.3     electrostatic radii, 2.29.86.79
     modification, 2.30.177     error, 2.29.86.33
     neighbor, 2.30.96.3     field, 2.29.86.34
     parray, 5.7.3.2          alignment, 2.29.86.35
     pattern, 5.7.4          map, 2.29.86.36
     position correspondence, 2.30.157.3          name, 2.29.86.37
     positional weights, 2.29.86.1     font, 2.29.86.38
     redundancy removal, 2.29.43.2          grob, 2.29.86.39
     search, 2.29.35.2     foreground, 2.29.86.40
     selection, 2.29.22.23     format, 2.29.86.41
     structure alignment, 2.31.1     grob, 2.29.86.42
     to alignment transfer, 2.30.119.3          coordinates, 2.29.86.42
     type, 5.8.3          label, 2.29.86.42
sequence-alignment mapping, 2.30.153.5, 2.30.153.6     group, 2.29.86.63
sequence-structure alignment, 2.30.5.1          column, 2.29.86.24
     output format, 2.18.21, 2.18.22     hydrogen, 2.29.86.25
sequenceBlock, 2.18.21     key, 2.29.86.43
sequenceColorScheme, 2.22.23     label, 2.29.86.44
sequenceLine, 2.18.22          3d label, 2.29.86.44.4
sequences, 3.4          chemical, 2.29.86.44.3
     not in alignments, 2.29.22.23          distance, 2.29.86.44.1
set, 2.29.86          table, 2.29.86.44.2
     alternative atom, 2.29.86.18     map, 2.29.86.45
     area, 2.29.86.1     molcart, 2.29.86.46
     atom, 2.29.86.3     molecular variables, 2.29.86.83
          ball label, 2.29.86.2     name, 2.29.86.47
     background image, 2.29.86.4          sequence, 2.29.86.47.1
     bfactor, 2.29.86.5     object, 2.29.86.48
     biological symmetry, 2.29.86.64     occupancy, 2.29.86.49
     bond topology, 2.29.86.7     plane, 2.29.86.50

     property, 2.29.86.52, 2.29.86.54, 2.29.86.55          radii, 2.29.86.86
          alignment, 2.29.86.55setResLabel, 2.32.80
          chemical view, 2.29.86.54setcomp_matrix, 2.29.86.20
          column, 2.29.86.53seticmff, 2.32.79
     radii graphical, 2.29.86.86setting conf properties, 2.29.86.61
     randomSeed, 2.29.86.56setvs_var, 2.29.86.83
     randomize, 2.29.86.56sf-term, 2.29.86.72
     resolution, 2.29.86.57sfWeight, 2.19.39
     selftether, 2.29.86.68sh24, 3.4
     similarity, 2.30.43.8, 2.30.133.2shadows, 2.23.5.34
     site, 2.29.86.26shell, 3.1, 5.8.5
          alignment, 2.29.86.27     functions, 2.29.40
          residue, 2.29.86.29     intro, 1.7.1
     slide, 2.29.86.30     progression, 2.29.75
     sstructure backbone, 2.29.86.59     warning message, 2.30.188
          sequence, 2.29.86.60shineStyle, 2.22.24
          to sequence, 2.29.86.60shininess, 2.19.40
     stack, 2.29.86.61show, 2.29.87, 2.29.87.39
          energy, 2.29.86.61, 2.29.91.1     alias, 2.29.87.7
     stereo, 2.29.86.58     aliases, 2.29.87.7
     swiss, 2.29.86.62     alignment, 2.29.87.8
          name, 2.29.86.62     area, 2.29.87.9
     symmetry, 2.29.86.65     atom, 2.29.87.10
          bio, 2.29.86.64          type, 2.29.87.11
          crystal, 2.29.86.63     atoms, 2.29.87.10
          group, 2.29.86.63     bond, 2.29.87.12
          to a torsion, 2.29.86.65     clash, 2.29.87.13
     table, 2.29.86.66     color, 2.29.87.14
     tautomer, 2.29.86.31     column, 2.29.87.15
     terms, 2.29.86.67     comp_matrix, 2.29.87.16
     tether, 2.29.86.69     database, 2.29.87.17
          append, 2.29.86.70     drestraint, 2.29.87.18
     texture, 2.29.86.32          type, 2.29.87.19
     type, 2.29.86.71     energy, 2.29.87.20
          mmff, 2.29.86.77          atom, 2.29.87.21
          molecule, 2.29.86.75     gradient, 2.29.87.22
          object, 2.29.86.74     hbond, 2.29.87.23
          property, 2.29.86.73          exact, 2.29.87.24
          sequence, 2.29.86.76     hbondexact, 2.29.87.24
          surface, 2.29.86.72     html, 2.29.87.25
     variable grid, 2.29.86.84     iarray, 2.29.87.26
     variablegrid, 2.29.86.84     integer, 2.29.87.27
     view, 2.29.86.80     key, 2.29.87.4
     vrestraint, 2.29.86.81     label, 2.29.87.28
     vrestraintvs_var, 2.29.86.82     library, 2.29.87.29
          radii, 2.29.86.78     link, 2.29.87.30
     vwelradii, 2.29.86.79     logical, 2.29.87.31
     vwradii, 2.29.86.78     map, 2.29.87.5
     window, 2.29.86.85     mol, 2.29.87.32
     xstick, 2.29.86.86     mol2, 2.29.87.33

     molecules, 2.29.87.6     by residue selection, 2.29.22.24
     object, 2.29.87.35     sequences, 5.8.6.1
     pdb, 2.29.87.36sixthe power, 2.22.6
     pharmacophore type, 2.29.87.53skin, 2.19.35, 5.8.7
     pmf, 2.29.87.37     intro, 1.4.1.2
     preferences, 2.29.87.38slide, 2.29.1.3, 2.30.141, 5.8.14
     profile, 2.29.87.39     transition time, 2.29.23.21
     residue, 2.29.87.40slides, 2.30.187
          type, 2.29.87.41slideshow, 2.29.1.3, 2.29.23.21, 2.30.141
     residuetype, 2.29.87.41sln, 5.8.8
     segment, 2.29.87.42smallest set of smallest rings, 2.30.127
     selftether, 2.29.87.1smart, 2.23.14.6
     sequence, 2.29.87.43smarts, 2.30.69.2
     shell variable, 2.29.87.3smiles, 2.23.14.6, 2.26
     site, 2.29.87.2     to chem-table element, 2.30.106
     stack, 2.29.87.44smooth alignment, 2.30.143.4
     svariable, 2.29.87.3     interpolation, 2.29.91.3
     table, 2.29.87.45     map, 2.30.143.5
          as database, 2.29.87.17     rarray, 2.30.143.1
     term, 2.29.87.46     surface, 2.32.88
     tethers, 2.29.87.47soap, 2.27
     version, 2.29.87.48soft trim, 2.30.175
     volume, 2.29.87.51solid sphere, 2.23.5.11
          map, 2.29.87.52solubility, 2.30.111
     volumemap, 2.29.87.52solvation, 2.22.25, 2.23.14.2
     vrestraint, 2.29.87.49     energy, 2.19.39, 2.22.25
          type, 2.29.87.50solvent accessible area, 2.18.23
     vrestraints, 2.29.87.49          surface, 2.23.5.55, 2.23.5.56, 2.29.87.9
showcomp_matrix, 2.29.87.16sort, 2.29.88, 2.29.88.4
showing weak hydrogen bonds, 2.23.5.25     array, 2.29.88.1
side chain, 2.32.90     arrays, 2.29.88.1
          flexibility, 2.32.90     column, 2.29.88.3
sigma function, 2.30.43.8, 2.30.133.2          table, 2.29.88.3
     level, 2.23.7.5     molecules, 2.29.88.5
signal recognition measure, 2.32.21     object, 2.29.88.4
similar chains, 2.30.134.13     stack, 2.29.88.6
similarity, 2.29.35.9, 2.29.35.10     table, 2.29.88.2
simple expressions, 2.10.1.1sortSeqByLength, 2.32.81
     string substitution, 2.30.123.2space group, 2.29.66
simplified representation, 2.23.5.16     transformations, 2.30.173
     compound, 2.30.176sparse atoms, 2.23.14.3
     mesh structure, 2.29.15.2spawn background job, 2.29.62.1
simulation duration, 2.19.47special values, 2.30.165
     temperature, 2.19.46specificity, 2.30.133.4
     intro, 1.4.2spectral decomposition, 2.30.44
sinking number, 2.19.35split, 2.29.89
site, 2.29.11.2, 5.8.6     column values, 2.29.89.5
     arrows, 2.29.86.26     grob, 2.29.89.1
     table, 5.8.6.1     group, 2.29.89.2
sites, 2.29.22.26          array, 2.29.89.3

     object, 2.29.89.6     matching, 2.10, 2.30.87
          to molecules, 2.29.89.6     variables, 2.21
     sequence, 2.29.89.4strings, 2.21
     table cell, 2.29.89.5strip, 2.29.93
     tree, 2.29.89.7struct, 2.30.96.2
splitting selection, 2.8.11structural alignment, 2.29.3.5, 2.30.5.2
spreadsheet, 2.29.81.44          optimization, 2.29.35.1
sprintf, 2.29.90     superposition, 2.29.3.5
sql, 2.29.78, 2.29.86.46, 2.30.49.1, 2.30.96.12, 2.30.99.5, 2.30.179.2     analysis, 3.3
sqlite, 3.5.1     comparison, 2.30.23.2
sqrt, 2.30.37     factors, 3.11.1
square matrix to element pairs, 2.30.157.5     structure, 3.11.1
ssThreshold, 2.19.41sub-alignment to selection, 2.30.125
ssWeight, 2.19.42sub-matrix, 2.30.88.2
ssbond, 5.4.5subalignment, 2.30.5.3, 5.1.1
ssearch, 2.18.17, 2.29.92submap, 2.30.84
ssearchStep, 2.19.43subroutine, 2.29.61
ssign sstructure segment, 2.29.5.2subset, 2.6
stack, 2.18.12, 2.18.13, 2.18.15, 2.22.7, 2.29.86.61, 2.29.91, 2.29.91.1, 2.30.65.6, 2.30.157.6, 5.3.12, 5.8.9substring, 2.30.87, 2.30.153, 2.30.153.1
     bin size, 2.29.14substructure, 2.29.35.9, 2.29.35.10
     cleaning, 2.29.22.17     search, 2.29.35.4
     extension, 2.29.4.2superimpose, 2.23.14, 2.29.94
     multiplication, 2.29.4.2     faq, 3.3.1
     merge, 3.7.7     how to, 3.3.1
standard chemical form, 2.29.67.4     minimize, 2.29.95
     deviation, 2.30.130support, 1.3
standardization, 2.29.22.11suppressing view changes, 2.29.23.21
     chemical, 2.29.67surface, 2.19.35, 2.30.106, 5.8.15
startup, 3.1.2.3     accessibility, 2.29.87.9
static RMSD, 2.30.152     area, 2.32.2, 5.8.15
     and dynamic hbonds, 2.23.5.24     charge, 5.7.13
statistical thermodynamics, 2.30.46     color, 2.29.86.16
stereo, 2.23.5.52, 2.29.30, 2.29.86.58     dot density, 2.23.5.55
     reconstruction, 3.8.9     energy, 2.22.25, 2.29.86.72
stereo-specific hydrogens, 2.29.22.11     mesh, 2.30.189.2
stereoisomer, 2.29.30     point selection, 2.30.189
stereoisomers, 2.20.16     term, 2.19.39
stick, 5.8.10surfaceAccuracy, 2.18.23
store, 2.29.91surfaceMethod, 2.22.25
     conf, 2.29.91, 2.29.91.1surfaceTension, 2.19.44
     frame, 2.29.91.3svariable, 5.8.12
     image, 2.29.62.20     map, 2.30.157.7
     stack object, 2.29.91.2swapping protein fragments, 3.8.7
     torsion type, 2.29.91swiss, 2.29.86.62
strength of hydrogen bond, 2.29.23.14swissFields, 2.24.10
string, 5.8.11swissprot, 2.29.86.26
     array, 2.30.132, 5.8.1symmetrization of a matrix, 2.30.88.3
     filtering, 2.30.175symmetry, 2.30.173
     inversion, 2.30.153.1     faq, 3.10
     label, 2.29.23.12     group, 2.18.2

syntax highlighting, 5.8.2texture, 5.5.3
sys, 2.29.96tga, 5.9.3
system, 5.10.2then, 2.29.98
     command, 2.29.96thickness, 2.23.9.14
     copy, 2.21.26thread to template, 2.29.63.4
     file move, 2.21.28threading, 2.30.5.1
     list file, 2.21.27     letter code, 2.30.169, 2.30.170
     remove, 2.21.29thumbnails, 2.30.67
table, 2.29.22.4, 2.29.86.52, 2.29.86.53, 2.29.86.54, 2.29.88.3, 5.9.1tif, 5.9.6
     actions, 5.9.2.4time, 2.30.38, 2.30.153.2
     column, 2.30.96timeLimit, 2.19.47
          format, 2.29.86.41tolFunc, 2.19.49
          plot, 2.29.62.32tolGrad, 2.19.48
          transformations, 2.30.101topological psa, 5.7.12
     creation, 2.29.43.3torScan, 2.32.84
     display style, 5.9.1torsion rmsd comparison, 2.29.14.2
     expression, 5.9.2     scan, 2.32.84
     from matrix, 2.30.157.4torsions, 2.30.99.3
     grid view, 5.9.1     score, 2.31.2
     of atoms and distances, 2.30.157.10tpsa, 5.7.12
     operations, 5.9.2.1trajectory, 2.29.60.2, 2.29.91, 2.29.91.3, 5.6.14
     plot, 5.9.2.3     file, 2.33.17
     principal component analysis, 2.29.62.29     frame writing, 2.29.23.17
     print, 2.29.87.45     smoothing, 2.29.23.17
     row, 2.29.69.4transform, 2.29.99, 2.29.99.2
          label mark, 2.29.86.44.2     general, 2.29.99
          mark, 2.30.78     grob coordinates, 2.29.99.2
     selected row numbers, 2.30.69     molecules, 2.29.99.2
     subset, 5.9.2.2     sarray, 2.29.99.1
     show html, 2.29.105.1transformation, 2.30.119, 5.9.7
targa, 5.9.3     vector, 5.9.7
target coordinates, 5.9.4     and symmetry, 3.10
tautomer, 2.29.31transforming points, 2.30.189.4
tempCycle, 2.19.46translate, 2.29.100
tempLocal, 2.19.45transparency, 2.29.86.42, 5.5.3
temperature, 2.19.46     background, 2.29.107.36
     variations in optimizer, 2.19.46     grob, 2.29.23.11
template docking, 3.13.2.6     grobs, 2.23.5.57
tensor product of two vectors, 2.30.88tree, 2.29.62.37, 2.30.96.5
terminal font, 2.33.14     cluster, 2.13
     window, 2.29.44     delete, 2.29.22.36
terms, 2.17     label format, 2.30.96.5
     hydrogen bonding, 2.19.21     representatives, 2.13.1
test, 2.29.97trim string array, 2.29.99.1
     binary, 2.29.97.1trimming grid map values, 2.30.175
testing if argument exists, 2.30.58true positives, 2.30.133.4
tether, 2.23.14.11, 2.29.107.9, 5.9.4, 5.9.5truncate alignment, 2.29.62.34
text, 2.30.87     values, 2.30.175
     search in tables, 2.30.55.2     grob, 2.23.5.9, 2.23.5.10
     to script, 5.8.2tsShapeData, 2.23.14.11

two alignments, 2.30.43.13vector, 2.30.99.6
     dimensional plot, 2.30.143.2     dot product, 2.30.184.1
     set comparison, 2.30.43.8, 2.30.133.2     length, 2.30.100
     sets, 2.30.69.10     product, 2.30.184.1
txdoc browser, 2.29.81.4     transformation, 2.30.101
type, 2.30.179.1vertex, 2.29.13.4.2
tzMethod, 2.22.26     connectivity, 2.30.88.13
tzWeight, 2.19.50vertexes, 2.29.13.4.2
uncharge functional groups, 2.29.67.2vertical alignment block, 2.29.62.34
unclip, 2.29.23.2     workspace, 2.23.8.6
underline, 2.29.86.38.1vertices, 2.29.13.4.2
undisplay, 2.29.101vicinity, 2.19.51
     graphics, 2.29.102video, 2.29.107.31
     window, 2.29.102view, 2.23.5.9, 2.23.5.10, 2.29.86.55
unfix, 2.29.103     point, 2.30.187
union, 2.30.69.10     restoration, 2.30.72
unique, 2.29.13.1, 5.10.1     transition, 2.29.86.80
     atomic order, 2.29.62.39views, 5.8.14
     column values, 2.29.43.4virtual, 5.10.3
     names, 2.30.96     arrays, 2.29.1.1.1
     new object name, 2.30.96     chemistry, 2.29.67, 2.30.99.4
     smiles, 2.29.62.39     field, 2.29.7.2
unix, 2.29.96, 5.10.2     ligand screening, 3.13, 3.13.1, 3.13.2, 3.13.3
     grep, 2.29.81.1               intro, 1.4.2.7
unlink alignments, 2.29.22.21visitsAction, 2.22.28
     sequences, 2.29.22.21vls, 3.13, 3.13.1, 3.13.2, 3.13.3
     variables, 2.29.22.21     cluster, 3.13.3.6
update database, 2.29.67.5     faq, 3.13.3
     speadsheet, 2.29.1.1.1     intro, 1.4.2.7
updates, 1.1     job queueing, 3.13.3.6
updating atom pairs, 2.20.27     overview, 3.13.1
upper case, 2.30.168     parallelization, 3.13.3.5
url string parsing, 2.30.157     results, 3.13.3.8
user atom display, 2.23.5.3     scores storage, 3.13.3.7
     commands, 2.29.81.3     threshold, 3.13.3.2
     defaults, 2.29.107.42vls_intro, 3.13.3.1
     environment, 3.1.2.2volume, 5.10.4
     menu, 2.23.10.1vrestraint, 5.10.5
     menus, 2.28     file, 2.33.23
user-defined properties, 2.29.86.34     type, 5.10.6
     solvation parameters, 2.30.7          file, 2.33.22
user_startup, 3.1.2.4vs_, 2.8.9
     icm, 3.1.2vs_out, 2.24.15
     guide, 3vwCutoff, 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, 2.29.86.81vwSoftMaxEnergy, 2.19.55
     selection, 2.8.9wait, 2.29.104
vdW gap, 2.30.148warning, 2.23.14.3

     suppression, 2.20.28     object, 2.29.107.32
water.dielectric constant, 2.19.15          parray, 2.29.107.34
waterRadius, 2.19.56          simple, 2.29.107.33
wavefront format, 2.29.62.11     pdb, 2.23.14.13, 2.29.107.35
web, 2.11, 2.29.105     png, 2.29.107.36
     table, 2.29.105.1     postscript, 2.29.107.37
webEntrezOption, 2.22.30     pov, 2.29.107.38
weighted rmsd, 2.23.14     povray, 2.29.107.38
while, 2.29.106     project, 2.29.107.2
whole string, 2.30.123.1     rarray, 2.29.107.4
window averaging, 2.30.143.1     sarray, 2.29.107.5
     layout, 2.30.153.9     sequence, 2.29.107.39
     width and height, 2.30.187     session, 2.29.107.40
windowSize, 2.18.24     several array, 2.29.107.8
     movie, 2.29.107.31     simple object, 2.29.107.33
wire, 5.10.7     stack, 2.29.107.41
wireBondSeparation, 2.19.57     system preference, 2.29.107.42
wireStyle, 2.22.31     table, 2.29.107.10
workspace, 2.29.102          mol, 2.29.107.11
write, 2.29.107          with links, 2.29.107.19
     album, 2.29.107.21     tether, 2.29.107.9
     alignment, 2.29.107.1     tethers, 2.29.107.9
     array, 2.29.107.8     trajectory, 2.29.23.17
          table, 2.29.107.8     vs_var, 2.29.107.43
     binary, 2.29.107.2writevs_var, 2.29.107.43
     blast, 2.29.107.25x-ray crystallography, 2.29.87.21
     column, 2.29.107.12xml, 2.29.81.56, 2.30.87, 5.1.6
     database, 2.29.107.13     drugbank example, 2.12
     drestraint, 2.29.107.14xpdb, 2.29.81.2
          type, 2.29.107.15xplor format, 2.29.81.27
     factor, 2.29.107.16xrMethod, 2.22.32
     gamess, 2.29.107.17xrWeight, 2.19.58
     grob, 2.29.107.18xray density to rectangular energy map, 2.29.62.31
     html, 2.29.107.19xstick, 5.10.8
     iarray, 2.29.107.3     radii, 2.29.86.2
     image, 2.29.107.20xyz morphing, 3.8.8
          alignment, 2.29.107.23zega, 5.10.9
          chemical, 2.29.107.22     intro, 1.4.3.6
          parray, 2.29.107.21|, 2.14.3
     index, 2.29.81.24, 2.29.107.24 
          blast, 2.29.107.25 
          fasta, 2.29.107.24 
     library, 2.29.107.26 
     map, 2.29.107.27 
     matrix, 2.29.107.6 
     model, 2.29.107.28 
     mol, 2.29.107.29 
     mol2, 2.29.107.30 
     molcart, 2.29.107.7 
     movie, 2.29.107.31 

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