Index

&, 2.12.3Ceil, 2.28.23
2D labels, 2.27.53.1Cell, 2.28.24
     to 3D, 3.13.2.3Charge, 2.28.25
     smooth, 2.28.135.2Chemical, 2.28.26
3D chemical builder, 1.4.2.8Cluster, 2.28.27
     font size, 2.27.23.12Collada, 5.5.3
     label, 2.27.23.12, 2.27.82.32Collection, 2.28.27.1
     labels, 2.27.53.1Color, 2.28.28
     mol file, 2.29.84     from gradient, 2.28.28.1
     plots intro, 1.4.3.7     image, 2.28.28.2
     smoothing, 2.28.135.3Connolly surface, 5.8.7
     superposition, 2.29.22Consensus, 2.28.29
     transformations, 2.27.95.2Corr, 2.28.30
3dxml, 5.5.3Cos, 2.28.31
=, 2.12.1Cosh, 2.28.32
A, 5.1Count, 2.28.33
Abs, 2.28.1CubicRoot, 2.28.34
Acc, 2.28.2D, 5.4
Acos, 2.28.3DAE, 5.5.3
Acosh, 2.28.4DE, 2.27.34.2
Adobe, 2.19.23DNA Representation, 1.4.1.3
Align, 2.28.5     alignment, 2.27.3.3
     sequence, 2.28.5.1     melting temperature, 2.28.153
Angle, 2.28.6     views, 1.4.1.3
Area, 2.28.7Date, 2.28.35
     residue contacts, 2.28.7.1Deletion, 2.28.36
Asin, 2.28.8Disgeo, 2.28.37
Asinh, 2.28.9Distance, 2.28.38
Ask, 2.28.10     2 alignments, 2.28.38.11
Askg, 2.28.11          matrices, 2.28.38.7
Atan, 2.28.12     Dayhoff, 2.28.38.9
Atan2, 2.28.13     Tanimoto, 2.28.38.6
Atanh, 2.28.14     alignment, 2.28.38.10
Atom, 2.28.15     as_, 2.28.38.3
Augment, 2.28.16          rarray, 2.28.38.4
Axis, 2.28.17     atoms, 2.28.38.3
B, 5.2     chemical, 2.28.38.6, 2.28.38.13
BPMC, 5.2.5     dayhoff, 2.28.38.9
Bfactor, 2.28.18     iarray, 2.28.38.1
Boltzmann, 2.28.19          alignment, 2.28.38.10
Box, 2.28.20     matrix, 2.28.38.5, 2.28.38.7
Bracket, 2.28.21     multiple atomic, 2.28.38.4
C, 5.3     rarray, 2.28.38.2
CCP4, 5.6.6     tether, 2.28.38.8
CONSENSUS, 2.21.1     tree, 2.28.38.12
CONSENSUSCOLOR, 2.21.2          cluster, 2.28.38.12
CONSENSUS_strength, 2.17.9     H, 5.5
Cad, 2.28.22, 2.28.22.1, 2.28.22.2EDS server, 2.29.42
Cad1, 2.28.22.1EST-alignment, 2.27.3.3
Cadalign, 2.28.22.2Eigen, 2.28.39

Error, 2.28.41     hbondWidth, 2.21.5.24
     soap, 2.28.42     hetatmZoom, 2.21.5.26
Exist, 2.28.43     hydrogenDisplay, 2.21.5.27
     molcart, 2.28.43.1     light, 2.21.5.28
Existenv, 2.28.44     lightPosition, 2.21.5.29
Exp, 2.28.46     mapLineWidth, 2.21.5.30
Extension, 2.28.45     occupancyDisplay, 2.21.5.31
FILTER, 2.21.3     occupancyRadiusRatio, 2.21.5.32
     Z, 2.21.3.1     quality, 2.21.5.33, 2.28.81.1
     gz, 2.21.3.2     rainbowBarStyle, 2.21.5.34
     uue, 2.21.3.3     resLabelDrag, 2.21.5.35
FTP, 2.21.4     resLabelShift, 2.21.5.36
     createFile, 2.21.4.1     ribbonCylinderRadius, 2.21.5.37
     keepFile, 2.21.4.2     ribbonRatio, 2.21.5.38
     proxy, 2.21.4.3     ribbonWidth, 2.21.5.39
Field, 2.28.47, 2.28.47.1     ribbonWorm, 2.21.5.40
     user, 2.28.47.1     rocking, 2.21.5.41
File, 2.28.48     rockingRange, 2.21.5.42
Find, 2.28.49     rockingSpeed, 2.21.5.43
     chemical, 2.28.49.3     selectionLevel, 2.21.5.44
          pattern, 2.28.49.3     selectionStyle, 2.21.5.45
     in array, 2.28.49.1     sketchAccents, 2.21.5.25
          table, 2.28.49.2     stereoMode, 2.21.5.46
FlexLM license info, 2.28.176     stickRadius, 2.21.5.26, 2.21.5.47
Floor, 2.28.50     surfaceDotDensity, 2.21.5.49
Formula, 2.28.51     surfaceDotSize, 2.21.5.48
GRAPHICS, 2.21.5     surfaceProbeRadius, 2.21.5.50
     atomLabelShift, 2.21.5.1     transparency, 2.21.5.51
     atomValueCircles, 2.21.5.2     wormRadius, 2.21.5.52
     ballRadius, 2.21.5.3, 2.21.5.26GRID, 2.21.6
     ballStickRatio, 2.21.5.4     gcghExteriorPenalty, 2.21.6.1
     chainBreakLabelDisplay, 2.21.5.7     gpGaussianRadius, 2.21.6.6
     chainBreakStyle, 2.21.5.6     margin, 2.21.6.2
     clashWidth, 2.21.5.5     maxEl, 2.21.6.3
     cpkClipCaps, 2.21.5.8     maxVw, 2.21.6.5
     displayLineLabels, 2.21.5.9     minEl, 2.21.6.4
     displayMapBox, 2.21.5.10GROB, 2.21.7
     dnaBallRadius, 2.21.5.11     arrowRadius, 2.21.7.3
     dnaRibbonRatio, 2.21.5.12     atomSphereRadius, 2.21.7.1
     dnaRibbonWidth, 2.21.5.13     contourSigmaIncrement, 2.21.7.5
     dnaRibbonWorm, 2.21.5.14     relArrowHead, 2.21.7.4
     dnaStickRadius, 2.21.5.15     relArrowSize, 2.21.7.2
     formalChargeDisplay, 2.21.5.16GUI, 2.21.8
     grobLineWidth, 2.21.5.17     dialog customize programming, 2.26
     hbondAngleSharpness, 2.21.5.21     plot, 2.27.59.31
     hbondBallPeriod, 2.21.5.22     tableRowMarkColors, 2.21.8.4
     hbondBallStyle, 2.21.5.23     windowLayout, 2.21.8.5
     hbondMinStrength, 2.21.5.20     workspaceFolderStyle, 2.21.8.8
     hbondRebuild, 2.21.5.19     workspaceStyle, 2.21.8.6
     hbondStyle, 2.21.5.18     workspaceTabStyle, 2.21.8.7

Getenv, 2.28.53IcmSequence, 2.28.60
Gradient, 2.28.54Image, 2.28.61
Graphics, 1.4.1     collection, 3.9.2.1
Grob, 2.28.55     frame by frame, 3.9.2.2
Group, 2.28.56Index, 2.28.62
HTTP.proxy, 2.21.4.4     chemical, 2.28.62.1
Hartree-Fock, 2.27.77.20, 2.27.103.17     element in array, 2.28.62.7
Header, 2.28.57     regexp, 2.28.62.3
Histogram, 2.28.58     string, 2.28.62.2
     N, 5.6     table label, 2.28.62.5
ICM desktop, 2.21.8.5          selection, 2.28.62.4
     documents, 2.27.77.3     tree, 2.28.62.8
     modules, 1.4.4     unique elements, 2.28.62.6
     object, 2.29.13Indexx, 2.28.63
     residue library, 2.19.24Info, 2.28.65
ICM-shell, 3.1, 5.8.5     image, 2.28.66
     intro, 1.7.1Insertion, 2.28.64
     script, 2.27.8Integer, 2.28.67
ICMFF force field, 2.29.78Integral, 2.28.68
ICMHOME, 3.1.2.1Interrupt, 2.28.69
     shell variable, 3.1.2.1Introduction, 1
IMAGE, 2.21.9JSON, 2.27.77.53
     bondLength2D, 2.21.9.15LIBRARY, 2.21.10
     color, 2.21.9.8     men, 2.21.10.1
     compress, 2.21.9.9     res, 2.21.10.2
     gammaCorrection, 2.21.9.7Label, 2.28.70
     generateAlpha, 2.21.9.10Laplacian, 2.28.71
     lineWidth, 2.21.9.3Latent, 2.28.175.3
     lineWidth2D, 2.21.9.14LatentVector, 2.28.175.3
     orientation, 2.21.9.16Length, 2.28.72
     paperSize, 2.21.9.17LinearFit, 2.28.73
     previewResolution, 2.21.9.13LinearModel, 2.28.74
     previewer, 2.21.9.12Log, 2.28.75
     printerDPI, 2.21.9.2LogP, 2.28.103
     quality, 2.21.9.1LogS, 2.28.103
     rgb2bw, 2.21.9.18M_out, 2.22.5
     scale, 2.21.9.4Map, 2.28.76
     stereoAngle, 2.21.9.6Markush structures, 2.27.50
     stereoBase, 2.21.9.5Mass, 2.28.77
     stereoText, 2.21.9.11Match, 2.28.79
     writeScale, 2.21.9.19Mathews, 2.28.125.2
I_out, 2.22.4Matrix, 2.28.80
Iarray, 2.28.59, 2.28.59.4, 2.28.59.5     alignment, 2.28.80.8
     atom numbers, 2.28.59.4     boundary, 2.28.80.9
     bits to integers, 2.28.59.3     grob connectivity, 2.28.80.12
     inverse, 2.28.59.2     histogram, 2.28.80.11
     residue numbers, 2.28.59.5     new, 2.28.80.1
     reverse, 2.28.59.2     residue areas, 2.28.80.7
     stack, 2.28.59.6          comparison, 2.28.80.4
Icm Options, 2.1     stack, 2.28.80.10

     symmetrical, 2.28.80.3     Yratio, 2.21.12.5
     table, 2.28.80.5     box, 2.21.12.13
     tensor, 2.28.80.6     color, 2.21.12.7
Max, 2.28.81     font, 2.21.12.10
     image graphic, 2.28.81.1     fontSize, 2.21.12.2
MaxHKL, 2.28.82     labelFont, 2.21.12.11
Mean, 2.28.83     lineWidth, 2.21.12.3
Method, 2.20.12     logo, 2.21.12.6
Min, 2.28.84     markSize, 2.21.12.4
Mod, 2.28.86     numberOffset, 2.21.12.1
Mol, 2.28.87     orientation, 2.21.12.8
MolPSA, 5.7.12     rainbowStyle, 2.21.12.12
Moment, 2.28.78     seriesLabels, 2.21.12.9
     of Inertia, 2.28.78PLS, 2.28.91.6
Money, 2.28.85     error, 2.28.125.2
NOE averaging, 2.20.5     models, 2.28.125.2
Name, 2.28.88Parray, 2.28.98
     chemical, 2.28.88.6Parray-object, 2.28.98
          property, 2.28.88.1Path, 2.28.97
     close sequence, 2.28.88.3Pattern, 2.28.99
     image, 2.28.88.9Pi, 2.28.100
     molcart, 2.28.88.10Polar Surface Area, 5.7.12
     object parray, 2.28.88.8Potential, 2.28.101
     sequence, 2.28.88.7Power, 2.28.102
     soap, 2.28.88.2Predict, 2.28.103
     string, 2.28.88.4Probability, 2.28.104
     tree, 2.28.88.5Profile, 2.28.105
Namex, 2.28.89Property, 2.28.106
     image, 2.28.89.2Putarg, 2.28.107
     sequence, 2.28.89.1Putenv, 2.28.108
Newick tree format, 2.28.145.3R-groups, 2.27.50
Next, 2.28.90, 2.28.90.1REBEL, 3.7.2
     covalent neighbors, 2.28.90.1     faq, 3.7.2
Nof, 2.28.91     file, 2.27.50
     chemical, 2.28.91.2R_2out, 2.22.7
     distance, 2.28.91.3R_out, 2.22.6
     latent, 2.28.91.6Radius, 2.28.109
     library, 2.28.91.4Random, 2.28.110
     molcart, 2.28.91.5     string, 2.28.110.1
     soap, 2.28.91.7Rarray, 2.28.111
     tree, 2.28.91.1     reverse, 2.28.111.2
Norm, 2.28.92     sequence projection, 2.28.111.1
Normalize, 2.28.93     alignment projection, 2.28.111.3
NotInList, 2.28.94          strength, 2.28.111.5
     R, 5.7     property assignment, 2.28.111.4
OBJECT, 2.21.11RarrayAlignment, 2.28.111.5
Obj, 2.28.95Rarrayinverse, 2.28.111.2
Occupancy, 2.28.96Real, 2.28.112
PBS, 3.13.3.6     array, 2.28.111
PLOT, 2.21.12Reference, 2.28.114

Remainder, 2.28.113Select_by atom numbers, 2.28.126.10
Replace, 2.28.115Select_by_sequence, 2.28.126.13
     chemical, 2.28.115.4Select_by_text, 2.28.126.9
     exact, 2.28.115.1Select_lists, 2.28.126.12
     regexp, 2.28.115.3Select_patching, 2.28.126.11
     simple, 2.28.115.2Select_projection, 2.28.126.8
Res, 2.28.116, 2.28.117Sequence, 2.28.127
Resali, 2.28.117     array, 2.28.127.2
Resolution, 2.28.118Sequence(dna reverse), 2.28.127.1
Rfactor, 2.28.120Shuffle, 2.28.128
Rfree, 2.28.121Sign, 2.28.129
Ring, 2.28.119Simulations, 1.4.2
Rmsd, 2.28.122Sin, 2.28.130
     of subset, 2.21.14Sinh, 2.28.131
Rot, 2.28.123Site, 2.28.132
S, 5.8Slide, 2.28.133
SAR analysis, 2.27.59.27, 2.27.85.2Smiles, 2.28.134
SC, 2.27.34.2Smooth, 2.16.23, 2.28.135, 2.28.135.1, 2.28.135.3
SEQUENCE.restoreOrigNames, 2.21.12.14     matrix, 2.28.135.2
SITE, 2.21.13Smoothrs, 2.28.135.3
     defSelect, 2.21.13.2SoapMessage, 2.28.141
     labelOffset, 2.21.13.3SolveQuadratic, 2.28.136
     labelStyle, 2.21.13.4SolveQubic, 2.28.137
     labelWrap, 2.21.13.5Sort, 2.28.142
     showSeqSkip, 2.21.13.6Sphere, 2.21.14.3, 2.28.140
     wrapComment, 2.21.13.7Split, 2.28.143
SLN notation, 2.28.145.9     chemical, 2.28.143.4
SMARTS, 2.24, 2.27.10, 2.28.91.2     multisep, 2.28.143.3
SOAP, 2.28.88.2, 2.28.91.7, 2.28.170.1     regexp, 2.28.143.2
     request message, 2.28.141     tree, 2.28.143.1
SSSR, 2.28.119Sql, 2.28.138
S_out, 2.22.8Sqrt, 2.28.139
Sarray, 2.28.124Srmsd, 2.28.144
     index, 2.28.124.1Sstructure, 2.28.146
Score, 2.28.125String, 2.28.145, 2.28.145.7
     alignment, 2.28.125.6     alternative, 2.28.145.6
     conservation, 2.28.125.5     mol, 2.28.145.2
     model, 2.28.125.2     selection, 2.28.145.7
     overlap, 2.28.125.1     slide gui, 2.28.145.8
     predictions, 2.28.125.3     substring, 2.28.145.1
     sequence, 2.28.125.4     chemical formula, 2.28.145.9
Select, 2.28.126Sum, 2.28.147
     break, 2.28.126.1     chemical, 2.28.147.1
          atom property, 2.28.126.7     image, 2.28.147.2
          nmembers, 2.28.126.4Swissprot, 2.27.103.23
          string, 2.28.126.9Symgroup, 2.28.148
     expand, 2.28.126.6T, 5.9
     fix, 2.28.126.2TOOLS, 2.21.14
     graphical, 2.28.126.5     edsDir, 2.21.14.1
     neighbors, 2.28.126.3     membrane, 2.21.14.2

     pdbReadNmrModels, 2.21.14.4     soap, 2.28.174
     superimposeMaxDeviation, 2.21.14.7Vector, 2.28.16, 2.28.175, 2.28.175.1, 2.28.175.3
     superimposeMaxIterations, 2.21.14.5     symmetry transformation, 2.28.175.2
     superimposeMinAtomFraction, 2.21.14.6Vectorproduct, 2.28.175.1
     tsShape, 2.21.14.9Vectorsymmetrytransformation, 2.28.175.2
     tsWeight, 2.21.14.10Version, 2.28.176
     writePdbRenameRes, 2.21.14.11View, 2.28.178
Table, 2.28.149Volume, 2.28.177
     alignment numbers, 2.28.149.3WEBAUTOLINK, 2.21.16
     distance, 2.28.149.9WEBLINK, 2.21.15
     matrix, 2.28.149.4Warning, 2.28.179
     model, 2.28.149.7Wavefront format, 2.27.77.21
     pairs, 2.28.149.5XML, 2.10
     stack, 2.28.149.6Xyz, 2.28.180
     url_decoder, 2.28.149.1     axes, 2.28.180.7
Table(alignment), 2.28.149.2     chemical match, 2.28.180.5
Table(stack), 2.28.149.6     fract, 2.28.180.3
Tan, 2.28.150     mesh, 2.28.180.2
Tanh, 2.28.151     points, 2.28.180.1
Tanimoto, 2.28.59.3     transformed xyz, 2.28.180.4
     distance, 2.27.59.35     vector2matrix, 2.28.180.6
          matrix, 2.28.38.6ZEGA, 5.10.9
Temperature, 2.28.153     intro, 1.4.3.6
Tensor, 2.28.152_NAME, 2.27.82.40
Time, 2.28.154_chemBatch, 3.1.2.5
Tointeger, 2.28.155_confGen, 3.13.2.3
Tolower, 2.28.156_dockScan, 3.13.2.6
Toreal, 2.28.157_macro, 2.30.1
Torsion, 2.28.158     file, 2.30.1
Tostring, 2.28.159_startup, 3.1.2.3
Toupper, 2.28.160     file, 2.30.2
Tr123, 2.28.161     icm, 2.30.2
Tr321, 2.28.162a_, 2.8.1
Trace, 2.28.163abbr, 1.6
Trans, 2.28.164abbreviations, 1.6
Transform, 2.28.165absolute to cell x y z, 2.28.180.3
Transpose, 2.28.166accFunction, 2.22.2
Trim, 2.28.167acceptor, 3.6.1
     sequence, 2.28.168access large sdf file, 2.27.77.23
Turn, 2.28.169accessMethod, 2.20.1
Type, 2.28.170accessible residues, 3.3.6
     molcart, 2.28.170.2     surface, 2.27.59.14, 5.8.15
     soap, 2.28.170.1accessing sections, 2.27.103.23
     Z, 5.10accuracy, 2.28.125.2
Unique, 2.28.171activate fog, 2.27.23.24
Unix, 2.28.172     alignment, 2.27.82.33
Uppsala, 2.29.42     document, 2.27.82.33
     server, 2.29.43     tab, 2.27.82.33
V_, 2.8.1     table, 5.9.2.4
Value, 2.28.173add, 2.27.1

          function, 2.27.1.1.1     sequence reordering, 2.28.5
     matrix, 2.27.1.2     strength, 2.28.111.5
     slide, 2.27.1.3     structural, 2.27.3.4, 2.28.5
     table, 2.27.1.4     to sequence transfer, 2.28.111.1
          row, 2.27.1.4          text conversion, 2.28.145.3
addBfactor, 2.17.1     weighted, 2.28.5
adding atoms to non-ICM objects, 2.27.7.1     gapExtension, 2.17.15
     columns to table, 2.27.1.1     gapOpen, 2.17.16
     hydrogens, 2.29.13alignment_as_text, 2.28.145.3
     in place, 2.12.4aliphatic amines, 2.27.64.2
     to slideshow, 2.27.1.3all, 5.1.2
admet selection, 3.13.3.4     torsions table, 3.3.11
advanced chemical search, 3.6alpha, 2.21.5.51, 2.27.82.35, 5.1.3
     operations, 2.12.6     channel, 2.21.9.10
     ops, 2.12.6alternative flag, 2.27.82.15
ali_seq_project, 2.28.145.4amber, 5.1.4
alias, 2.27.2amino acid, 2.19.24, 2.28.161, 2.28.162
align, 2.27.3          labels, 2.27.3.1
     3D, 2.27.3.4and, 2.12.3
          faq, 3.3.2angles, 2.28.91.3
          heavy, 2.27.3.5angular hbond dependence, 2.21.5.21
          how to, 3.3.2animated story, 5.8.14
     chemical, 2.27.81.1animation, 2.27.23.5, 2.27.23.6, 3.9
     fragments, 2.27.3.3annotation, 2.27.82.23
     intro, 1.4.3.3append, 5.1.5
     number, 2.27.3.1     a tables, 2.27.1.4
     res numbers, 2.27.3.1     column, 2.27.4.3
     sequence, 2.27.3.2     command, 2.27.4
     sequences, 2.27.3.2     sequence, 2.27.4.1
alignMethod, 2.20.2          to group, 2.27.4.1
alignMinCoverage, 2.17.2     stack, 2.27.4.2
alignMinMethod, 2.17.2     tables, 2.27.48
alignOldStatWeight, 2.17.3          by shared column, 2.27.4.3
alignSS, 2.29.1appending, 2.27.1.1
alignTwoSequences, 2.29.2     an element, 2.12.4
aligned residues, 2.28.117     menu items, 2.21.10.1
alignment, 5.1.1     representations to a slide, 2.27.23.21
     as table, 2.28.149.2     rows to matrix, 2.27.1.2
     block length, 2.16.21area under curve, 2.29.21
          secondary structure, 2.29.1arguments, 2.27.58
     cleaning, 2.28.135.4arithmetic operations, 2.12.2
     color by property, 2.27.82.29arithmetics, 2.12
     coloring, 2.19.1array, 2.27.66.4, 5.7.3.1
     distance, 2.28.126.13     assignment, 2.12.1
     editor, 2.4     derivative, 2.28.135.1
     extraction, 2.28.5     overlap, 2.28.125.1
     gap format, 5.1.1.1     parray, 2.27.22.29
     intro, 1.4.3.4     size, 2.28.91
     projection, 2.28.145, 2.28.145.4, 2.28.145.5     subset, 2.6
     score, 2.28.125.5arrow from selection, 2.29.36

as2_out, 2.22.13     site analysis, 3.4.2
as_, 2.8.8biological symmetry, 2.27.82.8
as_graph, 2.21.5.44, 2.21.5.45, 2.28.126.5     vector, 2.28.59.3
as_out, 2.22.12     to integers compression, 2.28.59.3
assign, 2.27.5blast files, 2.27.103.24
     ring conformation to template, 2.27.60.4blast-formatted database, 2.27.34.3, 2.27.103.24
     sstructure, 2.27.5.1blending, 2.27.103.30
          segment, 2.16.19, 2.27.5.2     images, 2.28.147.2
assignment, 2.12.1bold, 2.27.82.31.1
atom, 2.27.13.1, 5.1.6bond angle bending, 2.30.5
     code file, 2.30.4     errors, 2.27.83.11
     coordinates, 2.28.180.1     stretching, 2.30.6
     flickering, 2.27.82.2     to protein, 2.27.66.3
     label font, 2.30.15bonded atoms, 2.28.90.1
     name, 2.28.70born radii, 2.27.83.8
     pairs, 2.27.82.59, 2.27.82.60, 2.28.149.9boundary element, 5.2.4
     proximity to surface, 2.27.83.8          matrix, 2.28.80.9
     selection by number, 2.28.59.4box, 2.28.20
     type, 2.28.170break, 2.27.6
     user field, 2.28.47.1brightness, 2.21.5.28
atomLabelStyle, 2.20.3build, 2.27.7
atomSingleStyle, 2.20.4     atom, 2.27.7.1
atomic coordinate transfer, 2.27.82.2     column, 2.27.7.2
     solvation contributions, 2.28.7     faq, 3.8.1
     in residue, 2.28.56     from string, 2.27.7.7
     alternative position, 2.27.82.15     helix, 3.10.5
     selecting, 2.8.8     how to, 3.8.1
     translate, 2.27.82.2     hydrogen, 2.27.7.8
attenuation by occupancy, 2.27.59.25     loop, 2.27.7.5
auc enrichment, 2.29.21     model, 2.27.7.4, 2.27.103.9
auto saving log, 2.20.10     molcart, 2.27.7.9
autoSavePeriod, 2.16.1     sequence, 2.27.7.3
avi, 2.27.103.30     smiles, 2.27.7.6
axis, 5.1.7     string, 2.27.7.7
axisLength, 2.17.4built-in functions, 5.5.5
background, 2.28.28.2     atoms, 2.27.14
ball, 5.2.2     contact surface, 2.27.14
base, 5.2.1     molecule, 2.27.13.1
basis set, 2.27.77.20, 2.27.103.17     number of bonds, 2.28.126.3
batch chemical processing, 3.1.2.5     variables, 2.27.14
     docking, 3.13.2.6calcArea, 2.29.3
beta, 5.2.3calcBindingEnergy, 2.29.4
bfactor circles, 2.21.5.2calcDihedralAngle, 2.29.5
biased probability monte carlo, 2.27.65calcEnergyStrain, 2.29.20
binary file table of contents, 2.27.77.2calcEnsembleAver, 2.29.6
     files, 2.27.103.2calcMaps, 2.29.7
     key, 2.27.82.36calcPairSeqIdsFromAli, 2.29.8
binding energy, 3.7.4calcPepHelicity, 2.29.9
     pocket finding, 3.4.2calcProtUnfoldingEnergy, 2.29.10
     pockets, 2.27.85.1calcRmsd, 2.29.11

calc_nosauc, 2.29.21     similarity, 3.5
calculate phases, 3.11.2     spreadsheet, 2.27.12, 2.27.77.44, 2.27.77.45, 2.27.77.46, 2.27.82.40, 2.27.103.11
call, 2.27.8     structure from smiles, 2.27.82.6
carboxylic acid, 2.27.64.2     substructure, 2.27.34.4
cartesian cooridnates, 2.28.180          mask, 2.27.59.21
cartridge, 3.5     superposition, 2.20.6, 2.28.122
cavities, 2.27.85.1     table, 2.23
cavity, 5.3.1     view, 2.27.82.46
     analysis, 3.3.13chemistry, 2.23, 2.28.26
ccp4 maps, 2.27.77.26chiral isomer generation, 2.27.29
cd, 2.27.82.18chirality, 2.18.16, 2.27.29
cell axis vectors, 2.28.180.7choosing ligands, 3.13.1.2
     specific icm commands, 5.9.2.4cif, 2.27.77.44
center, 2.11.1, 2.27.9circular permutation of coordinates, 2.27.63
chain breaks, 2.21.5.6, 2.21.5.7, 2.28.126.1clamp values to range, 2.28.167
     symbol, 2.27.82.8clashThreshold, 2.17.5
change atom position, 2.27.82.2     labels, 2.28.155
     sequence position in multiple alignment, 2.27.66.6clear, 2.27.10
     unix directory, 2.27.82.18     graphical selection, 2.27.10
changing local stick radii, 2.27.82.77     screen, 2.27.10
     surface dot size, 2.21.5.48click and lock, 5.9.2.4
channel, 2.21.14.2clipping plane, 2.21.5.8, 5.3.3
charge, 5.3.2closer than threshold, 2.28.38.7
     compounds, 2.27.64.2closest sequence, 2.28.88.3
     change, 2.27.82.9     value, 2.28.49.1
chem formula, 2.28.145.9cluster, 2.28.143.1
chemSuper3D, 2.29.22     center, 2.28.62.8
chemical, 2.23, 2.27.34.9     centers, 2.11.1
     2D drawings, 2.27.59.9     selection, 2.28.62.8
     SMARTS search, 2.27.34.5     tree, 2.28.88.5
     database, 3.5          size, 2.28.91.1
     decomposition, 2.27.59.27, 2.27.85.2clustering, 2.11, 2.27.59.35, 2.27.85.7
     descriptors, 5.7.12clusters, 2.11, 2.11.1
     diversity, 3.14.6.3cnMethodAverage, 2.20.5
     drawing, 2.21.9.14cnWeight, 2.17.6
          quality, 2.21.9.15coil, 5.3.4
     formula, 2.28.145.9collection, 2.10, 5.3.6
     fragment counting, 2.28.91.2color, 2.21.5.28, 2.27.11
     keys, 2.27.59.21     accessibility, 2.27.13
     match coordinates, 2.28.180.5     background, 2.27.13.2
     matching, 2.27.34.4, 2.27.77.45, 2.27.77.46, 2.28.122, 2.28.144          example, 3.2.7
     models, 2.28.88.1          accessibility, 3.2.11
     modification, 2.27.62, 2.27.64, 2.29.37          alignment, 2.27.13.3
     name, 2.28.88.6          atom contributions, 2.27.12
     normalization, 2.27.64          bfactor, 3.2.9
          rules, 2.27.64.4          charge, 3.2.12
     pattern, 2.24, 2.27.81.1          electrostatic potential, 2.16.5
          search, 2.28.49.3          hydrophobicity, 3.2.10
     reaction product generation, 2.27.59.32          pharmacophore, 2.27.12
     search, 2.27.34.10, 2.27.81.1, 2.28.91.2          potential, 2.29.25

     chemical, 2.27.12, 2.27.81.1     array, 2.23
     file, 2.30.15compress, 2.27.15
     grob, 2.27.13.4     binary, 2.27.15.3
          by atom selection, 2.27.13.4.3     conf, 2.27.15.2
               atoms, 2.21.7.1     grob, 2.27.15.1
          map, 2.27.13.4.4     in place, 2.27.15.3
          matrix, 2.27.13.4.2     objects, 2.27.15
          potential, 2.27.13.4.5     stack, 2.27.15.2
          unique, 2.27.13.4.1compressed table view, 2.27.82.21
     label, 2.27.13.5conditional buttons, 5.5.5
     map, 2.27.13.6     string, 2.28.145.6
          by value, 2.27.23.16conf, 2.27.82.52, 2.27.103.40, 2.28.149.6, 5.3.12, 5.8.9
     molecule, 2.27.13.1     data, 2.28.149.6
     names, 2.28.28confgen, 3.13.2.3
     object, 2.27.11.2configuration, 2.30.14
     specification, 2.27.11.1     memory usage, 2.16.6
     surface by conservation, 2.27.13.3conformation comparison, 2.20.6
     volume, 2.27.13.7conformational generator, 2.27.60.1, 3.13.2.3
column, 5.3.5     interpolation, 2.27.23.6
     function, 2.27.7.2     stack, 2.27.103.40, 5.3.12, 5.8.9
     selection, 2.28.88          compression, 2.27.15.2
combinatorial compounds, 2.28.26          file, 2.30.7
     libraries, 2.27.59.32, 2.28.91.4     transition, 2.29.38
     PDB, 2.29.90conformer storage, 2.27.57.5, 2.27.87.2
     transformations, 3.10.4conformers, 3.13.2.3
combining plots, 2.27.59.31connect, 2.27.16
     receptor and ligand stacks, 2.27.4.2     chains with alignments, 2.27.52
command, 2.28.88.4, 5.3.10     molcart, 2.27.16.1
     line editing, 2.2consensus, 2.17.7
          help, 2.27.43     coloring, 2.17.9, 2.21.2
          options, 2.1     definitions, 2.21.1
     word list, 3.1.5consensusStrength, 2.17.7
commands, 2.20.10conservation, 2.28.111.5, 2.28.125.5
communication protocols, 2.25constant, 2.5
comp, 2.28.94constants, 2.5
comp_matrix, 2.27.82.17, 2.27.83.15, 5.3.11contact areas, 2.28.80
compare, 2.16.11, 2.16.14, 2.27.14continue, 2.27.17
     angles, 2.27.14.2contour surfaces, 2.21.7.5
     atom, 2.27.14.1contouring density, 2.27.59.14
     by rmsd without superposition, 2.27.14.1contrast, 2.21.5.28
     chemical tables, 2.27.34.10conversion to real array, 2.28.157
     patch only, 2.27.14.3convert, 2.27.18, 2.27.18.2, 3.13.2
     rmsd, 2.27.14.1     3D to chemical, 2.28.26
     surface, 2.27.14.3     3D/0D to 2D, 2.27.59.9
     variables, 2.27.14.2     ICM object to PDB, 2.27.89
compareMethod, 2.20.6     and reroot, 2.27.18.4
comparing two sarrays, 2.28.94     chemical 3D, 2.29.81
comparison operations, 2.12.5               and optmimize geometry, 2.29.82
complete view, 2.28.133     comp, 2.27.18.1
compound accessibilities, 3.14.4.1     comparison, 2.27.18.1

     mol, 2.27.18.3     working directory, 2.28.97
     object 3D and optmimize geometry, 2.29.83cursor action, 5.9.2.4
          macro, 2.29.13custom field, 2.27.82.44
     pdb, 3.8.2     interaction, 2.27.83.35
     to 3D, 2.27.82.7customization, 3.1.2
          ICM object, 2.29.84     and paste chemicals, 2.21.9.14, 2.21.9.15
          iarray, 2.28.155cyclic temperature protocol, 2.17.43
          icm-object, 2.27.18cylinder, 2.21.14.2
          integer, 2.28.155cz32, 4.5
convert2Dto3D, 2.29.83database, 5.4.1
convert3Dto3D, 2.29.84     browser, 2.27.57.3
convertObject, 2.29.13     connection, 2.27.16.1
converting a chemical, 2.27.18.3     file, 3.5.1
          pdb-chemical, 3.13.2     import, 2.27.59.26
     alignment to table, 2.28.149.2date, 2.27.21
     chemicals, 3.13.2.4     array, 2.27.21
     table columns into matrix, 2.28.80.5dcMethod, 2.20.7
     to, 2.28.112dcWeight, 2.17.8
cool, 2.29.40decomposition, 2.27.59.27, 2.27.85.2
     pictures, 2.21.5.25defCell, 2.22.1
cooling schedule, 2.17.43defSymGroup, 2.16.2
coordinate frame, 2.17.4, 2.27.23.4default atom colors, 2.27.82.13
copy, 2.27.19     value, 5.8.2
     chemical image, 2.21.9.15define axis, 3.10.3
     file, 2.19.26defining space box, 2.28.20
     site, 2.27.82.24dehtml, 2.28.115.3
correlation matrix, 2.28.152delete, 2.27.22
covalent bound count, 2.28.126.3     3D graphics panel, 2.27.98
     neighbors, 2.28.90.1     alias, 2.27.22.2
covalently attached molecule, 2.28.90.1     array element, 2.27.22.6
cpk, 5.3.13          index, 2.27.22.6
create a covalent bond, 2.27.59.2          selection, 2.27.22.1
     pharmacophore, 2.29.85     atom, 2.27.22.7
creating a local patch object, 2.27.18.2     bond, 2.27.22.14
credits, 4.5     boundary, 2.27.22.15
crypt, 2.27.20     chemical, 2.27.22.35
crystal axis vectors, 2.28.16          fragment, 2.27.22.35
     symmetry transformation, 3.10.2          selection, 2.27.22.35
          transformations, 2.28.165     class, 2.27.22
crystallographic cell, 2.27.63     conf, 2.27.22.16
     occupancy, 2.28.96     directory, 2.27.22.8
     symmetry intro, 1.4.2.4     disulfide bond, 2.27.22.25
crystallography, 2.28.118     drestraint, 2.27.22.17
csv format, 2.27.77.41     element, 2.27.22.29
csym, 1.4.2.4     file, 2.27.22.9
cube, 2.21.14.2     from array, 2.27.22.6
current, 5.3.9     hydrogen, 2.27.22.11
     icm-process number, 2.16.4     label, 2.27.22.18, 2.27.22.19
     map, 5.3.7          chemical, 2.27.22.19
     object, 5.3.8     link, 2.27.22.20

     molcart, 2.27.22.3display, 2.27.23
     molecule, 2.27.22.13     GUI window, 2.27.23.26
     object, 2.27.22.12     box, 2.27.23.7
     parray, 2.27.22.34     clash, 2.17.5, 2.27.23.8
          element, 2.27.22.34     drestraint, 2.27.23.9
     peptide bond, 2.27.22.26     field, 2.21.5.2
     plot, 2.27.22.4     from script, 2.27.23.3
     salts, 2.27.64.3     gradient, 2.27.23.10
     selection, 2.27.22.5     grob, 2.27.23.11
     selftether, 2.27.22.32          label, 2.27.23.12
     sequence, 2.27.22.22     gui, 2.27.23.26
     session, 2.27.22.10     hbond, 2.27.23.13
     shell object, 2.27.22.1     label, 2.27.23.15
     site, 2.27.22.23     map, 2.21.5.10, 2.27.23.16
     sstructure, 2.27.22.24     model, 2.27.23.1
     stack, 2.27.22.27     new, 2.27.23.2
          object, 2.27.22.28     off-screen, 2.27.23.3
     system, 2.27.22.9     offscreen, 2.27.23.3
     table, 2.27.22.30     origin, 2.27.23.4
          rows, 2.27.22.30     ribbon, 2.27.23.18
     term, 2.27.22.31     rotate, 2.27.23.5
     tether, 2.27.22.33     site, 2.27.23.19
     tree, 2.27.22.34     skin, 2.27.23.20
     variable, 2.27.22.6     slide, 2.27.23.21
     views, 2.27.22     stack, 2.27.23.6
     backbone, 2.28.126.1     string, 2.27.23.22
     restraint, 2.27.22.17     surface, 2.27.23.20
deleting sites by number, 2.27.22.23          area, 2.21.5.2
delphi, 2.29.25     tethers, 2.27.23.23
density correlation, 2.17.8, 3.11.3     trajectory, 2.27.23.17
     fitting, 2.20.7     volume, 2.27.23.24
     in unit cell, 2.27.59.23     window, 2.3, 2.27.23.25
densityCutoff, 2.17.10distance, 2.21.5.19, 5.4.3
dependent columns, 2.27.1.1.1     averaging, 2.20.5
depth cueing, 2.27.13.7, 5.4.2     contact-based, 2.28.22, 2.28.22.1
depth-cueing, 2.17.14     geometry, 5.4.4
desolvation, 2.20.24     matrix, 2.28.149.5, 2.29.8
detecting bad covalent geometry, 2.27.83.11          between stack conformations, 2.28.80.10
     proximity, 2.28.38.7     restraint, 5.4.6
dialog generation, 2.28.11          file, 2.30.9
     in html documents, 2.27.42          type file, 2.30.8
          tables, 2.27.42     restraints, 2.27.82.19
     scripting, 2.28.11distances, 2.28.91.3
dielConst, 2.17.11distribution, 1.3
dielConstExtern, 2.17.12     comparison, 2.28.125
dielectric constant, 2.17.11disulfide bond, 5.4.5
diff, 2.28.94diverse subset, 3.14.6.3
dihedral angle, 2.27.59.19dividing chemical into individual molecules, 2.28.143.4
          calculation, 3.3.10dna to protein sequence translation, 2.28.164.1
directory, 2.27.22.8, 2.27.59.5, 2.28.124     translate, 2.28.164.1

docking, 2.29.87     intro, 1.4.2.9
     intro, 3.13.2.1ellipsoid, 2.28.152
     result viewing, 2.29.28elseif, 2.27.25
     simple models, 3.14.3endfor, 2.27.26
     timing, 3.13.1.3endif, 2.27.27
     with template, 3.13.2.7endmacro, 2.27.28
documents, 5.5.8endwhile, 2.27.32
dominant color, 2.28.28.2energetics, 3.7
donor, 3.6.1     function, 2.21.14.3
     plot intro, 1.4.3.2     terms, 2.15
dots, 2.27.71ensemble average, 3.7.5
dotted surface, 2.21.5.50entropy of alignment, 2.28.125.5
double click action, 5.9.2.4     atom, 2.27.18.4
drestraint, 2.27.83.17, 5.4.6enumerate, 2.27.29, 2.27.30, 2.27.31
     generate from structure, 2.27.59.7     chiral, 2.27.29
     global weight, 2.17.6     library, 2.27.31
     set, 2.27.82.19     tautomer, 2.27.30
     type, 5.4.7enumeration, 2.28.26
drop, 2.17.13eps files, 2.19.23
drug, 2.10error SOAP services, 2.28.42
ds3D, 2.29.31     ignoring, 2.19.25
dsCellBox, 2.29.15error/warning bits cleanup, 2.27.10
dsChem, 2.29.17errorAction, 2.20.9
dsCustom, 2.29.18     vrestraint vs_var, 2.27.82.73
dsPocket, 2.29.28evalSidechainFlex, 2.29.88
dsPropertySkin, 2.29.19evol tree intro, 1.4.3.5
dsPrositePdb, 2.29.24evolutionary tree intro, 1.4.3.5
dsRebel, 2.16.5, 2.29.25exact, 2.27.34.9, 2.27.34.10
dsSeqPdbOutput, 2.29.26     match, 2.28.115.1
dsSkinLabel, 2.29.27example scripts, 3.14
dsStackConf, 2.29.29exit, 2.27.33
dsVarLabels, 2.29.30exitSeslogStyle, 2.20.10
dsXyz, 2.29.32expanding substructure match, 2.27.82.61
dump database, 2.27.103.7export, 2.27.103.7
dynamic gui, 5.5.5     animation, 2.27.103.30
ecepp, 5.5.1     pdb, 2.21.14.11
edit, 2.27.24exporting sdf, 2.27.103.11
     files, 2.21.14.1expression shortcuts, 2.9.1.2
electro intro, 1.4.2.9     comparison, 2.12.5
electroMethod, 2.20.8     arithmetics, 2.12.2
     density, 2.21.7.5, 2.29.42, 2.29.43     assignment, 2.12.1
          around selection, 2.17.22     comparison, 2.12.5
          map generation, 2.17.1     logical, 2.12.3
          maps, 2.21.14.1extending to bonded hydrogens, 2.28.126.6
electrostatic boundary matrix, 2.28.80.9               terminal atoms, 2.28.126.6
     isopotential surfaces, 2.27.59.13external process, 2.27.59.1
     potential, 2.27.13.4.5extracting from Markush, 2.27.50
     solvation, 3.7.2     icm script arguments, 2.28.52
     surface, 2.29.25     stack from object, 2.27.57.5
     troubleshooting, 5.7.13ez25, 3.7

false negatives, 2.28.125.2findSymNeighbors, 2.29.16
family, 2.27.82.31.1find_related_sequences, 2.29.33
faq, 1.3finding long covalent bonds, 2.28.126.1
     cheminformatics, 3.14.6     to density, 2.20.7
     chemsuper, 3.14.5fix, 2.27.35
     molcart dump, 3.14.6.2fixed branches, 2.28.126.2
          query, 3.14.6.1flattening 3D molecule, 2.29.17
     multiple chem overlay, 3.14.5.1flow control, 2.13
     residue table, 3.14.4.1fog, 2.17.14, 2.27.13.7, 2.27.23.24, 5.4.2
fast Fourier transform, 2.27.59.24     color, 2.17.14
     sequence search, 2.27.34.3fogStart, 2.17.14
fasta, 2.21.12.14, 5.5.2fold search, 5.8.4
     format, 2.27.103.1foldbank.db, 2.30.3
feature table, 2.28.149.8folding procedure, 3.14.1
     in sequences, 2.27.82.23font, 2.27.53.1
ffMethod, 2.20.11     size, 2.27.82.31.1, 2.30.14
field name, 2.28.88.2     specification, 2.27.82.31.1
file, 2.27.103.23for, 2.27.36
     exists, 2.28.43fork, 2.27.37
     list, 2.28.52formal charge, 2.21.5.16, 5.3.2
     length, 2.28.48formatdb, 2.27.103.24
     object origin, 2.28.48fprintf, 2.27.38
     permissions, 2.28.48fractional coordinates, 2.28.180.3
     time modified, 2.28.48     to abs coordinates, 2.28.16
     type, 2.28.48fragmented molecule, 2.27.18.2
files, 2.30frame, 2.27.87, 2.27.103.30
filling volume, 2.21.5.8fullscreen, 2.27.82.76
filter, 2.27.34.10, 2.27.57.3function, 2.27.58
     functions, 5.5.4     columns, 2.27.1.1.1
filtering table rows, 5.5.4     selecting in objects, 2.8.10
find, 2.27.34gamess, 5.5.6
     alignment, 2.27.34.1     expansion, 2.28.135.4
     and replace a chemical pattern, 2.27.64.1gapExtension, 2.17.15
               chemical fragment, 2.27.64gapFunction, 2.22.3
     chemical, 2.27.34.5gapOpen, 2.17.16
          pattern, 2.27.64gaussian averaging, 2.28.135.2
          substructure, 2.28.62.1gcMethod, 2.20.12
     database, 2.17.2, 2.27.34.2genbank, 2.21.12.14
          fast, 2.27.34.3generate intermediate conformers, 2.29.38
     family of commands, 2.27.34generating movie images, 3.9.2.1
     in sarray, 2.28.62.7genomics, 1.4.3.1
     molcart, 2.27.34.9, 3.5     clustering, 2.27.41.2
     molecule, 2.27.34.4     intro, 1.4.3.1
     pattern, 2.27.34.8geometry optimization, 2.27.60.1
     pdb, 2.27.34.6     started, 1.7
     pharmacophore, 2.27.34.11getting data from outside, 2.25
     prosite, 2.27.34.7     started, 1.7
     table, 2.27.34.10global, 2.27.39
findFuncMin, 2.29.33, 2.29.34glossary, 5
findFuncZero, 2.29.35goto, 2.27.40

gpWeights, 2.17.17header, 2.27.1.1
graph matching, 2.28.122helical axis, 2.29.36
graphical box, 2.27.23.7     cylinders, 2.21.5.37
     row selection, 2.28.62.4helicity, 3.7.6
     selection, 2.28.126.5     content calculation, 3.7.6
graphics, 2.27.82.3, 2.28.176, 3.2, 5.3.3help, 2.27.43, 2.27.43.1, 2.27.43.2
     card, 2.21.5.46     browser, 2.27.43.1
     controls, 2.3, 2.30.15, 5.4.2     commands, 2.27.43.3
     exists, 2.28.43     functions, 2.27.43.4
     intro, 1.4.1, 1.4.1.4     getting, 3.1.1
     learning, 3.2.1     word, 2.27.43.2
     attributes, 2.17.4     getting, 3.1.1
     fogStart, 2.17.14heterogenous environment, 2.21.14.2
     view vector, 2.27.82.71hidden blocks, 5.1.1.1
greedy matching, 2.9.1.4     display, 2.27.23.3
grid potentials, 2.27.59.25     hydrogens, 2.21.5.27
grob, 5.5.3     stack in object, 2.27.87.2
     coloring, 2.27.13hierarchical, 2.11
     files, 2.30.10highEnergyAction, 2.20.13
     inside-out flip, 2.27.82.35his-tags, 2.28.168
     normal directions, 2.27.82.35histogram, 2.27.59.31
     translate, 2.27.96     2D, 2.28.80
group, 2.27.41history, 2.27.44, 2.27.103.39
     by column, 2.27.41.4     delete, 2.27.22.10
     column, 2.27.41.4     of ICM, 1.2
     replacement, 2.27.62homodel, 2.29.41
     sequence, 2.27.41.1homology modeling, 1.4.2.2, 2.27.7.4, 2.27.82.59, 2.27.82.60, 2.29.1, 3.14.4
          unique, 2.27.41.2          faq, 3.14.4
     table, 2.27.41.3          intro, 1.4.2.2
grouping table by a column, 2.27.82.21     output, 2.27.7.4.3
gui, 2.27.42, 5.9.2.4     steps, 2.27.7.4.1
     exists, 2.28.43     to export a molcart table, 3.14.6.2
     functions, 5.5.5html, 2.27.42, 2.28.88.4, 5.5.8
     panels, 2.27.98     document order, 2.27.82.33
     programming, 2.26, 2.27.42, 2.27.82.21     tag removal, 2.28.115.3
gzip files, 2.27.15.3html-formatted text, 5.5.8
hash, 2.10hydration, 2.21.14.2, 2.28.7
     table, 5.3.6     parameters, 2.30.13
haze, 2.17.14hydrogen bond, 2.21.5.20, 2.21.5.21, 2.27.59.17, 5.5.7
hb, 2.17.18     bonding parameters, 2.30.12
hbCutoff, 2.17.18          cutoff, 2.17.18
hbond, 2.21.5.20, 2.21.5.21, 2.27.22.6, 5.5.7     bonds, 2.28.91.3
     color, 2.27.23.14     display, 2.21.5.27
     display, 2.21.5.22, 2.21.5.23     placement, 2.27.82.22
     energy, 2.27.23.14hydrophobicity profile, 3.3.12
     list, 2.28.149.9iProc, 2.16.4
     show, 2.27.83.21iSee, 5.8.14
hbondMinStrength, 2.21.5.20i_out, 2.16.3
     faq, 3.3.4iarray, 2.27.22.6, 2.28.49.1, 2.28.59.2, 2.28.62.7, 5.6.1
     how to, 3.3.4     making, 2.28.59.1

     algorithms, 4.3     rs, 2.30.23
     application refs, 4.4     rst, 2.30.22
          literature, 4.3     sar, 2.30.36
     archive, 2.27.77.2     se, 2.30.30
     arguments, 2.28.52     seq, 2.30.29
     binary, 2.28.97     tab, 2.30.25
     branching, 2.13.2     tot, 2.30.26
     commands, 2.27     trj, 2.30.17
     controls, 2.13     var, 2.30.21
     flags, 2.1     vwt, 2.30.27
     functions, 2.28icmCavityFinder, 2.29.14
     graphics, 3.2icmMacroShape, 2.29.86
     history, 1.2icmPmfProfile, 2.29.23
     jumps, 2.13.3icmPocketFinder, 2.29.87
     learning, 3.1.4icmscript, 2.27.77.3
     loops, 2.13.1     arguments, 2.28.52
     macros, 2.29if, 2.27.45
     main refs, 4.2ignoring swiss secondary structure, 2.22.9
     menus, 2.21.10.1illegal smiles, 2.28.62.1
     method literature, 4.4image, 3.2.6
     molecules, 2.14     annotation, 3.2.5
     object file, 2.30.18     center, 3.2.8
     session, 2.20.10     format, 5.9.3
     shell, 3.1     high quality, 3.2.2
     support, 1.3     parray, 5.7.3.3
     table, 2.21     resolution, 3.2.2
     ali, 2.30.31     rotation, 3.2.3
     all, 2.30.32implicit continuous solvation, 2.30.13
     bbt, 2.30.5     solvation, 2.27.82.63
     bst, 2.30.6imposing tether, 2.27.82.59, 2.27.82.60
     cfg, 2.30.14     place, 2.12.4
     clr, 2.30.15          ops, 2.12.4
     cmp, 2.30.33incidence, 2.28.80.12
     cn, 2.30.9increasing the number of shell variables, 2.30.14
     cnf, 2.30.7increment charge, 2.27.82.9
     cnt, 2.30.8index expressions, 2.6
     cod, 2.30.4     in array, 2.28.62.3
     col, 2.30.24     substring, 2.28.62.2
     gro, 2.30.10     table, 2.27.103.23
     hbt, 2.30.12          entry, 2.28.124.1
     hdt, 2.30.13          sdf-file path, 2.28.97
     htm, 2.30.11indices of labeled table rows, 2.28.62.5
     iar, 2.30.35          selected table rows, 2.28.62.4
     map, 2.30.16infinity, 2.28.157
     mat, 2.30.37info, 2.27.46
     ob, 2.30.18     molcart, 2.27.46.1
     pdb, 2.30.28inner join, 2.27.48
     prf, 2.30.34insert rows, 2.27.1.4
     rar, 2.30.38integer, 5.6.2
     res, 2.30.20     array, 2.28.59, 5.6.1

interaction cutoff, 2.18.27l_showWater, 2.18.25
     lists, 2.18.27, 2.21.14.3l_updateLists, 2.18.27
interactive docking, 1.4.2.8l_warn, 2.18.28
interatomic potential, 2.27.82.44, 2.27.83.35l_wrapLine, 2.18.29
interface comparison, 2.27.14.3l_writeStartObjMC, 2.18.30
     residues, 3.3.5l_xrUseHydrogen, 2.18.31
     torsions, 3.3.7label, 2.27.23.22, 5.6.3
     view, 2.29.28     fonts, 2.30.15
intermolecular bond, 2.27.66.3latent, 2.28.91.6
internal coordinate file, 2.30.21learn, 2.27.49
     coordinates, 2.8.9     atom, 2.27.49.1
     positional restraints, 5.9.4left join, 2.27.48
interpolate, 2.28.28.1     triangle of a matrix, 2.28.80.3
interpolation, 2.28.28.1library to replacement groups, 2.27.59.27, 2.27.85.2
interruptAction, 2.20.14ligand binding, 2.29.28
inverting array order, 2.28.59.2, 2.28.111.2     dock faq, 3.13.2
italic, 2.27.82.31.1     docking, 3.13, 3.13.1, 3.13.2
iterative overlay, 2.27.90          intro, 1.4.2.6
     superposition, 2.21.14, 2.27.91     editing, 1.4.2.8
join, 2.27.48     editor, 2.29.37
     tables, 2.27.48     fit, 3.13
keep, 2.27.47     setting, 3.13.2
kernel models quality, 2.28.125.2     view, 2.21.5.26
     mapping, 2.30.15light, 2.21.5.29
kmz, 5.5.3limits, 2.30.14
l_antiAlias, 2.18.1line thickness in 2D chemicals, 2.21.9.14
l_autoLink, 2.18.2lineWidth, 2.17.19
l_bpmc, 2.18.3linear chemical notation, 2.24
l_breakRibbon, 2.18.4     regression, 2.28.74
l_bufferedOutput, 2.18.5     group, 2.27.50
l_bug, 2.18.6     internal variables of molecular object, 2.27.51
l_caseSensitivity, 2.18.7     ms2ali, 2.27.52
l_commands, 2.18.8     sequences to 3D objects, 2.27.52
l_confirm, 2.18.9     to alignment, 2.27.52
l_easyRotate, 2.18.10     variable, 2.27.51
l_info, 2.18.11     variables, 2.27.51
l_minRedraw, 2.18.12linked alignment, 2.28.88
l_neutralAcids, 2.18.13     sequence, 2.28.88
l_out, 2.18.14linux shell, 2.27.92, 5.10.2
l_print, 2.18.15list, 2.27.53
l_racemicMC, 2.18.16     binary, 2.27.54
l_readMolArom, 2.18.17     database, 2.27.55
l_showAccessibility, 2.18.18     font, 2.27.53.1
l_showMC, 2.18.19     html documents, 2.28.88
l_showMinSteps, 2.18.20     molcart, 2.27.56
l_showResCodeInSelection, 2.18.21          database, 2.27.56
l_showSites, 2.18.23     of files, 2.28.124
l_showSpecialChar, 2.18.22     updates, 2.27.60
l_showSstructure, 2.18.24listUpdateThreshold, 2.17.20
l_showTerms, 2.18.26literature, 4.1

     conf, 2.27.57.1     hbond, 2.27.59.17
     frame, 2.27.57.2     image, 2.27.59.20
     molcart, 2.27.57.3     key, 2.27.59.21
     object, 2.27.57.6     map, 2.27.59.22
     solution, 2.27.57.4          cell, 2.27.59.23
     stack object, 2.27.57.5          factor, 2.27.59.24
loadEDS, 2.29.42          potential, 2.27.59.25
loadEDSweb, 2.29.43          xray, 2.27.59.30
local, 3.5.1     molcart, 2.27.59.26
logarithm, 2.28.75     molsar, 2.27.59.27
logical, 5.6.4     pca, 2.27.59.28
     operations, 2.12.3     peptide bond, 2.27.59.29
     variables, 2.18     plot, 2.27.59.31
logical_ops, 2.12.3     reaction, 2.27.59.32
logicals, 2.18     sequence, 2.27.59.34
long axes, 2.28.152          alignment, 2.27.59.33
loop database rebuilding, 2.27.103.27          from alignment, 2.27.59.33
     interrupt, 2.17.44     torsion, 2.27.59.19
     modeling, 1.4.2.3     tree, 2.27.59.35
          intro, 1.4.2.3     unique, 2.27.59.36
     search, 2.27.7.4.2makeAxisArrow, 2.29.36
     resolution shape, 2.29.86makeIndexChemDb, 2.29.44
ma29, 3.11makeIndexSwiss, 2.29.45
macro, 2.27.58, 5.6.5makePdbFromStereo, 2.29.46
macro_def, 5.6.5makePharma, 2.29.85
main ICM references, 4.2makeSimpleDockObj, 2.29.47
     concepts, 3.10.1makeSimpleModel, 2.29.48
make, 2.27.59making predictive models, 2.27.49
     3d label, 2.27.59.15manual style, 1.5
     angle, 2.27.59.18map, 2.17.22, 2.21.5.10, 5.6.6
     background, 2.27.59.1     aa property to sequence, 2.28.111.1
     bond, 2.27.59.2     averaging, 2.28.135.5
          chain, 2.27.59.3     calculation, 2.27.59.24
          multi, 2.27.59.3     conversion, 2.27.59.30
     boundary, 2.27.59.4     file, 2.30.16
     directory, 2.27.59.5     fitting, 2.20.7
     distance, 2.27.59.16     format, 5.6.6
     disulfide bond, 2.27.59.6     mean value, 2.28.83
     drestraint, 2.27.59.7     min value, 2.28.84
     factor, 2.27.59.8     name, 2.28.76
     flat, 2.27.59.9     operations, 5.6.6
          chem_array, 2.27.59.9     transformations, 2.28.135.5
     grob, 2.29.36     trimming, 2.28.21
          from image, 2.27.59.11     value sigma, 2.28.122
               matrix, 2.27.59.12     contouring, 2.27.59.14
          image, 2.27.59.11mapAtomMargin, 2.17.22
          map, 2.27.59.10mapSigmaLevel, 2.17.21
          matrix, 2.27.59.12mapping properties to sequence, 2.28.111.4
          potential, 2.27.59.13     and factors, 3.11
          skin, 2.27.59.14mass-spectrometry functions, 2.27.29, 2.27.30, 2.27.31

     hydrogens, 2.27.82.61     triangles, 2.28.177
matrix, 5.6.7mkUniqPdbSequences, 2.29.49
     derivatives, 2.28.71mm26, 3.8
     new, 2.28.80.1mmcif, 5.6.10
     map value, 2.28.81mmff, 5.6.9
maxColorPotential, 2.16.5     type, 2.28.170
maxMemory, 2.16.6     show atom types, 2.27.83.10
     movie, 3.9.2mnSolutions, 2.16.8
mcBell, 2.17.23mncalls, 2.16.9
mcJump, 2.17.24mncallsMC, 2.16.10
mcShake, 2.17.25mnconf, 2.16.11
mcStep, 2.17.26mnhighEnergy, 2.16.12
mean force, 2.27.82.44, 2.27.83.35mnreject, 2.16.13
membrane, 2.21.14.2mnvisits, 2.16.14
memorizing positions, 3.2.4model reliability, 2.29.23
menu, 2.27.61modify, 2.27.62
     script, 3.1.3     and reroot, 2.27.18.4
merge PDB, 2.29.90     chem, 2.27.64
     arrays to table, 2.27.41.3          charge, 2.27.64.2
     continuation lines, 2.27.77.37          delete salt, 2.27.64.3
     objects, 2.27.66.2          normalize, 2.27.64.4
     parts of molecule, 2.27.66.3     chemical find replace, 2.27.64.1
     pdb, 3.4.4     molcart, 2.27.64.5
     sarray into string, 2.28.147     rotate, 2.27.63
     stacks, 3.7.7modifyGroupSmiles, 2.29.37
     tables, 2.27.4.3, 2.27.48modules, 1.4.4
merge2, 3.8.7mol, 2.27.77.45, 2.27.77.46, 2.27.103.11, 2.27.103.23, 5.6.11
mergePdb, 2.29.90     file, 2.28.145.2
     several chemical, 2.28.147.1     to icm, 2.27.18.3
merging into one molecule, 2.27.66.3     translation, 3.2.4
mesh, 2.28.177mol-file to chem-table element, 2.28.98
     score, 3.13.3.3mol2, 5.6.12
mfMethod, 2.20.15molcart, 2.27.16.1, 3.5
mfWeight, 2.17.27     connection options, 3.5.2
mimel, 5.6.8molecular, 2.28.51, 5.7.3.1
mimelDepth, 2.17.28     arrays, 5.7.3
mimelMolDensity, 2.17.29     manipulations, 3.8
minNumGrad, 2.27.60     modifications, 3.8.5
minTetherWindow, 2.16.7     object, 5.7.1
minimization exit criteria, 2.27.60     objects, 2.14
minimize, 2.16.9, 2.27.60     surface, 2.27.83.8, 5.8.7
     cartesian, 2.27.60.1     views, 1.4.1.1
     loop, 2.27.60.2     volume, 2.28.103
     stack, 2.27.60.3molecule, 2.7
     tether, 2.16.7, 2.27.60.4     create, 3.8.4
     drop, 2.17.13     properties, 2.27.82.29
minimizeMethod, 2.20.16     rotation, 3.2.3
missing bonds, 2.27.66.3     translation, 3.2.3, 3.2.4
     loop, 2.21.5.6, 2.21.5.7     create, 1.7.2
     residues, 2.28.47.1     intro, 1.7.2, 2.7

     selecting, 2.8.6nProc, 2.16.17
monte carlo, 2.27.65nSsearchStep, 2.16.16
montecarlo, 2.16.10, 2.16.12, 2.16.13, 2.16.14, 2.16.18, 2.20.6, 2.27.65name, 2.28.70
     local, 2.16.15     atom fields, 2.27.82.29
     trajectory, 2.27.23.17naming compounds, 2.27.82.40
moprphing, 2.29.38nearest sequence, 2.28.84
more, 5.6.13nested script, 5.8.2
morph, 2.27.23.6nice, 2.29.39
     to tether target, 2.29.38     image, 3.2.2
morph2tz, 2.29.38non-redundant, 3.4.3
morphing, 2.27.23.6, 2.27.82.59, 2.27.82.60, 2.27.87.3normal distribution, 2.28.110
mouse controls, 2.3normalize chemicals, 2.27.64.4
     file, 2.27.103.30     defined, 2.28.157
move, 2.27.66nota, 1.5
     alignment sequence, 2.27.66.6notational conventions, 1.5
     atoms, 2.27.82.2nucleotides, 2.19.24
     bonding, 2.27.66.3number of dots, 2.21.5.49
     column, 2.27.66.5          elements, 2.28.91
     element, 2.27.66.4          hydrogen bonds, 2.27.83.21
     file, 2.19.28, 2.27.78.3          molecules in objects, 2.28.126.4
     fragments together, 2.27.66.3          occurrences, 2.28.91
     molecule, 2.27.66.1          residues in molecules, 2.28.126.4
     ms_molecule, 2.27.66.1          van der Waals contacts, 2.27.83.12
     multiple molecules, 2.27.66.2     transfer from sequence, 2.27.3.1
     object, 2.27.66.2nvis, 2.28.59.6
     sequence, 2.27.66.6object, 2.27.13.1, 5.7.1
     table column, 2.27.66.5     parray, 5.7.3.1
movie, 2.27.87.3     properties, 2.27.82.29
     images by frame, 3.9.2.2     stack, 5.8.9
     molecular simulation, 3.9.2     to chemarray, 2.28.26
     rotate view, 3.9.1     user fields, 2.28.47.1
     zooming, 3.9.1     assign comment, 2.27.82.14
moving selection to another object, 2.28.126.8     source file, 2.28.48
mpeg, 2.27.103.30     translate, 2.27.96
ms_, 2.8.6     merge, 3.8.6
multi center drestraint, 2.20.5     selecting, 2.8.5
multi-part molecule, 2.27.18.2obsolete, 2.17.51
multiple NMR models, 2.21.14.4occlusion shading, 2.27.13
     alignment, 2.27.3.2octanol transfer, 2.28.103
          to pairwise similarities, 2.29.8off, 2.27.77.21
     conformation storage, 5.8.9     format, 5.5.3
     mol as text, 2.28.145.2oligonucleotide melting, 2.28.153
     object file, 2.27.77.2on-line help, 2.27.43.1, 2.27.43.2
     sequence alignment intro, 1.4.3.4     third, 2.28.34
     smiles file format, 2.27.77.42only, 5.7.2
mutate residue, 2.27.62openGL window, 2.27.98
mutating residue, 3.8.5operating system, 2.27.92, 2.28.176, 5.10.2
mute, 5.6.15optimal chemical superposition, 3.14.5.1
mysql, 2.27.16.1optimization, 2.27.65
nLocalDeformVar, 2.16.15     Hbond, 2.29.89

optimizeHbonds, 2.29.89     grid type definitions, 2.27.82.64
or, 2.12.3     object, 3.6.1
order, 2.27.66.6     objects, 3.6
original sequence names, 2.21.12.14pharmacophores, 3.6
os_, 2.8.5     psi plot, 2.29.57
other variables, 2.22pipe, 2.27.77.40
output, 2.16.3planar angle, 2.27.59.18
overlay by atom pairs, 2.27.90plot, 2.27.68
          chemical substructure, 2.29.22     3D 2Dfunction, 3.12.3
overview, 1.4          shape, 3.12.4
pK shift, 3.7.3     area, 2.27.69
packing density, 3.3.8     histogram, 3.12.2
pair-distances, 2.27.22.6     how to, 3.12
pairdistance parray, 2.21.5.19     simple, 3.12.1
pairwise interactions, 2.27.82.44plot2DSeq, 2.29.50
panel layout, 2.21.8.5plotBestEnergies, 2.29.53
paragraphs, 2.27.103.23plotCluster, 2.29.55
parallelization, 2.16.4, 2.16.17plotFlexibility, 2.29.54
parray, 2.27.22.6, 5.7.3plotMatrix, 2.29.56
parrayTo3D, 2.29.82plotRama, 2.29.57
parrayToMol, 2.29.81plotRose, 2.29.58
parse SOAP message, 2.28.174plotSeqDotMatrix, 2.29.51
parsing, 2.28.79plotSeqDotMatrix2, 2.29.52
     web pages, 2.27.77.43plotSeqProperty, 2.29.59
partial least squares, 2.27.49     3d, 1.4.3.7
     slide display, 2.27.23.21plotting van der Waals, 3.7.1
     sum, 2.28.68          faq, 3.7.1
passing arguments, 5.8.2pls, 2.27.49
     by reference, 2.27.58     column contributions, 2.28.149.7
pattern, 5.7.4     model, 2.28.149.7
     search, 2.27.34.2     weights, 2.28.149.7
pause, 2.27.67pmf, 2.20.15
pdb, 5.6.10, 5.7.6     residue profile, 2.29.23
     file creation time, 2.28.35pmf-file, 2.30.19
     files, 2.30.28pmffile, 2.30.19
     format, 2.27.77.44png, 2.27.103.35, 5.7.5
     merge, 3.4.4pocket, 2.29.28, 2.29.87, 3.13.1.1
     sequence generation, 3.4.3point coordinates, 2.28.180.1
pdbDirStyle, 2.20.17pointer array, 5.7.3
peptide, 5.7.7polar hydrogens, 2.21.5.27
     docking, 3.12.5     surface area, 2.28.103
     folding, 1.4.2.1polarization charge, 3.7.2, 5.7.13
          intro, 1.4.2.1positional constraint, 2.21.14.9
personal gui controls, 3.1.2postscript, 2.19.23
     setup, 3.1.2potential surface coloring, 5.7.13
ph30, 3.12pov-ray, 2.27.103.37
ph4, 5.7.8pow, 2.28.34
     object faq, 3.6.1precision, 2.28.125.2
pharmacophore, 2.27.12, 3.5, 5.7.8predictSeq, 2.29.60
     faq, 3.6prediction model, 2.28.74

     score, 2.28.125     how to, 3.3.3
preference, 2.20random array, 2.28.110
preferences, 3.1.2.3     order, 2.28.128
prepSwiss, 2.29.61randomSeed, 2.16.18
previous atom, 2.28.90.1randomize, 2.16.18, 2.27.76
principal axes, 2.28.152     angles, 2.27.76.1
     component analysis, 3.3.9     coordinates, 2.27.76
     inertia moments, 2.28.78     torsions, 2.27.76
print, 2.27.70rarray, 2.27.22.6, 2.28.49.1, 2.28.111.2, 5.7.11
     bar, 2.27.71     properties, 2.28.111.4
     image, 2.27.73rdBlastOutput, 2.29.67
     to string, 2.27.86rdSeqTab, 2.29.68
printMatrix, 2.29.62reaction, 2.27.59.32
printPostScript, 2.29.63     group file, 2.27.50
printTorsions, 2.29.64read, 2.27.77, 2.27.77.52, 2.27.77.53
printf, 2.27.72     FILTER, 2.27.77.5
profile, 5.7.9     alignment, 2.27.77.11
program overview, 1.4     all, 2.27.77.6
progress bar, 2.27.71     binary, 2.27.77.2
progression, 2.27.71     color, 2.27.77.12
project setup, 3.13.2.2     column, 2.27.77.47
projected alignment, 2.28.88.3     comp_matrix, 2.27.77.13
projecting surface charge, 3.7.2     conf, 2.27.77.14
property, 2.27.82.45, 2.27.82.46     csd, 2.27.77.15
     grids, 2.17.17     csv, 2.27.77.41
     map, 2.27.82.64     database, 2.27.77.16
     superposition, 2.27.82.64     drestraint, 2.27.77.17
prosite, 5.7.10          type, 2.27.77.18
     pattern, 5.7.4     entries from database, 2.27.77.7
protein docking, 2.28.180.2     factor, 2.27.77.19
          intro, 1.4.2.5     from file, 2.27.77.1
     grid docking, 3.14.2          string, 2.27.77.4
     health, 2.29.57     fromstring, 2.27.77.4
     topology, 2.21.5.37     ftp http, 2.27.77.8
psa, 5.7.12     gamess, 2.27.77.20
purple box, 2.28.20     grob, 2.27.77.21
quadratic equation, 2.28.136     html, 2.27.77.3
quantum mechanics, 2.27.77.20, 2.27.103.17          file, 2.27.77.3
qubic equation, 2.28.137     iarray, 2.27.77.22
query, 3.14.6.1     index, 2.27.77.23
     molcart, 2.27.74          table, 2.27.77.7
question mark operator, 2.28.145.6     json, 2.27.77.53
quit, 2.27.75     library, 2.27.77.24
     property transfer via alignment, 2.28.111.3          mmff, 2.27.77.25
r_2out, 2.17.31     librarymmff, 2.27.77.25
r_out, 2.17.30     map, 2.27.77.26
radii.electrostatic, 2.28.109     matrix, 2.27.77.27
     van der Waals, 2.28.109     mol, 2.18.13, 2.27.77.7, 2.27.77.28
rainbow, 2.28.28.1     mol2, 2.27.77.7, 2.27.77.29
ramachandran faq, 3.3.3     object, 2.27.77.31

     pdb, 2.21.14.4, 2.27.77.32refresh view, 2.27.23.2
          sequence, 2.27.77.33refs, 4.1
     profile, 2.27.77.34regexp, 2.9, 2.28.79
     prosite, 2.27.77.35     back references, 2.9.1.3
     rarray, 2.27.77.36     syntax, 2.9.1
     sarray, 2.27.77.37regression, 2.27.49
     sequence, 2.27.77.7, 2.27.77.38regul, 2.29.66
          database, 2.27.77.38.1regular expression, 2.9, 2.28.62.3, 2.28.79
     smiles, 2.27.77.42          filter, 2.27.77.1
     stack, 2.27.77.39     expression, 2.28.115.3
     string, 2.27.77.40regularization, 2.16.7, 2.27.60.4, 5.7.15
     table, 2.27.77.41     procedure, 3.8.3
          csv, 2.27.77.41rejectAction, 2.20.18
          html, 2.27.77.43relational database, 2.28.138
          mmcif, 2.27.77.44relative accessible area of atoms, 2.20.1
          mol, 2.27.77.46release notes, 1.1
          mol2, 2.27.77.45remarkObj, 2.29.69
     trajectory, 2.27.77.30remove expression tags, 2.28.168
          and save a fragment, 2.27.77.30.1     file, 2.27.22.9
          write, 2.27.77.30.1     trailing blanks, 2.28.167
     unix, 2.27.77.9removing html tags, 2.27.77.43
          cat, 2.27.77.10     outliers, 2.28.167
     variable, 2.27.77.48rename, 2.27.78
     view, 2.27.77.49     chemicals, 2.27.82.40
     vrestraint, 2.27.77.50     file, 2.27.78.3
          type, 2.27.77.51     molcart, 2.27.78.2
     with filter, 2.27.77.5     object, 2.27.78.1
     xml, 2.27.77.52     system, 2.27.78.3
readMolNames, 2.22.10     atom, 2.27.78.1
readcomp_matrix, 2.27.77.13     molecule, 2.27.78.1
reading external tool output, 2.27.59.1     residue, 2.27.78.1
     from standard input, 2.27.77.40renaming, 2.21.12.14
     pdb from ftp, 2.19.18reorder, 2.27.66.6
               web, 2.19.19     alignment sequences, 2.27.103.1
     restraint, 2.27.77.50     array, 2.28.128
real, 5.7.14     objects, 2.27.84.3
     array, 5.7.11replace matching array element, 2.28.115.1
     shell variables, 2.17     without interpretation, 2.28.115.2
     space refinement, 2.27.59.30replacing scaffold in a library, 2.27.64.1
reals, 2.17reproducible randomness, 2.16.18
rebel, 2.16.5, 5.7.13reroot, 2.27.18.4
rebuild molcart index, 2.27.7.9     selections, 3.3.6
recalculate dependent values, 2.27.7.2resLabelShift, 2.17.32
     values, 2.27.1.1.1resLabelStyle, 2.20.19
receptor, 3.13.1.1reserved names, 2.22
     preparation, 3.13.1.1residue, 2.27.13.1, 5.7.16
redefine hydrogen coordinates, 2.27.82.22     accumulators, 2.28.56
references, 4     alignment, 2.27.82.59, 2.27.82.60
refineModel, 2.29.65     conservation, 2.28.111.5
reflections, 2.21.5.28     contact area matrix, 2.28.80.7

     field, 2.27.82.29rounding a real, 2.28.145
     gap, 2.21.5.6, 2.21.5.7     output, 2.27.83.43
     label, 2.27.3.1rsWeight, 2.17.33
     library file, 2.30.20rs_, 2.8.7
     name, 2.28.70run script, 2.27.8
          translation, 2.21.14.11running a docking job, 3.13.2.6
     number, 2.28.59.5     dock job, 3.13.2.5
          table, 2.28.149.3     script from html, 5.8.2
     property averaging, 2.28.135.3s-s bond, 5.4.5
          calculation, 2.28.56s_alignment_rainbow, 2.19.1
     proximity, 2.28.80.7s_blastdbDir, 2.19.2
     ranges, 2.8.11s_editor, 2.19.3
     selection, 2.18.21s_entryDelimiter, 2.19.4
          as string, 2.28.145.7s_errorFormat, 2.19.5
          function, 2.28.116s_fieldDelimiter, 2.19.6
     table, 3.14.4.1s_helpEngine, 2.19.7
     tethering, 2.27.82.59, 2.27.82.60s_icmPrompt, 2.19.10
     user field, 2.28.47.1s_icmhome, 2.19.8, 3.1.2.1
residue_selections, 2.8.11s_imageViewer, 2.19.11
     selecting, 2.8.7s_inxDir, 2.19.9
resizing, 2.28.61s_javaCodeBase, 2.19.12
restraining molecules to shapes, 2.21.14.9s_labelHeader, 2.19.13
restraints, 2.15, 2.27.82.59, 2.27.82.60s_lib, 2.19.14
     torsion, 2.27.82.72s_logDir, 2.19.15
return, 2.27.79s_out, 2.19.16
reverse complement, 2.28.127.1s_pdbDir, 2.19.17
     lighting, 2.27.82.35s_pdbDirFtp, 2.19.18
     normals, 2.27.82.35s_pdbDirWeb, 2.19.19
reversing order, 2.28.59.2s_printCommand, 2.19.21
rgb, 5.7.17s_projectDir, 2.19.20
     matrix, 2.28.28s_prositeDat, 2.19.22
ribbon, 5.7.18s_psViewer, 2.19.23
     bullets, 2.21.5.6s_reslib, 2.19.24
     diagram, 2.21.5.37s_skipMessages, 2.19.25
ribbonColorStyle, 2.20.20s_sysCp, 2.19.26
ribbonStyle, 2.20.21s_sysLs, 2.19.27
right join, 2.27.48s_sysMv, 2.19.28
rigid chemical superposition, 2.27.90s_sysRm, 2.19.29
ring, 2.28.119s_tempDir, 2.19.30
     sampling, 3.13.2.3s_translateString, 2.19.31
     templates, 2.27.82.7s_userDir, 2.19.32
rocking, 2.27.23.5s_usrlib, 2.19.33
root mean square deviation, 2.28.125.2s_webEntrezLink, 2.19.34
roots, 2.28.136, 2.28.137s_webViewer, 2.19.35
rotate, 2.27.80s_xpdbDir, 2.19.36
     grob, 2.27.80.2sa23, 3.3
     object, 2.27.80.1sampling grid, 2.28.180.2
     view, 2.27.80.3sarray, 2.27.22.6, 5.8.1
rotation, 2.27.23.5     transformation in place, 2.27.95.1
     angle, 2.28.17save print, 3.2.6

saving graphics to album, 2.27.59.20selecting by b-factor, 2.28.126
     image, 2.27.103.35               y z, 2.28.126
scaffolds, 2.27.50     columns, 5.9.1
scoring, 3.13.1.4     from clusters, 3.14.6.3
screen X, 2.28.178     neighboring elements, 2.28.90
     coordinates, 2.28.178     residues, 3.3.6
script, 2.28.88.4, 5.8.2     saving, 2.28.59.4
     file name, 2.28.48selection, 2.8, 2.28.126, 2.28.126.6
     inside ICM, 5.8.2     elements, 2.8.4
     name, 5.8.2     examples, 2.8.3
     image generation, 2.27.23.3     functions, 2.8.10
scripting molecular movements, 3.2.4     gap patching, 2.28.126, 2.28.126.11
sdf, 2.27.103.23     level, 2.8, 2.28.170
     file, 2.27.77.45, 2.27.77.46, 2.27.82.40, 2.27.103.11, 2.28.145.2, 5.7.3     levels, 2.8.2
     to chem-table, 2.28.98     simplification, 2.28.126.11
search for chemical pattern, 2.28.49.3     transfer, 2.28.126, 2.28.145.7
     pdb headers, 3.4.5     type, 2.8
     prosite, 3.4.1     types, 2.8.1
     sequence pattern, 2.27.34.8     variable, 2.22.11
searchObjSegment, 2.29.72     atoms, 2.8.8
searchPatternDb, 2.29.70     functions, 2.8.10
searchPatternPdb, 2.29.71     molecules, 2.8.6
searchSeqDb, 2.29.73     objects, 2.8.5
searchSeqFullPdb, 2.29.75     output, 2.22.14
searchSeqPdb, 2.29.74     residues, 2.8.7
searchSeqProsite, 2.29.76     torsions, 2.8.9
searchSeqSwiss, 2.29.77     variables, 2.8.9
searches and alignments, 3.4selections, 2.27.82.29
second moments, 2.28.152     in molecular objects, 2.8
secondary structure derivation from 3D, 2.27.5.1selftether, 2.21.14.9, 5.9.4
          schematic, 2.21.5.37seq_ali_project, 2.28.145.5
segMinLength, 2.16.19sequence, 2.28.161, 2.28.162, 5.8.3
segment, 5.8.4     alignment, 2.28.5.1, 2.29.2
select, 2.27.81          intro, 1.4.3.3
     atoms by number of bonded atoms, 2.28.126.3     analysis intro, 1.4.3
          of the fixed torsions, 2.28.126.2     assembly, 2.27.41.2
     by bfactor, 2.28.126.7     belongs to alignment, 2.28.62
          center of mass, 2.28.126.14     conservation, 2.28.125.5
          coordinates, 2.28.126.7     distance, 2.28.126
          iarray, 2.28.126          matrix from alignment, 2.28.80.8
          length, 2.28.126.13     dotplot, 1.4.3.2
          occupancy, 2.28.126.7     from pdb, 2.27.59.34
          user field, 2.28.126.7     identity, 2.29.8
     chemical, 2.27.81.1     intro, 1.4.3
     lines, 2.27.77.1     modification, 2.28.168
     tether partners, 2.28.126.12     neighbor, 2.28.88.3
     vw partners, 2.28.126.12     parray, 5.7.3.2
selectMinGrad, 2.17.34     pattern, 5.7.4
selectSphereRadius, 2.17.35     position correspondence, 2.28.149.3
selected stack conformations, 2.27.22.16     positional weights, 2.27.82.1

     search, 2.27.34.2     group, 2.27.82.54
     selection, 2.27.22.22          column, 2.27.82.21
     structure alignment, 2.29.1     hydrogen, 2.27.82.22
     to alignment transfer, 2.28.111.3     key, 2.27.82.36
     type, 5.8.3     label, 2.27.82.37
sequence-alignment mapping, 2.28.145.4, 2.28.145.5          3d label, 2.27.82.37.4
sequence-structure alignment, 2.28.5.1          chemical, 2.27.82.37.3
     output format, 2.16.20, 2.16.21          distance, 2.27.82.37.1
sequenceBlock, 2.16.20          table, 2.27.82.37.2
sequenceColorScheme, 2.20.22     map, 2.27.82.38
sequenceLine, 2.16.21     molcart, 2.27.82.39
sequences, 3.4     molecular variables, 2.27.82.74
     not in alignments, 2.27.22.22     name, 2.27.82.40
set, 2.27.82          sequence, 2.27.82.40.1
     alternative atom, 2.27.82.15     object, 2.27.82.41
     area, 2.27.82.1     occupancy, 2.27.82.42
     atom, 2.27.82.2     plane, 2.27.82.43
     background image, 2.27.82.3     pmf, 2.27.82.44
     bfactor, 2.27.82.4     property, 2.27.82.45, 2.27.82.46
     biological symmetry, 2.27.82.55          chemical view, 2.27.82.46
     bond topology, 2.27.82.6     radii graphical, 2.27.82.77
          type, 2.27.82.5     randomSeed, 2.27.82.47
          and formal charges, 2.27.82.6     randomize, 2.27.82.47
     cartesian, 2.27.82.7     resolution, 2.27.82.48
     chain, 2.27.82.8     selftether, 2.27.82.59
     charge, 2.27.82.9     site, 2.27.82.23
          formal, 2.27.82.10          residue, 2.27.82.25
          mmff, 2.27.82.11     slide, 2.27.82.26
     chargemmff, 2.27.82.11     sstructure backbone, 2.27.82.50
     chiral, 2.27.82.12          sequence, 2.27.82.51
     color, 2.27.82.13          to sequence, 2.27.82.51
     comment, 2.27.82.14, 2.27.82.15     stack, 2.27.82.52
          sequence, 2.27.82.16          energy, 2.27.82.52, 2.27.87.1
     comp_matrix, 2.27.82.17     stereo, 2.27.82.49
     current map, 2.27.82.38     swiss, 2.27.82.53
          object, 2.27.82.41          name, 2.27.82.53
     directory, 2.27.82.18     symmetry, 2.27.82.56
     drestraint, 2.27.82.19          bio, 2.27.82.55
          type, 2.27.82.20          crystal, 2.27.82.54
     electrostatic radii, 2.27.82.70          group, 2.27.82.54
     error, 2.27.82.28          to a torsion, 2.27.82.56
     field, 2.27.82.29     table, 2.27.82.57
          name, 2.27.82.30     terms, 2.27.82.58
     font, 2.27.82.31     tether, 2.27.82.60
          grob, 2.27.82.32          append, 2.27.82.61
     foreground, 2.27.82.33     texture, 2.27.82.27
     format, 2.27.82.34     type, 2.27.82.62
     grob, 2.27.82.35          mmff, 2.27.82.68
          coordinates, 2.27.82.35          molecule, 2.27.82.66
          label, 2.27.82.35          object, 2.27.82.65

          sequence, 2.27.82.67     iarray, 2.27.83.24
          surface, 2.27.82.63     integer, 2.27.83.25
     variable grid, 2.27.82.75     key, 2.27.83.3
     variablegrid, 2.27.82.75     label, 2.27.83.26
     view, 2.27.82.71     library, 2.27.83.27
     vrestraint, 2.27.82.72     link, 2.27.83.28
     vrestraintvs_var, 2.27.82.73     logical, 2.27.83.29
          radii, 2.27.82.69     map, 2.27.83.4
     vwelradii, 2.27.82.70     mol, 2.27.83.30
     vwradii, 2.27.82.69     mol2, 2.27.83.31
     window, 2.27.82.76     molecule, 2.27.83.32
     xstick, 2.27.82.77     molecules, 2.27.83.5
          radii, 2.27.82.77     object, 2.27.83.33
setResLabel, 2.29.79     pdb, 2.27.83.34
setcomp_matrix, 2.27.82.17     pharmacophore type, 2.27.83.51
seticmff, 2.29.78     pmf, 2.27.83.35
setting conf properties, 2.27.82.52     preferences, 2.27.83.36
setvs_var, 2.27.82.74     profile, 2.27.83.37
sf-term, 2.27.82.63     residue, 2.27.83.38
sfWeight, 2.17.36          type, 2.27.83.39
sh24, 3.4     residuetype, 2.27.83.39
shadows, 2.21.5.29     segment, 2.27.83.40
shell, 3.1, 5.8.5     sequence, 2.27.83.41
     intro, 1.7.1     shell variable, 2.27.83.2
     progression, 2.27.71     site, 2.27.83.1
     warning message, 2.28.179     stack, 2.27.83.42
shineStyle, 2.20.23     svariable, 2.27.83.2
shininess, 2.17.37     table, 2.27.83.43
show, 2.27.83, 2.27.83.37          as database, 2.27.83.16
     alias, 2.27.83.6     term, 2.27.83.44
     aliases, 2.27.83.6     tethers, 2.27.83.45
     alignment, 2.27.83.7     version, 2.27.83.46
     area, 2.27.83.8     volume, 2.27.83.49
     atom, 2.27.83.9          map, 2.27.83.50
          type, 2.27.83.10     volumemap, 2.27.83.50
     atoms, 2.27.83.9     vrestraint, 2.27.83.47
     bond, 2.27.83.11          type, 2.27.83.48
     clash, 2.27.83.12     vrestraints, 2.27.83.47
     color, 2.27.83.13showcomp_matrix, 2.27.83.15
     column, 2.27.83.14showing weak hydrogen bonds, 2.21.5.20
     comp_matrix, 2.27.83.15side chain, 2.29.88
     database, 2.27.83.16          flexibility, 2.29.88
     drestraint, 2.27.83.17sigma level, 2.21.7.5
          type, 2.27.83.18signal recognition measure, 2.29.21
     energy, 2.27.83.19similar chains, 2.28.126.13
     gradient, 2.27.83.20similarity, 2.27.34.9, 2.27.34.10
     hbond, 2.27.83.21simple expressions, 2.9.1.1
          exact, 2.27.83.22     string substitution, 2.28.115.2
     hbondexact, 2.27.83.22simplify mesh structure, 2.27.15.1
     html, 2.27.83.23simulation duration, 2.17.44

     intro, 1.4.2          to molecules, 2.27.85.6
site, 2.27.11.2, 5.8.6     sequence, 2.27.85.4
     arrows, 2.27.82.23     table, 2.27.85.3
     table, 2.28.149.8          cell, 2.27.85.5
     by residue selection, 2.27.22.23          to columns, 2.27.85.3
     sequences, 2.28.149.8     tree, 2.27.85.7
sixthe power, 2.20.5splitting selection, 2.8.11
skin, 5.8.7sprintf, 2.27.86
     intro, 1.4.1.2sql, 2.27.74, 2.27.82.39, 2.28.43.1, 2.28.88.10, 2.28.91.5, 2.28.170.2
slide, 2.27.1.3, 2.28.133, 5.8.14sqlite, 3.5.1
     transition time, 2.27.23.21sqrt, 2.28.34
slides, 2.28.178square matrix to element pairs, 2.28.149.5
slideshow, 2.27.1.3, 2.27.23.21, 2.28.133ssThreshold, 2.17.38
sln, 5.8.8ssWeight, 2.17.39
smallest set of smallest rings, 2.28.119ssbond, 5.4.5
smarts, 2.28.62.1ssearch, 2.16.16, 2.27.88
smiles, 2.24ssearchStep, 2.17.40
     to chem-table element, 2.28.98ssign sstructure segment, 2.27.5.2
smooth alignment, 2.28.135.4stack, 2.16.11, 2.16.12, 2.16.14, 2.20.6, 2.27.82.52, 2.27.87, 2.27.87.1, 2.28.59.6, 2.28.149.6, 5.3.12, 5.8.9
     interpolation, 2.27.87.3     bin size, 2.27.14
     map, 2.28.135.5     cleaning, 2.27.22.16
     rarray, 2.28.135.1     extension, 2.27.4.2
     surface, 2.29.86     multiplication, 2.27.4.2
soap, 2.25     merge, 3.7.7
soft trim, 2.28.167standard chemical form, 2.27.64.4
solid sphere, 2.21.5.8     deviation, 2.28.122
solubility, 2.28.103standardization, 2.27.22.11
solvation, 2.20.24, 2.21.14.2     chemical, 2.27.64
     energy, 2.17.36, 2.20.24startup, 3.1.2.3
solvent accessible area, 2.16.22static RMSD, 2.28.144
          surface, 2.21.5.49, 2.21.5.50, 2.27.83.8     and dynamic hbonds, 2.21.5.19
sort, 2.27.84, 2.27.84.3stereo, 2.21.5.46, 2.27.29, 2.27.82.49
     array, 2.27.84.1     reconstruction, 3.8.9
     arrays, 2.27.84.1stereo-specific hydrogens, 2.27.22.11
     molecules, 2.27.84.4stereoisomer, 2.27.29
     object, 2.27.84.3stereoisomers, 2.18.16
     stack, 2.27.84.5stick, 5.8.10
     table, 2.27.84.2store, 2.27.87
sortSeqByLength, 2.29.80     conf, 2.27.87, 2.27.87.1
space group, 2.27.63     frame, 2.27.87.3
     transformations, 2.28.165     image, 2.27.59.20
sparse atoms, 2.21.14.3     stack object, 2.27.87.2
spawn background job, 2.27.59.1     torsion type, 2.27.87
special values, 2.28.157strength of hydrogen bond, 2.27.23.14
specificity, 2.28.125.2string, 5.8.11
split, 2.27.85     array, 2.28.124, 5.8.1
     column values, 2.27.85.5     filtering, 2.28.167
     grob, 2.27.85.1     inversion, 2.28.145.1
     group, 2.27.85.2     label, 2.27.23.12
     object, 2.27.85.6     matching, 2.9, 2.28.79

strings, 2.19     command, 2.27.92
strip, 2.27.89     copy, 2.19.26
struct, 2.28.88.2     file move, 2.19.28
structural alignment, 2.27.3.4, 2.28.5.2     list file, 2.19.27
          optimization, 2.27.34.1     remove, 2.19.29
     superposition, 2.27.3.4table, 2.27.22.4, 2.27.82.45, 2.27.82.46, 5.9.1
     analysis, 3.3     actions, 5.9.2.4
     comparison, 2.28.22.2     column, 2.28.88
     factors, 3.11.1          format, 2.27.82.34
     structure, 3.11.1          plot, 2.27.59.31
sub-alignment to selection, 2.28.117          transformations, 2.28.93
sub-matrix, 2.28.80.2     creation, 2.27.41.3
subalignment, 2.28.5.3     display style, 5.9.1
submap, 2.28.76     expression, 5.9.2
subroutine, 2.27.58     from matrix, 2.28.149.4
subset, 2.6     grid view, 5.9.1
substring, 2.28.79, 2.28.145, 2.28.145.1     of atoms and distances, 2.28.149.9
substructure, 2.27.34.9, 2.27.34.10     operations, 5.9.2.1
     search, 2.27.34.4     plot, 5.9.2.3
superimpose, 2.21.14, 2.27.90     principal component analysis, 2.27.59.28
     faq, 3.3.1     print, 2.27.83.43
     how to, 3.3.1     row, 2.27.66.4
     minimize, 2.27.91          label mark, 2.27.82.37.2
support, 1.3          mark, 2.28.70
suppressing view changes, 2.27.23.21     selected row numbers, 2.28.62
surface, 5.8.15     subset, 5.9.2.2
     accessibility, 2.27.83.8     show html, 2.27.101.1
     area, 2.29.3, 5.8.15targa, 5.9.3
     charge, 5.7.13target coordinates, 5.9.4
     color, 2.27.82.13tautomer, 2.27.30
     dot density, 2.21.5.49tempCycle, 2.17.43
     energy, 2.20.24, 2.27.82.63tempLocal, 2.17.42
     mesh, 2.28.180.2temperature, 2.17.43
     point selection, 2.28.180     variations in optimizer, 2.17.43
     term, 2.17.36template docking, 3.13.2.7
surfaceAccuracy, 2.16.22tensor product of two vectors, 2.28.80
surfaceMethod, 2.20.24terminal font, 2.30.14
surfaceTension, 2.17.41     window, 2.27.42
svariable, 5.8.12terms, 2.15
swapping protein fragments, 3.8.7     hydrogen bonding, 2.17.18
swiss, 2.27.82.53test, 2.27.93
swissFields, 2.22.9     binary, 2.27.93.1
swissprot, 2.27.82.23testing if argument exists, 2.28.52
symmetrization of a matrix, 2.28.80.3tether, 2.21.14.9, 2.27.103.9, 5.9.4, 5.9.5
symmetry, 2.28.165text, 2.28.79
     faq, 3.10     search in tables, 2.28.49.2
     group, 2.16.2     to script, 5.8.2
     problem, 2.27.63texture, 5.5.3
sys, 2.27.92tga, 5.9.3
system, 5.10.2then, 2.27.94

threading, 2.28.5.1undisplay, 2.27.97
     letter code, 2.28.161, 2.28.162     graphics, 2.27.98
thumbnails, 2.28.61     window, 2.27.98
tif, 5.9.6unfix, 2.27.99
time, 2.28.35unique, 2.27.13.1, 5.10.1
timeLimit, 2.17.44     atomic order, 2.27.59.36
tolFunc, 2.17.46     column values, 2.27.41.4
tolGrad, 2.17.45     names, 2.28.88
topological psa, 5.7.12     new object name, 2.28.88
torsion rmsd comparison, 2.27.14.2     smiles, 2.27.59.36
torsions, 2.28.91.3unix, 2.27.92, 5.10.2
tpsa, 5.7.12     grep, 2.27.77.1
trajectory, 2.27.57.2, 2.27.87, 2.27.87.3, 5.6.14unlink alignments, 2.27.22.20
     file, 2.30.17     sequences, 2.27.22.20
     frame writing, 2.27.23.17     variables, 2.27.22.20
     smoothing, 2.27.23.17update database, 2.27.64.5
transform, 2.27.95, 2.27.95.2     speadsheet, 2.27.1.1.1
     general, 2.27.95updates, 1.1
     grob coordinates, 2.27.95.2updating atom pairs, 2.18.27
     molecules, 2.27.95.2url string parsing, 2.28.149
     sarray, 2.27.95.1user atom display, 2.21.5.2
transformation, 5.9.7     environment, 3.1.2.2
     vector, 5.9.7     menu, 2.21.10.1
     and symmetry, 3.10user-defined properties, 2.27.82.29
transforming points, 2.28.180.4     solvation parameters, 2.28.7
translate, 2.27.96user_startup, 3.1.2.4
transparency, 2.27.82.35, 5.5.3     icm, 3.1.2
     background, 2.27.103.35     guide, 3
     grob, 2.27.23.11v_, 2.8.1
     grobs, 2.21.5.51van der Waals surface, 2.21.5.50
tree, 2.27.59.35, 2.28.88.5varLabelStyle, 2.20.26
     cluster, 2.11variable restraint, 2.27.82.72
     delete, 2.27.22.34     selection, 2.8.9
     label format, 2.28.88.5vector, 2.28.91.6
     representatives, 2.11.1     dot product, 2.28.175.1
trim string array, 2.27.95.1     length, 2.28.92
trimming grid map values, 2.28.167     product, 2.28.175.1
true positives, 2.28.125.2     transformation, 2.28.93
truncate alignment, 2.27.59.33vertex, 2.27.13.4.2
     values, 2.28.167     connectivity, 2.28.80.12
tsv table format, 2.27.77.41vertexes, 2.27.13.4.2
two alignments, 2.28.38.11vertical alignment block, 2.27.59.33
     dimensional plot, 2.28.135.2     workspace, 2.21.8.5
txdoc browser, 2.27.77.3vertices, 2.27.13.4.2
type, 2.28.170.1vicinity, 2.17.48
tzMethod, 2.20.25video, 2.27.103.30
tzWeight, 2.17.47view point, 2.28.178
uncharge functional groups, 2.27.64.2     restoration, 2.28.65
unclip, 2.27.23.2     transition, 2.27.82.71
underline, 2.27.82.31.1views, 5.8.14

     arrays, 2.27.1.1.1workspace, 2.27.98
     chemistry, 2.27.64, 2.28.91.4write, 2.27.103
     field, 2.27.7.2     album, 2.27.103.21
     ligand screening, 3.13, 3.13.1, 3.13.2, 3.13.3     alignment, 2.27.103.1
               intro, 1.4.2.7     array, 2.27.103.8
visitsAction, 2.20.27          table, 2.27.103.8
vls, 3.13, 3.13.1, 3.13.2, 3.13.3     binary, 2.27.103.2
     cluster, 3.13.3.6     blast, 2.27.103.24
     faq, 3.13.3     column, 2.27.103.12
     intro, 1.4.2.7     database, 2.27.103.13
     job queueing, 3.13.3.6     drestraint, 2.27.103.14
     overview, 3.13.1          type, 2.27.103.15
     parallelization, 3.13.3.5     factor, 2.27.103.16
     results, 3.13.3.8     gamess, 2.27.103.17
     scores storage, 3.13.3.7     grob, 2.27.103.18
     threshold, 3.13.3.2     html, 2.27.103.19
vls_intro, 3.13.3.1     iarray, 2.27.103.3
volume, 5.10.4     image, 2.27.103.20
vrestraint, 5.10.5          chemical, 2.27.103.22
     file, 2.30.23          parray, 2.27.103.21
     type, 5.10.6     index, 2.27.103.23
          file, 2.30.22          blast, 2.27.103.24
vs_, 2.8.9     library, 2.27.103.25
vs_out, 2.22.14     map, 2.27.103.26
vwCutoff, 2.17.49     matrix, 2.27.103.6
vwExpand, 2.17.50     model, 2.27.103.27
vwExpandDisplay, 2.17.51     mol, 2.27.103.28
vwMethod, 2.20.28     mol2, 2.27.103.29
vwSoftMaxEnergy, 2.17.52     molcart, 2.27.103.7
wait, 2.27.100     movie, 2.27.103.30
warning, 2.21.14.3     object, 2.27.103.31
     message, 2.28.179          parray, 2.27.103.33
     suppression, 2.18.28          simple, 2.27.103.32
water.dielectric constant, 2.17.12     pdb, 2.21.14.11, 2.27.103.34
waterRadius, 2.17.53     png, 2.27.103.35
wavefront format, 2.27.59.11     postscript, 2.27.103.36
web, 2.27.101     pov, 2.27.103.37
     table, 2.27.101.1     povray, 2.27.103.37
webEntrezOption, 2.20.29     project, 2.27.103.2
weighted rmsd, 2.21.14     rarray, 2.27.103.4
while, 2.27.102     sarray, 2.27.103.5
whole string, 2.28.115.1     sequence, 2.27.103.38
window averaging, 2.28.135.1     session, 2.27.103.39
     layout, 2.28.145.8     several array, 2.27.103.8
     width and height, 2.28.178     simple object, 2.27.103.32
windowSize, 2.16.23     stack, 2.27.103.40
     movie, 2.27.103.30     table, 2.27.103.10
wire, 5.10.7          mol, 2.27.103.11
wireBondSeparation, 2.17.54          with links, 2.27.103.19
wireStyle, 2.20.30     tether, 2.27.103.9

     trajectory, 2.27.23.17 
     vs_var, 2.27.103.41 
writevs_var, 2.27.103.41 
xml, 2.27.77.52, 2.28.79 
     drugbank example, 2.10 
xplor format, 2.27.77.26 
xrMethod, 2.20.31 
xrWeight, 2.17.55 
xray density to rectangular energy map, 2.27.59.30 
xstick, 5.10.8 
xyz morphing, 3.8.8 
zega, 5.10.9 
     intro, 1.4.3.6 
|, 2.12.3