ICM Manual v.3.8
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2019, Molsoft LLC
Dec 27 2021

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

Index

&, 2.14.3Bracket, 2.34.22
2D labels, 2.33.56.1C, 5.3
     to 3D, 3.16CCP4, 5.6.6
     trees, 2.33.63.38CGI, 2.11
     smooth, 2.34.146.2COLOR.bg, 2.19.9
3D chemical builder, 1.4.2.8     distanceAtom, 2.19.10
     font size, 2.33.23.12     label, 2.19.11
     label, 2.33.23.12, 2.33.87.39CONSENSUS, 2.23.1
     labels, 2.33.56.1CONSENSUSCOLOR, 2.23.2
     mol file, 2.36.86CONSENSUS_strength, 2.19.12
     plots intro, 1.4.3.7Cad, 2.34.23, 2.34.23.1, 2.34.23.2
     smoothing, 2.34.146.3Cad1, 2.34.23.1
     superposition, 2.36.22Cadalign, 2.34.23.2
     transformations, 2.33.100.2Ceil, 2.34.24
     tree, 2.33.63.38Cell, 2.34.25
     chemical similarity, 2.34.136Charge, 2.34.26
     pharmacophore comparison, 2.34.136.3Chemical, 2.34.27
3dxml, 5.5.3     Functions, 2.27
=, 2.14.1     Synthetic Accessibility, 2.30
A, 5.1Cluster, 2.34.28
ANN, 2.33.52Collada, 5.5.3
APF distance, 2.34.136Collection, 2.34.28.1
Abs, 2.34.1Color, 2.34.29
Acc, 2.34.2     from gradient, 2.34.29.1
Acos, 2.34.3     image, 2.34.29.2
Acosh, 2.34.4     protein, 2.34.29.3
Adobe, 2.21.23Compare, 2.34.30
Align, 2.34.5Connolly surface, 5.8.7
     sequence, 2.34.5.1Consensus, 2.34.31
AlignSS, 2.35.1Contour, 2.34.32
Angle, 2.34.6Corr, 2.34.33
Apple, 3.14.6.2Cos, 2.34.34
Area, 2.34.7Cosh, 2.34.35
     residue contacts, 2.34.7.1Count, 2.34.36
Asin, 2.34.8CubicRoot, 2.34.37
Asinh, 2.34.9D, 5.4
Ask, 2.34.10DAE, 5.5.3
Askg, 2.34.11DE, 2.33.35.2
Atan, 2.34.12DNA Representation, 1.4.1.3
Atan2, 2.34.13     alignment, 2.33.3.4
Atanh, 2.34.14     melting temperature, 2.34.164
Atom, 2.34.15     views, 1.4.1.3
Augment, 2.34.16Date, 2.34.38
Axis, 2.34.17Deletion, 2.34.39
B, 5.2Descriptor, 2.34.40, 2.34.41
BPMC, 5.2.6     numeric, 2.34.40
Bfactor, 2.34.19Det, 2.34.42
Blob, 2.34.18Disgeo, 2.34.43
Boltzmann, 2.34.20Distance, 2.34.44, 2.34.44.6
Box, 2.34.21     2 alignments, 2.34.44.13

     Dayhoff, 2.34.44.11Formula, 2.34.58
     Tanimoto, 2.34.44.7GRAPHICS, 2.23.5
     alignment, 2.34.44.12     alignmentRainbow, 2.23.5.1
     as_, 2.34.44.3     atomLabelShift, 2.23.5.2
          rarray, 2.34.44.4     atomValueCircles, 2.23.5.3
     atoms, 2.34.44.3     ballRadius, 2.23.5.4, 2.23.5.31
     chemical, 2.34.44.7, 2.34.44.15     ballStickRatio, 2.23.5.5
     chemset, 2.34.44.8     chainBreakLabelDisplay, 2.23.5.8
     dayhoff, 2.34.44.11     chainBreakStyle, 2.23.5.7
     hierarchical, 2.34.44.6     clashWidth, 2.23.5.6
     iarray, 2.34.44.1     clipStatic, 2.23.5.10
          alignment, 2.34.44.12     clippingPlane, 2.23.5.9
     matrix, 2.34.44.5, 2.34.44.9     cpkClipCaps, 2.23.5.11
     multiple atomic, 2.34.44.4     displayLineLabels, 2.23.5.12
     rarray, 2.34.44.2     displayMapBox, 2.23.5.13
     tether, 2.34.44.10     dnaBallRadius, 2.23.5.14
     tree, 2.34.44.14     dnaRibbonRatio, 2.23.5.15
          cluster, 2.34.44.14     dnaRibbonStyle, 2.23.5.16
     H, 5.5     dnaRibbonWidth, 2.23.5.17
     number, 2.34.44.6     dnaRibbonWorm, 2.23.5.18
EDS server, 2.36.42     dnaStickRadius, 2.23.5.19
EST-alignment, 2.33.3.4     formalChargeDisplay, 2.23.5.20
Eigen, 2.34.45     grobDotSize, 2.23.5.21
Energy, 2.34.46     grobLineWidth, 2.23.5.22
Entropy, 2.34.47     hbondAngleSharpness, 2.23.5.26
Error, 2.34.48     hbondBallPeriod, 2.23.5.27
     soap, 2.34.49     hbondBallStyle, 2.23.5.28
Exist, 2.34.50     hbondMinStrength, 2.23.5.25
     molcart, 2.34.50.1     hbondRebuild, 2.23.5.24
Existenv, 2.34.51     hbondStyle, 2.23.5.23
Exp, 2.34.53     hbondWidth, 2.23.5.29
Extension, 2.34.52     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, 2.34.91.1
     proxy, 2.23.4.3     rainbowBarStyle, 2.23.5.39
Field, 2.34.54, 2.34.54.1     resLabelDrag, 2.23.5.40
     user, 2.34.54.1     resLabelYShift, 2.23.5.41
File, 2.34.55     ribbonCylinderRadius, 2.23.5.42
Find, 2.34.56     ribbonGapDistance, 2.23.5.43
     chemical, 2.34.56.3     ribbonRatio, 2.23.5.44
          pattern, 2.34.56.3     ribbonWidth, 2.23.5.45
     in array, 2.34.56.1     ribbonWorm, 2.23.5.46
          table, 2.34.56.2     rocking, 2.23.5.47
FlexLM license info, 2.34.188     rockingRange, 2.23.5.48
Floor, 2.34.57     rockingSpeed, 2.23.5.49

     selectionStyle, 2.23.5.51ICM-shell, 3.1, 5.8.5
     sketchAccents, 2.23.5.30     intro, 1.7.1
     stereoMode, 2.23.5.52     script, 2.33.8
     stickRadius, 2.23.5.31, 2.23.5.53ICMFF force field, 2.36.79
     surfaceDotDensity, 2.23.5.55ICMHOME, 3.1.2.1
     surfaceDotSize, 2.23.5.54     shell variable, 3.1.2.1
     surfaceProbeRadius, 2.23.5.56IMAGE, 2.23.9
     transparency, 2.23.5.57     bondLength2D, 2.23.9.15
     wormRadius, 2.23.5.58     color, 2.23.9.8
GRID, 2.23.6     compress, 2.23.9.9
     gcghExteriorPenalty, 2.23.6.1     gammaCorrection, 2.23.9.7
     gpGaussianRadius, 2.23.6.6     generateAlpha, 2.23.9.10
     margin, 2.23.6.2     lineWidth, 2.23.9.3
     maxEl, 2.23.6.3     lineWidth2D, 2.23.9.14
     maxVw, 2.23.6.5     orientation, 2.23.9.16
     minEl, 2.23.6.4     paperSize, 2.23.9.17
GROB, 2.23.7     previewResolution, 2.23.9.13
     arrowRadius, 2.23.7.3     previewer, 2.23.9.12
     atomSphereRadius, 2.23.7.1     printerDPI, 2.23.9.2
     contourSigmaIncrement, 2.23.7.5     quality, 2.23.9.1
     relArrowHead, 2.23.7.4     rgb2bw, 2.23.9.18
     relArrowSize, 2.23.7.2     scale, 2.23.9.4
GUI, 2.23.8     stereoAngle, 2.23.9.6
     defaults, 3.14.6.2     stereoBase, 2.23.9.5
     dialog, 2.32     stereoText, 2.23.9.11
     plot, 2.33.63.32     writeScale, 2.23.9.19
     preferences, 2.33.83.4I_out, 2.24.4
     tableRowMarkColors, 2.23.8.5Iarray, 2.34.66, 2.34.66.4, 2.34.66.5
     windowLayout, 2.23.8.6     atom numbers, 2.34.66.4
     workspaceFolderStyle, 2.23.8.9     bits to integers, 2.34.66.3
     workspaceStyle, 2.23.8.7     inverse, 2.34.66.2
     workspaceTabStyle, 2.23.8.8     residue numbers, 2.34.66.5
GaussFit, 2.34.82     reverse, 2.34.66.2
Getarg, 2.34.59     stack, 2.34.66.6
Getenv, 2.34.60Icm Options, 2.1
Gradient, 2.34.61IcmSequence, 2.34.67
Graphics, 1.4.1Image, 2.34.68
Grob, 2.34.62     collection, 3.9.2.1
Group, 2.34.63     frame by frame, 3.9.2.2
HTTP.ignoreProxyDomains, 2.23.4.5InChI, 2.34.69
     proxy, 2.23.4.4InChi, 2.34.69
Hartree-Fock, 2.33.82.21, 2.33.108.17InList, 2.34.105
Header, 2.34.64Index, 2.34.70
Histogram, 2.34.65     chemical, 2.34.70.2
     N, 5.6     compare, 2.34.70.10
ICM desktop, 2.23.8.6     element in array, 2.34.70.8
     documents, 2.33.82.4     fork, 2.34.70.1
     modules, 1.4.4     regexp, 2.34.70.4
     object, 2.36.13     string, 2.34.70.3
     residue library, 2.21.24     table label, 2.34.70.6

     tree, 2.34.70.9Median, 2.34.93
     unique elements, 2.34.70.7Method, 2.22.13
Indexx, 2.34.71Min, 2.34.95
Info, 2.34.73Mod, 2.34.97
     image, 2.34.74Mol, 2.34.98
     model, 2.34.75MolLogP, 2.28
Insertion, 2.34.72MolLogS, 2.29
Integer, 2.34.76MolPSA, 5.7.12
Integral, 2.34.77MolSynth, 2.30
Interrupt, 2.34.78Moment, 2.34.88
Introduction, 1     of Inertia, 2.34.88
JSON, 2.33.82.57Money, 2.34.96
LIBRARY, 2.23.10N-terminus, 2.23.14.4
     men, 2.23.10.1NMR, 2.33.61.1
     res, 2.23.10.2NOE averaging, 2.22.6
Label, 2.34.79Name, 2.34.99
Laplacian, 2.34.80     chemical, 2.34.99.6
Latent, 2.34.187.3          property, 2.34.99.1
LatentVector, 2.34.187.3     close sequence, 2.34.99.3
Length, 2.34.81     conf, 2.34.99.7
LinearFit, 2.34.83     image, 2.34.99.11
LinearModel, 2.34.84     molcart, 2.34.99.12
Log, 2.34.85     object parray, 2.34.99.10
LogP, 2.28, 2.34.114     sequence, 2.34.99.8
LogS, 2.29, 2.34.114     soap, 2.34.99.2
M_out, 2.24.5     string, 2.34.99.4
Mac, 3.14.6.2     tree, 2.34.99.5
Map, 2.34.86Namex, 2.34.100
Markush structures, 2.33.53     image, 2.34.100.2
Mass, 2.34.87     sequence, 2.34.100.1
Match, 2.34.89Newick tree format, 2.34.156.4
Mathews, 2.34.136.4Next, 2.34.101, 2.34.101.1
Matrix, 2.34.90     covalent neighbors, 2.34.101.1
     alignment, 2.34.90.9Nof, 2.34.102
     boundary, 2.34.90.10     chemical, 2.34.102.2
     color, 2.34.90.4     distance, 2.34.102.3
     grob connectivity, 2.34.90.13     latent, 2.34.102.6
     histogram, 2.34.90.12     library, 2.34.102.4
     new, 2.34.90.1     molcart, 2.34.102.5
     residue areas, 2.34.90.8     soap, 2.34.102.7
          comparison, 2.34.90.5     tree, 2.34.102.1
     stack, 2.34.90.11Norm, 2.34.103
     sub, 2.34.90.2Normalize, 2.34.104
     symmetric, 2.34.90.3NotInList, 2.34.105
     table, 2.34.90.6     R, 5.7
     tensor, 2.34.90.7OBJECT, 2.23.11
Max, 2.34.91Obj, 2.34.106
     image graphic, 2.34.91.1Occupancy, 2.34.107
MaxHKL, 2.34.92PBS, 3.13.3.6
Mean, 2.34.94PLOT, 2.23.12

     box, 2.23.12.1Real, 2.34.123
     color, 2.23.12.2Reference, 2.34.125
     font, 2.23.12.3     Guide, 2
     fontSize, 2.23.12.4Remainder, 2.34.124
     gridLineWidth, 2.23.12.5Replace, 2.34.126
     labelFont, 2.23.12.13     chemical, 2.34.126.4
     lineWidth, 2.23.12.6     exact, 2.34.126.1
     logo, 2.23.12.10     regexp, 2.34.126.3
     markSize, 2.23.12.7     simple, 2.34.126.2
     numberOffset, 2.23.12.8Res, 2.34.127, 2.34.128
     orientation, 2.23.12.11Resali, 2.34.128
     rainbowStyle, 2.23.12.14Resolution, 2.34.129
     seriesLabels, 2.23.12.12Rfactor, 2.34.131
PLS, 2.34.102.6Rfree, 2.34.132
     error, 2.34.136.4Ring, 2.34.130
     models, 2.34.136.4Rmsd, 2.34.133
Parray, 2.34.109     of subset, 2.23.14
Parray-object, 2.34.109Rot, 2.34.134
Path, 2.34.108S, 5.8
Pattern, 2.34.110SAR analysis, 2.33.63.27, 2.33.63.28, 2.33.90.2, 2.33.90.3
Pi, 2.34.111SC, 2.33.35.2
Polar Surface Area, 5.7.12SEQUENCE.restoreOrigNames, 2.23.12.15
Potential, 2.34.112SITE, 2.23.13
Power, 2.34.113     defSelect, 2.23.13.2
Predict, 2.34.114     labelOffset, 2.23.13.3
Probability, 2.34.115     labelStyle, 2.23.13.4
Profile, 2.34.116     labelWrap, 2.23.13.5
Property, 2.34.117     showSeqSkip, 2.23.13.6
Protonation state, 2.34.160.11     wrapComment, 2.23.13.7
Putarg, 2.34.118SLN notation, 2.34.156.10
Putenv, 2.34.119SMARTS, 2.26, 2.33.10, 2.34.102.2
QSAR, 2.33.52SOAP, 2.34.99.2, 2.34.102.7, 2.34.182.1
R-groups, 2.33.53     request message, 2.34.152
REBEL, 3.7.2SSSR, 2.34.130
     faq, 3.7.2S_out, 2.24.8
     file, 2.33.53S_proteinTags, 2.24.9
RNA topology, 2.23.5.16Sarray, 2.34.135
R_2out, 2.24.7     index, 2.34.135.1
R_out, 2.24.6Score, 2.34.136
Radius, 2.34.120     alignment, 2.34.136.8
Random, 2.34.121     apf, 2.34.136.3
     string, 2.34.121.1     chemset, 2.34.136.2
Rarray, 2.34.122     conservation, 2.34.136.7
     reverse, 2.34.122.2     model, 2.34.136.4
     sequence projection, 2.34.122.1     overlap, 2.34.136.1
     alignment projection, 2.34.122.3     predictions, 2.34.136.5
          strength, 2.34.122.5     sequence, 2.34.136.6
     property assignment, 2.34.122.4Scripting Tutorials, 1.8
RarrayAlignment, 2.34.122.5Select, 2.34.137
Rarrayinverse, 2.34.122.2     break, 2.34.137.1

          atom property, 2.34.137.7Sum, 2.34.158
          nmembers, 2.34.137.4     chemical, 2.34.158.1
          string, 2.34.137.9     image, 2.34.158.2
     expand, 2.34.137.6Swissprot, 2.33.108.24
     fix, 2.34.137.2Symgroup, 2.34.159
     graphical, 2.34.137.5T, 5.9
     neighbors, 2.34.137.3TOOLS, 2.23.14
Select_by atom numbers, 2.34.137.10     edsDir, 2.23.14.1
Select_by_sequence, 2.34.137.13     membrane, 2.23.14.2
Select_by_text, 2.34.137.9     minSphereCubeSize, 2.23.14.3
Select_lists, 2.34.137.12     pdbChargeNterm, 2.23.14.4
Select_patching, 2.34.137.11     pdbReadNmrModels, 2.23.14.5
Select_projection, 2.34.137.8     rebelPatchSize, 2.18.5, 2.23.14.6
Sequence, 2.34.138     smilesXyzSeparator, 2.23.14.7
     array, 2.34.138.2     superimposeMaxDeviation, 2.23.14.10
Sequence(dna reverse), 2.34.138.1     superimposeMaxIterations, 2.23.14.8
Shannon, 2.34.47     superimposeMinAtomFraction, 2.23.14.9
Shuffle, 2.34.139     tsShape, 2.23.14.12
Sign, 2.34.140     tsWeight, 2.23.14.13
Simulations, 1.4.2     writePdbRenameRes, 2.23.14.14
Sin, 2.34.141Table, 2.34.160
Sinh, 2.34.142     alignment numbers, 2.34.160.3
Site, 2.34.143     distance, 2.34.160.10
Slide, 2.34.144     matrix, 2.34.160.4
Smiles, 2.34.145     model, 2.34.160.8
Smooth, 2.18.24, 2.34.146, 2.34.146.1, 2.34.146.3          chem, 2.34.160.9
     matrix, 2.34.146.2     pairs, 2.34.160.5
Smoothrs, 2.34.146.3     plot, 2.34.160.7
SoapMessage, 2.34.152     stack, 2.34.160.6
SolveQuadratic, 2.34.147     url_decoder, 2.34.160.1
SolveQubic, 2.34.148Table(alignment), 2.34.160.2
Sort, 2.34.153Table(stack), 2.34.160.6
Sphere, 2.23.14.3, 2.34.151Tan, 2.34.161
Split, 2.34.154Tanh, 2.34.162
     chemical, 2.34.154.4Tanimoto, 2.34.66.3
     multisep, 2.34.154.3     distance, 2.33.63.37
     regexp, 2.34.154.2          matrix, 2.34.44.7
     tree, 2.34.154.1Temperature, 2.34.164
Sql, 2.34.149Tensor, 2.34.163
Sqrt, 2.34.150Time, 2.34.165
Srmsd, 2.34.155Tointeger, 2.34.166
Sstructure, 2.34.157Tolower, 2.34.167
String, 2.34.156, 2.34.156.8Toreal, 2.34.168
     alternative, 2.34.156.7Torsion, 2.34.169
     date, 2.34.156.2Tostring, 2.34.170
     mol, 2.34.156.3Toupper, 2.34.171
     selection, 2.34.156.8ToxScore, 2.35.2
     slide gui, 2.34.156.9Tr123, 2.34.172
     substring, 2.34.156.1Tr321, 2.34.173
     chemical formula, 2.34.156.10Trace, 2.34.174

Transform, 2.34.176     icm, 2.37.2
Transpose, 2.34.177a_, 2.8.1
Trim, 2.34.178abbr, 1.6
     chemical, 2.34.179abbreviations, 1.6
     sequence, 2.34.180absolute to cell x y z, 2.34.192.4
Turn, 2.34.181accFunction, 2.24.2
Type, 2.34.182acceptor, 3.6.1
     molcart, 2.34.182.2access large sdf file, 2.33.82.24
     soap, 2.34.182.1accessMethod, 2.22.2
     Z, 5.10accessible residues, 3.3.6
Unique, 2.34.183     surface, 2.33.63.14, 5.8.15
Unix, 2.34.184accessing sections, 2.33.108.24
Uppsala, 2.36.42accuracy, 2.34.136.4
     server, 2.36.43acidity constant, 2.33.87.11, 2.33.87.12
V_, 2.8.1activate fog, 2.33.23.24
Value, 2.34.185     alignment, 2.33.87.40
     soap, 2.34.186     document, 2.33.87.40
Vector, 2.34.16, 2.34.187, 2.34.187.1, 2.34.187.3     tab, 2.33.87.40
     symmetry transformation, 2.34.187.2     table, 5.9.2.4
Vectorproduct, 2.34.187.1add, 2.33.1
Vectorsymmetrytransformation, 2.34.187.2     column, 2.33.1.1
Version, 2.34.188          function, 2.33.1.1.1
View, 2.34.190     matrix, 2.33.1.2
Volume, 2.34.189     slide, 2.33.1.3
WEBAUTOLINK, 2.23.16     table, 2.33.1.4
WEBLINK, 2.23.15          row, 2.33.1.4
Warning, 2.34.191addBfactor, 2.19.1
Wavefront format, 2.33.82.22adding atoms to non-ICM objects, 2.33.7.1
XML, 2.12     columns to table, 2.33.1.1
Xyz, 2.34.192     hydrogens, 2.36.13
     axes, 2.34.192.8     in place, 2.14.4
     chemical match, 2.34.192.6     to slideshow, 2.33.1.3
     fract, 2.34.192.4admet selection, 3.13.3.4
     mesh, 2.34.192.3advanced chemical search, 3.6
     points, 2.34.192.1     operations, 2.14.6
     rings, 2.34.192.2     ops, 2.14.6
     transformed xyz, 2.34.192.5ahfs, 2.34.44.6
     vector2matrix, 2.34.192.7ali_seq_project, 2.34.156.5
Z-shift, 2.19.35alias, 2.33.2
ZEGA, 5.10.9align, 2.33.3
     intro, 1.4.3.6     3D, 2.33.3.5
_NAME, 2.33.87.47          faq, 3.3.2
_chemBatch, 3.1.2.5          heavy, 2.33.3.6
_chemSuper, 3.15          how to, 3.3.2
_confGen, 3.16     chemical, 2.33.86.1
_dockScan, 3.13.2.5     fragments, 2.33.3.4
_macro, 2.37.1     intro, 1.4.3.3
     file, 2.37.1     number, 2.33.3.2
_startup, 3.1.2.3          chemical, 2.33.3.1
     file, 2.37.2     res numbers, 2.33.3.2

     sequences, 2.33.3.3     a tables, 2.33.1.4
alignMethod, 2.22.3     column, 2.33.4.3
alignMinCoverage, 2.19.2     command, 2.33.4
alignMinMethod, 2.19.2     sequence, 2.33.4.1
alignOldStatWeight, 2.19.3          to group, 2.33.4.1
alignTwoSequences, 2.36.1     stack, 2.33.4.2
aligned residues, 2.34.128     tables, 2.33.50
alignment, 2.33.22.26, 2.33.87.27, 2.33.87.35, 2.33.87.55, 5.1.1          by shared column, 2.33.4.3
     as table, 2.34.160.2appending, 2.33.1.1
     block length, 2.18.22     an element, 2.14.4
          secondary structure, 2.35.1     menu items, 2.23.10.1
     cleaning, 2.34.146.4     representations to a slide, 2.33.23.21
     color by property, 2.33.87.34     rows to matrix, 2.33.1.2
     coloring, 2.21.1area under curve, 2.36.21
     conservation, 2.36.8arguments, 2.33.62
     distance, 2.34.137.13arithmetic operations, 2.14.2
     editor, 2.4arithmetics, 2.14
     extraction, 2.34.5aromatic planes, 2.36.4
     gap format, 5.1.1.1array, 2.33.70.4, 5.1.6, 5.7.3.1
     intro, 1.4.3.4     assignment, 2.14.1
     projection, 2.34.156, 2.34.156.5, 2.34.156.6     derivative, 2.34.146.1
     score, 2.34.136.7     overlap, 2.34.136.1
     sequence reordering, 2.34.5     parray, 2.33.22.31
     strength, 2.34.122.5     size, 2.34.102
     structural, 2.33.3.5, 2.34.5     subset, 2.6
     to sequence transfer, 2.34.122.1arrow from selection, 2.36.36
          text conversion, 2.34.156.4     length, 2.33.87.26
     weighted, 2.34.5as2_out, 2.24.14
     gapExtension, 2.19.18as_, 2.8.8
     gapOpen, 2.19.19as_graph, 2.23.5.50, 2.23.5.51, 2.34.137.5
alignment_as_text, 2.34.156.4as_out, 2.24.13
aliphatic amines, 2.33.68.2assign, 2.33.5
all, 5.1.2     residue, 2.33.6.1
     torsions table, 3.3.11     ring conformation to template, 2.33.64.4
alpha, 2.23.5.57, 2.33.87.42, 5.1.3     sstructure, 2.33.5.1
     channel, 2.23.9.10          segment, 2.18.20, 2.33.5.2
alternative flag, 2.33.87.18assignment, 2.14.1
amber, 5.1.4atc code, 2.34.44.6
amino acid, 2.21.24, 2.34.172, 2.34.173atom, 2.33.13.1, 5.1.7
          colors, 2.34.29.3     centers within, 2.34.151
          labels, 2.33.3.2     code file, 2.37.4
and, 2.14.3     coordinates, 2.34.192.1
angle rotation, 2.36.84     flickering, 2.33.87.3
angles, 2.34.102.3     label font, 2.37.15
angular hbond dependence, 2.23.5.26     labels, 2.33.87.2
animated story, 5.8.14     name, 2.33.3.1, 2.34.79
animation, 2.33.23.5, 2.33.23.6, 3.9     pairs, 2.33.87.68, 2.33.87.69, 2.34.160.10
annotation, 2.33.22.26, 2.33.87.26, 2.33.87.27     proximity to surface, 2.33.88.9
apf, 3.15     selection by number, 2.34.66.4
append, 5.1.5     type, 2.34.182

atomLabelStyle, 2.22.4     to protein, 2.33.70.3
atomSingleStyle, 2.22.5     width, 2.23.9.14
atomic contributions, 2.33.88.20, 2.33.88.21bonded atoms, 2.34.101.1
     coordinate transfer, 2.33.87.3born radii, 2.33.88.9
     property fields, 3.15boundary element, 5.2.5
     solvation contributions, 2.34.7          matrix, 2.34.90.10
     in residue, 2.34.63box, 2.34.21
     alternative position, 2.33.87.18break, 2.33.6
     selecting, 2.8.8brightness, 2.23.5.33
     translate, 2.33.87.3build, 2.33.7
attenuation by occupancy, 2.33.63.25     atom, 2.33.7.1
auc enrichment, 2.36.21     column, 2.33.7.2
auto saving log, 2.22.11     faq, 3.8.1
autoSavePeriod, 2.18.1     from string, 2.33.7.8
avi, 2.33.108.31     helix, 3.10.5
axis, 5.1.8     how to, 3.8.1
axisLength, 2.19.4     hydrogen, 2.33.7.9
background, 2.34.29.2     loop, 2.33.7.6
     color, 2.19.9     model, 2.33.7.5, 2.33.108.9
ball, 2.33.87.2, 5.2.2     molcart, 2.33.7.10
base, 5.2.1     sequence, 2.33.7.3
     pair diagram, 2.23.5.16     smiles, 2.33.7.7
basis set, 2.33.82.21, 2.33.108.17     string, 2.33.7.8
batch chemical processing, 3.1.2.5     tautomer, 2.33.7.4
     docking, 3.13.2.5built-in functions, 5.5.5
beta, 5.2.3     plot, 2.33.87.53
bfactor circles, 2.23.5.3     atoms, 2.33.14
biased probability monte carlo, 2.33.69     contact surface, 2.33.14
binary file table of contents, 2.33.82.2     molecule, 2.33.13.1
     files, 2.33.108.2     number of bonds, 2.34.137.3
     string, 5.2.4     variables, 2.33.14
     key, 2.33.87.43cage, 2.36.4
binding energy, 3.7.4calcArea, 2.36.2
     pocket finding, 3.4.2calcBindingEnergy, 2.36.3
     pockets, 2.33.90.1calcDihedralAngle, 2.36.4
     side comparison, 2.36.8calcEnergyStrain, 2.36.20
     site analysis, 3.4.2calcEnsembleAver, 2.36.5
biological symmetry, 2.33.87.9calcMaps, 2.36.6
     vector, 2.34.66.3calcPairSeqIdsFromAli, 2.36.7
     to integers compression, 2.34.66.3calcPepHelicity, 2.36.9
blast, 2.33.108.25calcProtUnfoldingEnergy, 2.36.10
     files, 2.33.108.25calcRmsd, 2.36.11
blast-formatted database, 2.33.35.3, 2.33.108.25calcRoc, 2.36.21
blending, 2.33.108.31calcSeqContent, 2.36.12
     images, 2.34.158.2calcSeqSimilarity, 2.36.8
blob, 5.2.4calculate phases, 3.11.2
bold, 2.33.87.38.1call, 2.33.8
bond angle bending, 2.37.5canonical form, 2.34.45
     errors, 2.33.88.12carboxylic acid, 2.33.68.2
     stretching, 2.37.6cartesian cooridnates, 2.34.192

cavities, 2.33.90.1     search, 2.33.35.10, 2.33.86.1, 2.34.102.2
cavity, 5.3.1     similarity, 3.5
     analysis, 3.3.13     simplification, 2.34.178
ccp4 maps, 2.33.82.27     spreadsheet, 2.33.12, 2.33.82.48, 2.33.82.49, 2.33.82.50, 2.33.87.47, 2.33.108.11
cd, 2.33.87.21     structure from smiles, 2.33.87.7
cell axis vectors, 2.34.192.8     substructure, 2.33.35.4
     specific icm commands, 5.9.2.4          mask, 2.33.63.21
center, 2.13.1, 2.33.9     superposition, 2.22.7, 2.34.133, 3.15
cgi programming with icm, 2.11     table, 2.25
chain breaks, 2.23.5.7, 2.23.5.8, 2.34.137.1     text format, 5.6.11
     symbol, 2.33.87.9     topological descriptors, 2.34.40
change atom position, 2.33.87.3     view, 2.33.87.54
     sequence position in multiple alignment, 2.33.70.7chemistry, 2.25, 2.34.27
     unix directory, 2.33.87.21chiral isomer generation, 2.33.30
changing local stick radii, 2.33.87.86chirality, 2.20.16, 2.33.30
     surface dot size, 2.23.5.54choosing ligands, 3.13.1.2
channel, 2.23.14.2chroma, 2.34.90.4
charge, 2.23.14.4, 5.3.2cif, 2.33.82.48
     compounds, 2.33.68.2circular permutation of coordinates, 2.33.67
     prediction, 2.33.87.11, 2.33.87.12clamp values to range, 2.34.178
     state, 2.33.29clashThreshold, 2.19.5
     change, 2.33.87.10clashes, 2.33.63.16
chem formula, 2.34.156.10     labels, 2.34.166
chemSuper3D, 2.36.22classification, 2.34.44.6
chemical, 2.23.14.7, 2.25, 2.33.35.9, 2.34.69clear, 2.33.10
     2D drawings, 2.33.63.9     graphical selection, 2.33.10
     SMARTS search, 2.33.35.5     screen, 2.33.10
     atom annotation, 2.33.22.20click and lock, 5.9.2.4
     database, 3.5clipping plane, 2.23.5.9, 2.23.5.10, 2.23.5.11, 2.33.70.6, 5.3.3
     decomposition, 2.33.63.27, 2.33.90.2, 2.33.90.3closer than threshold, 2.34.44.9
     descriptors, 2.34.41, 5.7.12closest sequence, 2.34.99.3
     distance, 2.34.44.8, 2.34.136.2, 2.34.136.3     value, 2.34.56.1
     diversity, 3.14.6.4cluster, 2.34.154.1
     drawing, 2.23.9.14     center, 2.34.70.9
          quality, 2.23.9.15     centers, 2.13.1
     fingerprints, 2.9     selection, 2.34.70.9
     formula, 2.34.156.10     tree, 2.34.99.5
     fragment counting, 2.34.102.2          size, 2.34.102.1
     functions, 2.27clustering, 2.13, 2.33.63.37, 2.33.63.38, 2.33.90.7
     keys, 2.33.63.21clusters, 2.13, 2.13.1
     match coordinates, 2.34.192.6cnMethodAverage, 2.22.6
     matching, 2.33.35.4, 2.33.82.49, 2.33.82.50, 2.34.133, 2.34.155cnWeight, 2.19.6
     models, 2.34.99.1code, 2.34.44.6
     modification, 2.33.66, 2.33.68, 2.36.37coil, 5.3.4
     name, 2.34.99.6collection, 2.12, 5.3.6
     normalization, 2.33.68color, 2.23.5.33, 2.33.11
          rules, 2.33.68.4     accessibility, 2.33.13
     pattern, 2.26, 2.33.86.1     background, 2.33.13.2
          search, 2.34.56.3          example, 3.2.7
     reaction product generation, 2.33.63.33          accessibility, 3.2.11

          atom contributions, 2.33.12compare, 2.18.12, 2.18.15, 2.33.14
          bfactor, 3.2.9     angles, 2.33.14.2
          charge, 3.2.12     atom, 2.33.14.1
          electrostatic potential, 2.18.5     by rmsd without superposition, 2.33.14.1
          hydrophobicity, 3.2.10     chemical tables, 2.33.35.10
          pharmacophore, 2.33.12     patch only, 2.33.14.3
          potential, 2.36.25     rmsd, 2.33.14.1
          shape depth, 2.33.13     surface, 2.33.14.3
     chemical, 2.33.12, 2.33.86.1     variables, 2.33.14.2
     choice, 2.19.9compareMethod, 2.22.7
     file, 2.37.15comparing two sarrays, 2.34.105
     grob, 2.33.13.4comparison, 2.34.70.10
          by atom selection, 2.33.13.4.3     operations, 2.14.5
               atoms, 2.23.7.1complete view, 2.34.144
          map, 2.33.13.4.4compound accessibilities, 3.14.4.1
          matrix, 2.33.13.4.2     array, 2.25
          potential, 2.33.13.4.5     property prediction, 2.33.51.2
          unique, 2.33.13.4.1compress, 2.33.15
     label, 2.33.13.5     alignment, 2.33.15.1
     map, 2.33.13.6     binary, 2.33.15.4
          by value, 2.33.23.16     conf, 2.33.15.3
     molecule, 2.33.13.1     grob, 2.33.15.2
     names, 2.34.29     in place, 2.33.15.4
     object, 2.33.11.2     objects, 2.33.15
     preference, 2.19.10     stack, 2.33.15.3
     specification, 2.33.11.1compressed table view, 2.33.87.24
     surface by conservation, 2.33.13.3conditional buttons, 5.5.5
     table, 2.34.29.3     string, 2.34.156.7
     volume, 2.33.13.7conf, 2.33.87.61, 2.33.108.41, 2.34.160.6, 5.3.12, 5.8.9
column, 5.3.5     data, 2.34.160.6
     correlation, 2.33.89.3confgen, 3.16
     function, 2.33.7.2configuration, 2.37.14
     names, 2.33.83.1, 2.33.86.2     file, 2.33.108.42
     of grobs, 2.34.109     memory usage, 2.18.7
     selection, 2.34.99conformation comparison, 2.22.7
combinatorial compounds, 2.34.27conformational ensemble, 2.33.7.5.2
     libraries, 2.33.63.33, 2.34.102.4     generator, 2.33.64.1, 3.16
     PDB, 2.36.92     interpolation, 2.33.23.6
     transformations, 3.10.4     stack, 2.33.108.41, 5.3.12, 5.8.9
combining plots, 2.33.63.32          compression, 2.33.15.3
     receptor and ligand stacks, 2.33.4.2          file, 2.37.7
command, 2.34.99.4, 5.3.10     transition, 2.36.38
     line editing, 2.2conformer storage, 2.33.61.5, 2.33.92.2
          help, 2.33.45conformers, 3.16
          options, 2.1connect, 2.33.16
     word list, 3.1.5     chains with alignments, 2.33.55
commands, 2.22.11, 5.1.1     molcart, 2.33.16.1
communication protocols, 2.31consensus, 2.19.7
comp, 2.34.105     coloring, 2.19.12, 2.23.2
comp_matrix, 2.33.87.20, 2.33.88.16, 5.3.11     definitions, 2.23.1

conservation, 2.34.122.5, 2.34.136.7     neighbors, 2.34.101.1
constant, 2.5covalently attached molecule, 2.34.101.1
constants, 2.5cpk, 2.19.35, 5.3.13
contact areas, 2.34.90create a covalent bond, 2.33.63.2
continue, 2.33.17     pharmacophore, 2.36.87
contour lines, 2.34.32creating a local patch object, 2.33.18.2
     surfaces, 2.23.7.5credits, 4.5
contouring density, 2.33.63.14crypt, 2.33.20
contrast, 2.23.5.33crystal axis vectors, 2.34.16
conversion, 5.1.6     symmetry transformation, 3.10.2
     to real array, 2.34.168          transformations, 2.34.176
convert, 2.33.18, 2.33.18.2, 3.13.2crystallographic cell, 2.33.67
     3D to chemical, 2.34.27     occupancy, 2.34.107
     3D/0D to 2D, 2.33.63.9     symmetry intro, 1.4.2.4
     ICM object to PDB, 2.33.94crystallography, 2.34.129
     and reroot, 2.33.18.4csv format, 2.33.82.44
     chemical 3D, 2.36.82csym, 1.4.2.4
               and optmimize geometry, 2.36.83cube, 2.23.14.2
     comp, 2.33.18.1current, 5.3.9
     comparison, 2.33.18.1     map, 5.3.7
     fragments, 2.33.18.2     object, 5.3.8
     mol, 2.33.18.3     working directory, 2.34.108
     object 3D and optmimize geometry, 2.36.85cursor action, 5.9.2.4
          macro, 2.36.13custom alignment color, 2.23.5.1
     pdb, 3.8.2     field, 2.33.87.51
     to 3D, 2.33.87.8     interaction, 2.33.88.37
          ICM object, 2.36.86     menu, 2.32, 2.33.82.3
          iarray, 2.34.166customization, 3.1.2
          icm-object, 2.33.18     environment, 2.32
          integer, 2.34.166     and paste chemicals, 2.23.9.14, 2.23.9.15
convert2Dto3D, 2.36.85cyclic temperature protocol, 2.19.46
convert3Dto3D, 2.36.86cylinder, 2.23.14.2
convertObject, 2.36.13cz32, 4.5
converting a chemical, 2.33.18.3data visualization, 2.33.63.38
          pdb-chemical, 3.13.2database, 5.4.1
     alignment to table, 2.34.160.2     browser, 2.33.61.3
     chemicals, 3.13.2.3     connection, 2.33.16.1
     table columns into matrix, 2.34.90.6     file, 3.5.1
     to, 2.34.123     import, 2.33.63.26
cool, 2.36.40date, 2.33.21, 2.34.156.2
     pictures, 2.23.5.30     array, 2.33.21
cooling schedule, 2.19.46dcMethod, 2.22.8
coordinate frame, 2.19.4, 2.33.23.4dcWeight, 2.19.8
coordinates, 2.23.14.7decomposition, 2.33.63.27, 2.33.90.2, 2.33.90.3
copy, 2.33.19deep learning, 2.33.52
     chemical image, 2.23.9.15defCell, 2.24.1
     file, 2.21.26defSymGroup, 2.18.2
     site, 2.33.87.28default atom colors, 2.33.87.16
correlation matrix, 2.34.163     color of label, 2.19.11
covalent bound count, 2.34.137.3     parameters, 2.22.1

define axis, 3.10.3          rows, 2.33.22.32
defining space box, 2.34.21     term, 2.33.22.33
dehtml, 2.34.126.3     tether, 2.33.22.35
del, 2.33.22.9     tree, 2.33.22.36
delete, 2.33.22     variable, 2.33.22.6
     3D graphics panel, 2.33.103     views, 2.33.22
     alias, 2.33.22.2     backbone, 2.34.137.1
     array element, 2.33.22.6     restraint, 2.33.22.18
          index, 2.33.22.6deleting, 2.33.22.26
          selection, 2.33.22.1     sites by number, 2.33.22.24
     atom, 2.33.22.7delphi, 2.36.25
     bond, 2.33.22.14density correlation, 2.19.8, 3.11.3
     boundary, 2.33.22.15     fitting, 2.22.8
     chemical, 2.33.22.37     in unit cell, 2.33.63.23
          fragment, 2.33.22.37densityCutoff, 2.19.13
          selection, 2.33.22.37dependent columns, 2.33.1.1.1
     class, 2.33.22depth cueing, 2.33.13.7, 5.4.2
     column table, 2.33.22.16depth-cueing, 2.19.17
     conf, 2.33.22.17desolvation, 2.22.25
     directory, 2.33.22.8detecting bad covalent geometry, 2.33.88.12
     disulfide bond, 2.33.22.27     proximity, 2.34.44.9
     drestraint, 2.33.22.18dialog generation, 2.34.11
     element, 2.33.22.31     in html documents, 2.33.44
     file, 2.33.22.9          tables, 2.33.44
     from array, 2.33.22.6     scripting, 2.34.11
     hydrogen, 2.33.22.11dielConst, 2.19.14
     label, 2.33.22.19, 2.33.22.20dielConstExtern, 2.19.15
          chemical, 2.33.22.20dielectric constant, 2.19.14
     link, 2.33.22.21diff, 2.34.105
     map, 2.33.22.22dihedral, 2.36.4
     molcart, 2.33.22.3     angle, 2.33.63.19
     molecule, 2.33.22.13          calculation, 3.3.10
     object, 2.33.22.12directory, 2.33.22.8, 2.33.63.5, 2.34.135
     parray, 2.33.22.36display, 2.33.23
          element, 2.33.22.36     GUI window, 2.33.23.26
     peptide bond, 2.33.22.28     box, 2.33.23.7
     plot, 2.33.22.4     clash, 2.19.5, 2.33.23.8
     salts, 2.33.68.3     contact, 2.33.63.16
     selection, 2.33.22.5     drestraint, 2.33.23.9
     selftether, 2.33.22.34     field, 2.23.5.3
     sequence, 2.33.22.23     from script, 2.33.23.3
     session, 2.33.22.10     gradient, 2.33.23.10
     shell object, 2.33.22.1     grob, 2.33.23.11
     site, 2.33.22.24          label, 2.33.23.12
          alignment, 2.33.22.26     gui, 2.33.23.26
     sstructure, 2.33.22.25     hbond, 2.33.23.13
     stack, 2.33.22.29     label, 2.33.23.15
          object, 2.33.22.30     map, 2.23.5.13, 2.33.23.16
     system, 2.33.22.9     model, 2.33.23.1
     table, 2.33.22.32     new, 2.33.23.2

     offscreen, 2.33.23.3     global weight, 2.19.6
     origin, 2.33.23.4     set, 2.33.87.22
     ribbon, 2.33.23.18     type, 5.4.7
     rotate, 2.33.23.5drop, 2.19.16
     site, 2.33.23.19drug, 2.12
     skin, 2.33.23.20ds3D, 2.36.31
     slide, 2.33.23.21dsCellBox, 2.36.15
     stack, 2.33.23.6dsChem, 2.36.17
     string, 2.33.23.22dsCustom, 2.36.18
     surface, 2.33.23.20dsPocket, 2.36.28
          area, 2.23.5.3dsPropertySkin, 2.36.19
     tethers, 2.33.23.23dsPrositePdb, 2.36.24
     trajectory, 2.33.23.17dsRebel, 2.18.5, 2.23.14.6, 2.36.25
     volume, 2.33.23.24dsSeqPdbOutput, 2.36.26
     window, 2.3, 2.33.23.25dsSkinLabel, 2.36.27
distance, 2.23.5.24, 2.34.41, 5.4.3dsStackConf, 2.36.29
     averaging, 2.22.6dsVarLabels, 2.36.30
     contact-based, 2.34.23, 2.34.23.1dsXyz, 2.36.32
     geometry, 5.4.4dump database, 2.33.108.7
     matrix, 2.34.160.5, 2.36.7dynamic gui, 5.5.5
          between stack conformations, 2.34.90.11ecepp, 5.5.1
     restraint, 5.4.6edit, 2.33.24
          file, 2.37.9     files, 2.23.14.1
          type file, 2.37.8eigen value factorization, 2.34.45
     restraints, 2.33.87.22eigendecomposition of a matrix, 2.34.45
distances, 2.34.102.3eigenvalues, 2.34.45
distribution, 1.3eigenvectors, 2.34.45
     comparison, 2.34.136electro intro, 1.4.2.9
disulfide bond, 5.4.5electroMethod, 2.22.9
diverse subset, 3.14.6.4     density, 2.23.7.5, 2.33.87.36, 2.33.88.21, 2.36.42, 2.36.43
dividing chemical into individual molecules, 2.34.154.4          around selection, 2.19.25
dna to protein sequence translation, 2.34.175.1          map generation, 2.19.1
     translate, 2.34.175.1          maps, 2.23.14.1
dockScan, 3.13.2.5electrostatic boundary matrix, 2.34.90.10
docking, 2.36.89     coloring, 2.23.14.6
     intro, 3.13.2.1     isopotential surfaces, 2.33.63.13
     result viewing, 2.36.28     potential, 2.33.13.4.5
     simple models, 3.14.3     solvation, 3.7.2
     timing, 3.13.1.3     surface, 2.36.25
     with template, 3.13.2.6     troubleshooting, 5.7.13
documents, 5.5.8electrostatics, 2.23.14.6
dollar separated file, 2.33.82.44     intro, 1.4.2.9
dominant color, 2.34.29.2ellipsoid, 2.34.163
donor, 3.6.1elseif, 2.33.25
     plot intro, 1.4.3.2empty model, 2.34.109
dots, 2.33.76endfor, 2.33.26
dotted surface, 2.23.5.56endif, 2.33.27
double click action, 5.9.2.4endmacro, 2.33.28
drestraint, 2.33.88.18, 5.4.6endwhile, 2.33.33
     generate from structure, 2.33.63.7energetics, 3.7

     profile, 2.36.84faq, 1.3
     terms, 2.17     cheminformatics, 3.14.6
ensemble, 2.33.61.1, 2.33.92.1     chemsuper, 3.14.5
     average, 3.7.5     mac gui preferences, 3.14.6.2
entropy of alignment, 2.34.136.7     molcart dump, 3.14.6.3
     atom, 2.33.18.4          query, 3.14.6.1
enumerate, 2.33.29, 2.33.30, 2.33.31, 2.33.32     multiple chem overlay, 3.14.5.1
     charge, 2.33.29     residue table, 3.14.4.1
     chiral, 2.33.30fast Fourier transform, 2.33.63.24
     library, 2.33.32     sequence search, 2.33.35.3
     tautomer, 2.33.31fasta, 2.23.12.15, 5.5.2
enumeration, 2.34.27     format, 2.33.108.1
eps files, 2.21.23feature table, 5.8.6.1
equipotential surface, 2.34.32     in sequences, 2.33.87.26
error SOAP services, 2.34.49ffMethod, 2.22.12
     ignoring, 2.21.25field, 2.33.87.35
error/warning bits cleanup, 2.33.10     name, 2.34.99.2
errorAction, 2.22.10file, 2.33.108.24
     vrestraint vs_var, 2.33.87.82     exists, 2.34.50
evalSidechainFlex, 2.36.90     list, 2.34.59
evol tree intro, 1.4.3.5     length, 2.34.55
evolutionary tree intro, 1.4.3.5     object origin, 2.34.55
exact, 2.33.35.9, 2.33.35.10     permissions, 2.34.55
     match, 2.34.126.1     time modified, 2.34.55
example scripts, 3.14     type, 2.34.55
excel, 2.33.82.44files, 2.37
exit, 2.33.34filling volume, 2.23.5.11
exitSeslogStyle, 2.22.11filter, 2.33.35.10, 2.33.61.3
expanding substructure match, 2.33.87.70     functions, 5.5.4
export, 2.33.108.7filtering table rows, 5.5.4
     animation, 2.33.108.31find, 2.33.35
     pdb, 2.23.14.14     alignment, 2.33.35.1
exporting sdf, 2.33.108.11     and replace a chemical pattern, 2.33.68.1
expression shortcuts, 2.10.1.2               chemical fragment, 2.33.68
     tags, 2.24.9     chemical, 2.33.35.5
     comparison, 2.14.5          pattern, 2.33.68
     arithmetics, 2.14.2          substructure, 2.34.70.2
     assignment, 2.14.1     database, 2.19.2, 2.33.35.2
     comparison, 2.14.5          fast, 2.33.35.3
     logical, 2.14.3     family of commands, 2.33.35
extending to bonded hydrogens, 2.34.137.6     in sarray, 2.34.70.8
               terminal atoms, 2.34.137.6     molcart, 2.33.35.9, 3.5
external process, 2.33.63.1     molecule, 2.33.35.4
extracting from Markush, 2.33.53     motifs, 2.24.9
     icm script arguments, 2.34.59     pattern, 2.33.35.8
     stack from object, 2.33.61.5     pdb, 2.33.35.6
ez25, 3.7     pharmacophore, 2.33.35.11
factor, 5.8.13     prosite, 2.33.35.7
false negatives, 2.34.136.4     scaffold, 2.34.179
family, 2.33.87.38.1     table, 2.33.35.10

findFuncZero, 2.36.35geometry optimization, 2.33.64.1
findSymNeighbors, 2.36.16     started, 1.7
find_related_sequences, 2.36.33getting data from outside, 2.31
finding long covalent bonds, 2.34.137.1     started, 1.7
fingerprint, 2.34.41global, 2.33.41
fingerprints, 2.9glossary, 5
     to density, 2.22.8go, 2.34.44.6
fix, 2.33.36goto, 2.33.42
fixed branches, 2.34.137.2     term, 2.19.20, 2.33.87.73
flattening 3D molecule, 2.36.17gpWeights, 2.19.20
flexible superimpose, 2.36.50graph matching, 2.34.133
flow control, 2.15graphical box, 2.33.23.7
fog, 2.19.17, 2.33.13.7, 2.33.23.24, 5.4.2     row selection, 2.34.70.5
     color, 2.19.17     selection, 2.34.137.5
fogStart, 2.19.17graphics, 2.19.9, 2.33.87.4, 2.34.188, 3.2, 5.3.3
fold search, 5.8.4     card, 2.23.5.52
foldbank.db, 2.37.3     controls, 2.3, 2.37.15, 5.4.2
folding procedure, 3.14.1     exists, 2.34.50
font, 2.33.56.1     intro, 1.4.1, 1.4.1.4
     size, 2.33.87.38.1, 2.37.14     learning, 3.2.1
     sizes, 3.14.6.2     attributes, 2.19.4
     specification, 2.33.87.38.1     fogStart, 2.19.17
for, 2.33.37     view vector, 2.33.87.80
fork, 2.33.38, 2.34.70.1graphviz, 2.34.160.7
formal charge, 2.23.5.20, 2.33.87.12, 5.3.2greedy matching, 2.10.1.4
formatdb, 2.33.108.25grid energy, 2.33.88.21
fprintf, 2.33.39     potentials, 2.33.63.25
fractional coordinates, 2.34.192.4grob, 5.5.3
     to abs coordinates, 2.34.16     coloring, 2.33.13
fragmented molecule, 2.33.18.2     files, 2.37.10
frame, 2.33.92, 2.33.108.31     inside-out flip, 2.33.87.42
fullscreen, 2.33.87.85     normal directions, 2.33.87.42
function, 2.33.40, 2.33.62     vertex, 2.23.5.21
     columns, 2.33.1.1.1     translate, 2.33.101
functions, 5.1.1group, 2.33.43
     selecting in objects, 2.8.10     by column, 2.33.43.4
gamess, 5.5.6     column, 2.33.43.4
     expansion, 2.34.146.4     rename of table columns, 2.33.83.1
gapExtension, 2.19.18     replacement, 2.33.66
gapFunction, 2.24.3     select of table columns, 2.33.86.2
gapOpen, 2.19.19     sequence, 2.33.43.1
gaussian averaging, 2.34.146.2          unique, 2.33.43.2
gcMethod, 2.22.13     table, 2.33.43.3
genbank, 2.23.12.15grouping table by a column, 2.33.87.24
generalized arrays, 5.1.6gui, 2.33.44, 5.9.2.4
generate intermediate conformers, 2.36.38     exists, 2.34.50
generating movie images, 3.9.2.1     functions, 5.5.5
genomics, 1.4.3.1     panels, 2.33.103
     clustering, 2.33.43.2     programming, 2.32, 2.33.44, 2.33.87.24
     intro, 1.4.3.1gvim text editor, 5.8.2

hash, 2.12, 5.3.6html5, 2.11
     table, 5.3.6hue, 2.34.90.4
haze, 2.19.17hydration, 2.23.14.2, 2.34.7
hb, 2.19.21     parameters, 2.37.13
hbCutoff, 2.19.21hydrogen bond, 2.23.5.25, 2.23.5.26, 2.33.63.17, 5.5.7
hbond, 2.23.5.25, 2.23.5.26, 2.33.22.6, 5.5.7     bonding parameters, 2.37.12
     color, 2.33.23.14          cutoff, 2.19.21
     display, 2.23.5.27, 2.23.5.28     bonds, 2.34.102.3
     energy, 2.33.23.14     display, 2.23.5.32
     list, 2.34.160.10     placement, 2.33.87.25
     show, 2.33.88.23hydrophobicity profile, 3.3.12
hbondMinStrength, 2.23.5.25iSee, 5.8.14
     faq, 3.3.4i_2out, 2.18.4
     how to, 3.3.4i_out, 2.18.3
header, 2.33.1.1iarray, 2.33.22.6, 2.34.56.1, 2.34.66.2, 2.34.70.8, 5.6.1
helical axis, 2.36.36     making, 2.34.66.1
     cylinders, 2.23.5.42icb files, 5.8.14
helicity, 3.7.6     GUI, 2.33.87.40
     content calculation, 3.7.6     algorithms, 4.3
help, 2.33.45, 2.33.45.1, 2.33.45.2     application refs, 4.4
     browser, 2.33.45.1          literature, 4.3
     commands, 2.33.45.3     archive, 2.33.82.2
     functions, 2.33.45.4     arguments, 2.34.59
     getting, 3.1.1     binary, 2.34.108
     word, 2.33.45.2     branching, 2.15.2
     getting, 3.1.1     commands, 2.33
heterogenous environment, 2.23.14.2     controls, 2.15
hidden blocks, 5.1.1.1     flags, 2.1
     display, 2.33.23.3     functions, 2.34
     hydrogens, 2.23.5.32     graphics, 3.2
     stack in object, 2.33.92.2     history, 1.2
hierarchical, 2.13     jumps, 2.15.3
highEnergyAction, 2.22.14     learning, 3.1.4
his-tags, 2.34.180     loops, 2.15.1
histogram, 2.33.63.32     macros, 2.36
     2D, 2.34.90     main refs, 4.2
history, 2.33.46, 2.33.108.40     menus, 2.23.10.1
     delete, 2.33.22.10     method literature, 4.4
     of ICM, 1.2     molecules, 2.16
homodel, 2.36.41     object file, 2.37.18
homology modeling, 1.4.2.2, 2.33.7.5, 2.33.87.68, 2.33.87.69, 2.35.1, 3.14.4     preferences, 2.22.1
          faq, 3.14.4     session, 2.22.11
          intro, 1.4.2.2     shell, 3.1
     output, 2.33.7.5.3          functions, 2.35
     steps, 2.33.7.5.1     support, 1.3
     to export a molcart table, 3.14.6.3     table, 2.23
html, 2.11, 2.33.44, 2.34.99.4, 5.5.8     ali, 2.37.31
     document order, 2.33.87.40     all, 2.37.32
     tag removal, 2.34.126.3     bbt, 2.37.5
html-formatted text, 5.5.8     bst, 2.37.6

     clr, 2.37.15imposing tether, 2.33.87.68, 2.33.87.69
     cmp, 2.37.33     place, 2.14.4
     cn, 2.37.9          ops, 2.14.4
     cnf, 2.37.7incidence, 2.34.90.13
     cnt, 2.37.8increasing the number of shell variables, 2.37.14
     cod, 2.37.4increment charge, 2.33.87.10
     col, 2.37.24index expressions, 2.6
     gro, 2.37.10     in array, 2.34.70.4
     gui, 2.32     substring, 2.34.70.3
     hbt, 2.37.12     table, 2.33.108.24
     hdt, 2.37.13          entry, 2.34.135.1
     htm, 2.37.11          sdf-file path, 2.34.108
     iar, 2.37.35indices of labeled table rows, 2.34.70.6
     lps, 2.33.7.5.2          selected table rows, 2.34.70.5
     map, 2.37.16infinity, 2.34.168
     mat, 2.37.37info, 2.33.48
     ob, 2.37.18     molcart, 2.33.48.1
     pdb, 2.37.28inner join, 2.33.50
     prf, 2.37.34insert rows, 2.33.1.4
     rar, 2.37.38integer, 5.6.2
     res, 2.37.20     array, 2.34.66, 5.6.1
     rs, 2.37.23     output, 2.18.4
     rst, 2.37.22     shell variables, 2.18
     sar, 2.37.36intensity, 2.34.90.4
     se, 2.37.30interaction cutoff, 2.20.27
     seq, 2.37.29     lists, 2.20.27, 2.23.14.3
     tab, 2.37.25interactive docking, 1.4.2.8
     tot, 2.37.26interatomic distance, 2.19.10, 2.33.63.16, 2.34.151
     trj, 2.37.17     potential, 2.33.87.51, 2.33.88.37
     var, 2.37.21interface comparison, 2.33.14.3
     vwt, 2.37.27     residues, 3.3.5
icmCavityFinder, 2.36.14     torsions, 3.3.7
icmMacroShape, 2.36.88     view, 2.36.28
icmPmfProfile, 2.36.23intermolecular bond, 2.33.70.3
icmPocketFinder, 2.36.89internal coordinate file, 2.37.21
icmscript, 2.33.82.4     coordinates, 2.8.9
     arguments, 2.34.59     positional restraints, 5.9.4
if, 2.33.47interplanar angle, 2.36.4
ignoring swiss secondary structure, 2.24.10interpolate, 2.34.29.1
illegal smiles, 2.34.70.2interpolation, 2.34.29.1
image, 3.2.6interruptAction, 2.22.15
     annotation, 3.2.5inverting array order, 2.34.66.2, 2.34.122.2
     center, 3.2.8italic, 2.33.87.38.1
     format, 5.9.3iterative overlay, 2.33.95
     high quality, 3.2.2     superposition, 2.23.14, 2.33.96
     parray, 5.7.3.3javascript, 2.11
     resolution, 3.2.2join, 2.33.50
     rotation, 3.2.3     tables, 2.33.50
implicit continuous solvation, 2.37.13keep, 2.33.49
     solvation, 2.33.87.72kernel models quality, 2.34.136.4

kmz, 5.5.3     fit, 3.13
l_antiAlias, 2.20.1     setting, 3.13.2
l_autoLink, 2.20.2     view, 2.23.5.31
l_bpmc, 2.20.3light, 2.23.5.34
l_breakRibbon, 2.20.4lightness, 2.34.90.4
l_bufferedOutput, 2.20.5limits, 2.37.14
l_bug, 2.20.6line thickness, 2.23.12.5
l_caseSensitivity, 2.20.7          in 2D chemicals, 2.23.9.14
l_commands, 2.20.8lineWidth, 2.19.22
l_confirm, 2.20.9linear chemical notation, 2.26
l_easyRotate, 2.20.10     regression, 2.34.84
l_info, 2.20.11     group, 2.33.53
l_minRedraw, 2.20.12     internal variables of molecular object, 2.33.54
l_neutralAcids, 2.20.13     ms2ali, 2.33.55
l_out, 2.20.14     sequences to 3D objects, 2.33.55
l_print, 2.20.15     to alignment, 2.33.55
l_racemicMC, 2.20.16     variable, 2.33.54
l_readMolArom, 2.20.17     variables, 2.33.54
l_showAccessibility, 2.20.18linked alignment, 2.34.99
l_showMC, 2.20.19     sequence, 2.34.99
l_showMinSteps, 2.20.20linux shell, 2.33.97, 5.10.2
l_showResCodeInSelection, 2.20.21list, 2.33.56
l_showSites, 2.20.23     binary, 2.33.57
l_showSpecialChar, 2.20.22     database, 2.33.58
l_showSstructure, 2.20.24     directory, 2.33.59
l_showTerms, 2.20.26     font, 2.33.56.1
l_showWater, 2.20.25     html documents, 2.34.99
l_updateLists, 2.20.27     molcart, 2.33.60
l_warn, 2.20.28          database, 2.33.60
l_wrapLine, 2.20.29     of files, 2.34.135
l_writeStartObjMC, 2.20.30     updates, 2.33.64
l_xrUseHydrogen, 2.20.31listUpdateThreshold, 2.19.23
label, 2.33.23.22, 5.6.3literature, 4.1
     fonts, 2.37.15load, 2.33.61
large text, 2.33.82.40     conf, 2.33.61.1
latent, 2.34.102.6     frame, 2.33.61.2
learn, 2.33.51, 2.33.52, 2.34.109     molcart, 2.33.61.3
     ann, 2.33.52     object, 2.33.61.6
     atom, 2.33.51.1     solution, 2.33.61.4
     chemical, 2.33.51.2     stack object, 2.33.61.5
left join, 2.33.50loadEDS, 2.36.42
     triangle of a matrix, 2.34.90.3loadEDSweb, 2.36.43
library to replacement groups, 2.33.63.27, 2.33.90.2, 2.33.90.3local, 3.5.1
ligand based screening, 3.15logarithm, 2.34.85
     binding, 2.36.28logical, 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, 2.36.37long axes, 2.34.163

     interrupt, 2.19.47     reaction, 2.33.63.33
     library, 2.33.7.5.2     sequence, 2.33.63.35, 2.33.63.36
     modeling, 1.4.2.3          alignment, 2.33.63.34
          intro, 1.4.2.3          from alignment, 2.33.63.34
     search, 2.33.7.5.2          random, 2.33.63.36
     resolution shape, 2.36.88     torsion, 2.33.63.19
lower case, 2.34.167     tree, 2.33.63.37
ma29, 3.11          object, 2.33.63.38
macro, 2.33.62, 5.6.5     unique, 2.33.63.39
macro_def, 5.6.5makeAxisArrow, 2.36.36
main ICM references, 4.2makeIndexChemDb, 2.36.44
     concepts, 3.10.1makeIndexSwiss, 2.36.45
make, 2.33.63makePdbFromStereo, 2.36.46
     3d label, 2.33.63.15makePharma, 2.36.87
     angle, 2.33.63.18makeSimpleDockObj, 2.36.47
     background, 2.33.63.1makeSimpleModel, 2.36.48
     blast index, 2.33.108.25making predictive models, 2.33.51
     bond, 2.33.63.2manual style, 1.5
          chain, 2.33.63.3map, 2.19.25, 2.23.5.13, 2.23.6.1, 5.6.6
          multi, 2.33.63.3     aa property to sequence, 2.34.122.1
     boundary, 2.33.63.4     averaging, 2.34.146.5
     directory, 2.33.63.5     calculation, 2.33.63.24
     distance, 2.33.63.16     conversion, 2.33.63.31
     disulfide bond, 2.33.63.6     file, 2.37.16
     drestraint, 2.33.63.7     fitting, 2.22.8
     factor, 2.33.63.8     format, 5.6.6
     flat, 2.33.63.9     mean value, 2.34.94
          chem_array, 2.33.63.9     min value, 2.34.95
     grob, 2.36.36     name, 2.34.86
          from image, 2.33.63.11     operations, 5.6.6
               matrix, 2.33.63.12     transformations, 2.34.146.5
          image, 2.33.63.11     trimming, 2.34.22
          map, 2.33.63.10     value sigma, 2.34.133
          matrix, 2.33.63.12          on atoms, 2.33.87.36
          potential, 2.33.63.13     contouring, 2.33.63.14
          skin, 2.33.63.14mapAtomMargin, 2.19.25
     hbond, 2.33.63.17mapSigmaLevel, 2.19.24
     image, 2.33.63.20mapping chemical equivalences, 2.34.70
     index fasta, 2.33.82.24, 2.33.108.24     properties to sequence, 2.34.122.4
     key, 2.33.63.21     and factors, 3.11
     map, 2.33.63.22margin, 2.23.6.1
          cell, 2.33.63.23mass-spectrometry functions, 2.33.30, 2.33.31, 2.33.32
          factor, 2.33.63.24matching chemicals, 2.34.70.2
          potential, 2.33.63.25     hydrogens, 2.33.87.70
          xray, 2.33.63.31matrix, 5.6.7
     molcart, 2.33.63.26     derivatives, 2.34.80
     molsar, 2.33.63.27     new, 2.34.90.1
     pca, 2.33.63.29     plot, 2.34.32
     peptide bond, 2.33.63.30     map value, 2.34.91
     plot, 2.33.63.32maxColorPotential, 2.18.5, 2.36.25

     movie, 3.9.2     type, 2.34.182
mcBell, 2.19.26     show atom types, 2.33.88.11
mcJump, 2.19.27mnSolutions, 2.18.9
mcShake, 2.19.28mncalls, 2.18.10
mcStep, 2.19.29mncallsMC, 2.18.11
mean force, 2.33.87.51, 2.33.88.37mnconf, 2.18.12
median value, 2.34.93mnhighEnergy, 2.18.13
membrane, 2.23.14.2mnreject, 2.18.14
memorizing positions, 3.2.4mnvisits, 2.18.15
menu, 2.33.65model reliability, 2.36.23
     script, 3.1.3modify, 2.33.66
merge PDB, 2.36.92     and reroot, 2.33.18.4
     arrays to table, 2.33.43.3     chem, 2.33.68
     continuation lines, 2.33.82.39          charge, 2.33.68.2
     objects, 2.33.70.2          delete salt, 2.33.68.3
     parts of molecule, 2.33.70.3          normalize, 2.33.68.4
     pdb, 3.4.4     chemical column, 2.33.68.3
     sarray into string, 2.34.158          find replace, 2.33.68.1
     stacks, 3.7.7     molcart, 2.33.68.5
     tables, 2.33.4.3, 2.33.50     rotate, 2.33.67
merge2, 3.8.7modifyGroupSmiles, 2.36.37
mergePdb, 2.36.92modules, 1.4.4
     several chemical, 2.34.158.1mol, 2.33.82.49, 2.33.82.50, 2.33.108.11, 2.33.108.24, 5.6.11
merging into one molecule, 2.33.70.3     file, 2.34.156.3
mesh, 2.34.109, 2.34.189     to icm, 2.33.18.3
     point radius, 2.23.5.21     translation, 3.2.4
     score, 3.13.3.3mol-file to chem-table element, 2.34.109
mfMethod, 2.22.16mol-format, 2.23.14.7
mfWeight, 2.19.30mol2, 5.6.12
mimel, 5.6.8molcart, 2.33.16.1, 3.5
mimelDepth, 2.19.31     connection options, 3.5.2
mimelMolDensity, 2.19.32molecular, 2.34.58, 5.7.3.1
minNumGrad, 2.33.64     arrays, 5.7.3
minTetherWindow, 2.18.8     manipulations, 3.8
minimization exit criteria, 2.33.64     modifications, 3.8.5
minimize, 2.18.10, 2.33.64     object, 5.7.1
     cartesian, 2.33.64.1     objects, 2.16
     loop, 2.33.64.2     surface, 2.33.88.9, 5.8.7
     stack, 2.33.64.3     views, 1.4.1.1
     tether, 2.18.8, 2.33.64.4     volume, 2.34.114
     drop, 2.19.16molecule, 2.7
minimizeMethod, 2.22.17     create, 3.8.4
missing bonds, 2.33.70.3     properties, 2.33.87.34
     loop, 2.23.5.7, 2.23.5.8     rotation, 3.2.3
     residues, 2.34.54.1     translation, 3.2.3, 3.2.4
     triangles, 2.34.189     create, 1.7.2
mkUniqPdbSequences, 2.36.49     intro, 1.7.2, 2.7
mm26, 3.8     sort/reorder, 2.33.89.5
mmcif, 5.6.10     selecting, 2.8.6
mmff, 5.6.9molt, 3.5.1

montecarlo, 2.18.11, 2.18.13, 2.18.14, 2.18.15, 2.18.19, 2.22.7, 2.33.69mute, 5.6.15
     local, 2.18.16mysql, 2.33.16.1
     trajectory, 2.33.23.17nLocalDeformVar, 2.18.16
moprphing, 2.36.38nProc, 2.18.18
more, 5.6.13nSsearchStep, 2.18.17
morph, 2.33.23.6name, 2.34.79
     to tether target, 2.36.38     atom fields, 2.33.87.34
morph2tz, 2.36.38naming compounds, 2.33.87.47
morphing, 2.33.23.6, 2.33.87.68, 2.33.87.69, 2.33.92.3nearest sequence, 2.34.95
mouse controls, 2.3neato, 2.34.160.7
     file, 2.33.108.31neighbor joining, 2.33.63.38
move, 2.33.70neighbors, 2.34.151
     alignment sequence, 2.33.70.7nested script, 5.8.2
     atoms, 2.33.87.3neural network, 2.33.52
     bonding, 2.33.70.3     real array, 2.34.122
     column, 2.33.70.5nice, 2.36.39
     element, 2.33.70.4     image, 3.2.2
     file, 2.21.28, 2.33.83.3non-redundant, 3.4.3
     fragments together, 2.33.70.3normal distribution, 2.34.121
     molecule, 2.33.70.1normalize chemicals, 2.33.68.4
     ms_molecule, 2.33.70.1     defined, 2.34.168
     multiple molecules, 2.33.70.2nota, 1.5
     object, 2.33.70.2notational conventions, 1.5
     plane, 2.33.70.6nproc, 2.33.38
     sequence, 2.33.70.7nucleotides, 2.21.24
     table column, 2.33.70.5number, 2.18.18
movie, 2.33.92.3     of dots, 2.23.5.55
     images by frame, 3.9.2.2          elements, 2.34.102
     molecular simulation, 3.9.2          hydrogen bonds, 2.33.88.23
     rotate view, 3.9.1          molecules in objects, 2.34.137.4
     zooming, 3.9.1          occurrences, 2.34.102
moving selection to another object, 2.34.137.8          residues in molecules, 2.34.137.4
mpeg, 2.33.108.31          van der Waals contacts, 2.33.88.13
ms_, 2.8.6     transfer from sequence, 2.33.3.2
multi center drestraint, 2.22.6nvis, 2.34.66.6
multi-part molecule, 2.33.18.2object, 2.33.13.1, 5.7.1
multicore, 2.34.70.1     in table, 2.34.109
multiline input, 2.33.82.5     parray, 5.7.3.1
multiple NMR models, 2.23.14.5     properties, 2.33.87.34
     alignment, 2.33.3.3     stack, 5.8.9
          to pairwise similarities, 2.36.7     to chemarray, 2.34.27
     conformation storage, 5.8.9     user fields, 2.34.54.1
     conformations, 2.33.61.1, 2.33.92.1     assign comment, 2.33.87.17
     mol as text, 2.34.156.3     source file, 2.34.55
     object file, 2.33.82.2     translate, 2.33.101
     sequence alignment intro, 1.4.3.4     merge, 3.8.6
     smiles file format, 2.33.82.46     selecting, 2.8.5
multiprocessor, 2.33.38obsolete, 2.19.54
mutate residue, 2.33.66occlusion shading, 2.33.13
mutating residue, 3.8.5octanol transfer, 2.34.114

     format, 5.5.3pattern, 5.7.4
oligonucleotide melting, 2.34.164     search, 2.33.35.2
on-line help, 2.33.45.1, 2.33.45.2pause, 2.33.71
     third, 2.34.37pdb, 5.6.10, 5.7.6
only, 5.7.2     file creation time, 2.34.38
ontology, 2.34.44.6     files, 2.37.28
openGL window, 2.33.103     format, 2.33.82.48
operating system, 2.33.22.9, 2.33.97, 2.34.188, 5.10.2     merge, 3.4.4
optimal chemical superposition, 3.14.5.1     sequence generation, 3.4.3
optimization, 2.33.69pdbDirStyle, 2.22.18
     Hbond, 2.36.91peptide, 5.7.7
     hydrogen bond, 2.36.91     docking, 3.12.5
optimizeHbonds, 2.36.91     folding, 1.4.2.1
or, 2.14.3          intro, 1.4.2.1
order, 2.33.3.1, 2.33.70.7personal gui controls, 3.1.2
original sequence names, 2.23.12.15     setup, 3.1.2
os_, 2.8.5ph30, 3.12
other variables, 2.24ph4, 5.7.8
out-of density atoms, 2.33.88.21     object faq, 3.6.1
output, 2.18.3pharmacophore, 2.33.12, 3.5, 5.7.8
outside penalty, 2.23.6.1     faq, 3.6
overlap, 2.34.70.10     grid type definitions, 2.33.87.73
     by atom pairs, 2.33.95     object, 3.6.1
          chemical substructure, 2.36.22     objects, 3.6
overview, 1.4pharmacophores, 3.6
pK shift, 3.7.3     psi plot, 2.36.58
pKa, 2.33.22.20, 2.33.87.11, 2.33.87.12pipe, 2.33.82.43
     model, 2.33.87.12placeLigand, 2.36.50
packing density, 3.3.8planar angle, 2.33.63.18
pair-distances, 2.33.22.6plot, 2.33.72
pairdistance parray, 2.23.5.24     3D 2Dfunction, 3.12.3
pairwise interactions, 2.33.87.51          shape, 3.12.4
panel layout, 2.23.8.6     area, 2.33.73
paragraphs, 2.33.108.24     grid line width, 2.23.12.5
parallel, 2.18.18     histogram, 3.12.2
     computing, 2.34.70.1     how to, 3.12
     processing, 2.33.38     simple, 3.12.1
parallelization, 2.34.70.1plot2DSeq, 2.36.51
parameter list file, 3.14.6.2plotBestEnergies, 2.36.54
parray, 2.33.22.6, 5.7.3plotCluster, 2.36.56
parrayTo3D, 2.36.83plotFlexibility, 2.36.55
parrayToMol, 2.36.82plotMatrix, 2.36.57
parse SOAP message, 2.34.186plotRama, 2.36.58
parsing, 2.34.89plotRose, 2.36.59
     web pages, 2.33.82.47plotSeqDotMatrix, 2.36.52
partial least squares, 2.33.51plotSeqDotMatrix2, 2.36.53
     slide display, 2.33.23.21plotSeqProperty, 2.36.60
     sum, 2.34.77     3d, 1.4.3.7
passing arguments, 5.8.2plotting van der Waals, 3.7.1
     by reference, 2.33.62          faq, 3.7.1

     column contributions, 2.34.160.8, 2.34.160.9project setup, 3.13.2.2
     model, 2.34.160.8, 2.34.160.9projected alignment, 2.34.99.3
     weights, 2.34.160.8, 2.34.160.9projecting surface charge, 3.7.2
pmf, 2.22.16property, 2.33.87.52, 2.33.87.53, 2.33.87.54
     residue profile, 2.36.23     grids, 2.19.20
pmf-file, 2.37.19     map, 2.33.87.73
pmffile, 2.37.19     superposition, 2.33.87.73
png, 2.33.108.36, 5.7.5prosite, 5.7.10
pocket, 2.36.28, 2.36.89, 3.13.1.1     pattern, 5.7.4
point coordinates, 2.34.192.1protein docking, 2.34.192.3
     size, 2.23.5.21          intro, 1.4.2.5
pointer array, 5.7.3     engineering, 2.24.9
polar hydrogens, 2.23.5.32     grid docking, 3.14.2
     surface area, 2.34.114     health, 2.36.58
polarization charge, 3.7.2, 5.7.13     topology, 2.23.5.42
positional constraint, 2.23.14.12protonation states table, 2.34.160.11
postscript, 2.21.23psa, 5.7.12
potential surface, 2.23.14.6purple box, 2.34.21
          coloring, 5.7.13quadratic equation, 2.34.147
pov-ray, 2.33.108.38quantum mechanics, 2.33.82.21, 2.33.108.17
pow, 2.34.37qubic equation, 2.34.148
precision, 2.34.136.4query, 3.14.6.1
predict, 2.33.74     molcart, 2.33.79
predictSeq, 2.36.61question mark operator, 2.34.156.7
prediction model, 2.34.84quit, 2.33.80
     quality, 2.34.136     property transfer via alignment, 2.34.122.3
     score, 2.34.136r_2out, 2.19.34
predictive models, 2.33.51.2r_out, 2.19.33
preference, 2.22radii.electrostatic, 2.34.120
     system, 2.22.1     van der Waals, 2.34.120
preferences, 3.1.2.3rainbow, 2.34.29.1
prepSwiss, 2.36.62ramachandran faq, 3.3.3
previous atom, 2.34.101.1     how to, 3.3.3
principal axes, 2.34.163random array, 2.34.121
     component analysis, 3.3.9     order, 2.34.139
     inertia moments, 2.34.88     sequence, 2.33.63.36
print, 2.33.75randomSeed, 2.18.19
     bar, 2.33.76randomize, 2.18.19, 2.33.81
     image, 2.33.78     angles, 2.33.81.1
     to string, 2.33.91     coordinates, 2.33.81
printMatrix, 2.36.63     torsions, 2.33.81
printPostScript, 2.36.64rarray, 2.33.22.6, 2.34.56.1, 2.34.70.8, 2.34.122.2, 5.7.11
printTorsions, 2.36.65     properties, 2.34.122.4
printf, 2.33.77rdBlastOutput, 2.36.68
problem, 3.14.6.2rdSeqTab, 2.36.69
processors, 2.18.18reaction, 2.33.63.33
profile, 5.7.9     group file, 2.33.53
program overview, 1.4read, 2.33.82, 2.33.82.56, 2.33.82.57
progress bar, 2.33.76     FILTER, 2.33.82.6
progression, 2.33.76     alignment, 2.33.82.12

     binary, 2.33.82.2          csv, 2.33.82.44
     blob, 2.33.82.38          html, 2.33.82.47
     color, 2.33.82.13          mmcif, 2.33.82.48
     column, 2.33.82.51          mol, 2.33.82.50
     comp_matrix, 2.33.82.14          mol2, 2.33.82.49
     conf, 2.33.82.15     text, 2.33.82.40
     csd, 2.33.82.16     trajectory, 2.33.82.31
     csv, 2.33.82.44          and save a fragment, 2.33.82.31.1
     database, 2.33.82.17          write, 2.33.82.31.1
     drestraint, 2.33.82.18     unix, 2.33.82.10
          type, 2.33.82.19          cat, 2.33.82.11
     entries from database, 2.33.82.8     variable, 2.33.82.52
     factor, 2.33.82.20     view, 2.33.82.53
     file by chunk, 2.33.82.40     vrestraint, 2.33.82.54
     from file, 2.33.82.1          type, 2.33.82.55
          string, 2.33.82.5     with filter, 2.33.82.6
     fromstring, 2.33.82.5     xml, 2.33.82.56
     ftp http, 2.33.82.9readMolNames, 2.24.11
     gamess, 2.33.82.21readcomp_matrix, 2.33.82.14
     grob, 2.33.82.22reading external tool output, 2.33.63.1
     gui, 2.33.82.3     from standard input, 2.33.82.43
     html, 2.33.82.4     pdb from ftp, 2.21.18
          file, 2.33.82.4               web, 2.21.19
     iarray, 2.33.82.23     restraint, 2.33.82.54
     index, 2.33.82.24real, 5.7.14
          table, 2.33.82.8     array, 5.7.11
     json, 2.33.82.57     shell variables, 2.19
     library, 2.33.82.25     space refinement, 2.33.63.31
          mmff, 2.33.82.26reals, 2.19
     librarymmff, 2.33.82.26rebel, 2.18.5, 2.23.14.6, 5.7.13
     map, 2.33.82.27rebuild molcart index, 2.33.7.10
     matrix, 2.33.82.28recalculate dependent values, 2.33.7.2
     menu file, 2.33.82.3     values, 2.33.1.1.1
     mol, 2.20.13, 2.33.82.8, 2.33.82.29receptor, 3.13.1.1
     mol2, 2.33.82.8, 2.33.82.30     preparation, 3.13.1.1
     object, 2.33.82.32redefine hydrogen coordinates, 2.33.87.25
          parray, 2.33.82.32.1references, 4
     pdb, 2.23.14.4, 2.23.14.5, 2.33.82.2, 2.33.82.33refineModel, 2.36.66
          sequence, 2.33.82.34reflections, 2.23.5.33
     profile, 2.33.82.35refresh view, 2.33.23.2
     prosite, 2.33.82.36refs, 4.1
     rarray, 2.33.82.37regexp, 2.10, 2.34.89
     sarray, 2.33.82.39, 2.33.82.40     back references, 2.10.1.3
     sequence, 2.33.82.8, 2.33.82.41     syntax, 2.10.1
          database, 2.33.82.41.1regression, 2.33.51
     smiles, 2.33.82.46regul, 2.36.67
     stack, 2.33.82.42regular expression, 2.10, 2.34.70.4, 2.34.89
     string, 2.33.82.43          filter, 2.33.82.1
     table, 2.33.82.44     expression, 2.34.126.3
          chunk, 2.33.82.45regularization, 2.18.8, 2.33.64.4, 5.7.15

rejectAction, 2.22.19     selection, 2.20.21
relational database, 2.34.149          as string, 2.34.156.8
relative accessible area of atoms, 2.22.2          function, 2.34.127
release notes, 1.1     table, 3.14.4.1
remarkObj, 2.36.70     tethering, 2.33.87.68, 2.33.87.69
remove columns, 2.33.22.16     user field, 2.34.54.1
     expression tags, 2.34.180residue_selections, 2.8.11
     file, 2.33.22.9     selecting, 2.8.7
     trailing blanks, 2.34.178resizing, 2.34.68
removing html tags, 2.33.82.47resorting nodes edges, 2.34.160.7
     outliers, 2.34.178restore, 3.14.6.2
rename, 2.33.3.1, 2.33.83     defaults, 2.33.83.4
     chemicals, 2.33.87.47     preference, 2.33.83.4
     column table, 2.33.83.1restraining molecules to shapes, 2.23.14.12
     file, 2.33.83.3restraints, 2.17, 2.33.87.68, 2.33.87.69
     molcart, 2.33.83.2     torsion, 2.33.87.81
     system, 2.33.83.3return, 2.33.84
renaming, 2.23.12.15reverse complement, 2.34.138.1
reorder, 2.33.70.7     lighting, 2.33.87.42
     alignment sequences, 2.33.108.1     normals, 2.33.87.42
     array, 2.34.139reversing order, 2.34.66.2
     columns by function, 2.33.89.3rgb, 2.34.90.4, 5.7.17
     objects, 2.33.89.4     matrix, 2.34.29
replace matching array element, 2.34.126.1ribbon, 5.7.18
     without interpretation, 2.34.126.2     bullets, 2.23.5.7
replacing scaffold in a library, 2.33.68.1     diagram, 2.23.5.42, 2.23.5.43
reproducible randomness, 2.18.19ribbonColorStyle, 2.22.21
reroot, 2.33.18.4ribbonStyle, 2.22.22
     selections, 3.3.6right join, 2.33.50
resLabelShift, 2.19.35rigid chemical superposition, 2.33.95
resLabelStyle, 2.22.20ring, 2.34.130
reserved names, 2.24     center coordinates, 2.34.192.2
residue, 2.33.13.1, 5.7.16     sampling, 3.16
     accumulators, 2.34.63     templates, 2.33.87.8
     alignment, 2.33.87.68, 2.33.87.69rm, 2.33.22.9
     conservation, 2.34.122.5rocking, 2.33.23.5
     contact area matrix, 2.34.90.8root mean square deviation, 2.34.136.4
          areas, 2.34.7.1roots, 2.34.147, 2.34.148
     field, 2.33.87.34rotate, 2.33.85
     gap, 2.23.5.7, 2.23.5.8     grob, 2.33.85.2
     label, 2.19.35, 2.33.3.2     object, 2.33.85.1
     library file, 2.37.20     view, 2.33.85.3
     name, 2.34.79rotation, 2.33.23.5
          translation, 2.23.14.14     angle, 2.34.17
     number, 2.34.66.5rounding, 2.34.122
          table, 2.34.160.3     a real, 2.34.156
     property averaging, 2.34.146.3     output, 2.33.88.45
          calculation, 2.34.63rsWeight, 2.19.36
     proximity, 2.34.90.8rs_, 2.8.7
     ranges, 2.8.11ruler, 2.19.10

running a docking job, 3.13.2.5scaffolds, 2.33.53
     dock job, 3.13.2.4scoring, 3.13.1.4
     script from html, 5.8.2screen X, 2.34.190
s-s bond, 5.4.5     coordinates, 2.34.190
s_alignment_rainbow, 2.21.1script, 2.34.99.4, 5.8.2
s_blastdbDir, 2.21.2     file name, 2.34.55
s_editor, 2.21.3     inside ICM, 5.8.2
s_entryDelimiter, 2.21.4     name, 5.8.2
s_errorFormat, 2.21.5     image generation, 2.33.23.3
s_fieldDelimiter, 2.21.6scripting molecular movements, 3.2.4
s_helpEngine, 2.21.7sdf, 2.23.14.7, 2.33.108.24, 5.6.11
s_icmPrompt, 2.21.10     file, 2.33.82.49, 2.33.82.50, 2.33.87.47, 2.33.108.11, 2.34.156.3, 5.7.3
s_icmhome, 2.21.8, 3.1.2.1     to chem-table, 2.34.109
s_imageViewer, 2.21.11search for chemical pattern, 2.34.56.3
s_inxDir, 2.21.9     pdb headers, 3.4.5
s_javaCodeBase, 2.21.12     prosite, 3.4.1
s_labelHeader, 2.21.13     sequence pattern, 2.33.35.8
s_lib, 2.21.14searchObjSegment, 2.36.73
s_logDir, 2.21.15searchPatternDb, 2.36.71
s_out, 2.21.16searchPatternPdb, 2.36.72
s_pdbDir, 2.21.17searchSeqDb, 2.36.74
s_pdbDirFtp, 2.21.18searchSeqFullPdb, 2.36.76
s_pdbDirWeb, 2.21.19searchSeqPdb, 2.36.75
s_printCommand, 2.21.21searchSeqProsite, 2.36.77
s_projectDir, 2.21.20searchSeqSwiss, 2.36.78
s_prositeDat, 2.21.22searches and alignments, 3.4
s_psViewer, 2.21.23second moments, 2.34.163
s_reslib, 2.21.24secondary structure derivation from 3D, 2.33.5.1
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, 2.33.86
s_sysRm, 2.21.29     atoms by number of bonded atoms, 2.34.137.3
s_tempDir, 2.21.30          of the fixed torsions, 2.34.137.2
s_translateString, 2.21.31     based on alignment, 2.34.137.14
s_userDir, 2.21.32          bfactor, 2.34.137.7
s_usrlib, 2.21.33          center of mass, 2.34.137.15
s_webEntrezLink, 2.21.34          coordinates, 2.34.137.7
s_webViewer, 2.21.35          iarray, 2.34.137
s_xpdbDir, 2.21.36          length, 2.34.137.13
sa23, 3.3          occupancy, 2.34.137.7
sampling grid, 2.34.192.3          user field, 2.34.137.7
sarray, 2.33.22.6, 5.8.1     chemical, 2.33.86.1
     transformation in place, 2.33.100.1     column table, 2.33.86.2
save preferences, 2.33.108.42     lines, 2.33.82.1
     print, 3.2.6     tether partners, 2.34.137.12
     sdf file, 2.33.108.11     vw partners, 2.34.137.12
saving graphics to album, 2.33.63.20selectMinGrad, 2.19.37
     image, 2.33.108.36selectSphereRadius, 2.19.38
scaffold, 2.34.178selected stack conformations, 2.33.22.17

               y z, 2.34.137     redundancy removal, 2.33.43.2
     columns, 5.9.1     search, 2.33.35.2
     from clusters, 3.14.6.4     selection, 2.33.22.23
     neighboring elements, 2.34.101     structure alignment, 2.35.1
     residues, 3.3.6     to alignment transfer, 2.34.122.3
     saving, 2.34.66.4     type, 5.8.3
selection, 2.8, 2.34.137, 2.34.137.6sequence-alignment mapping, 2.34.156.5, 2.34.156.6
     elements, 2.8.4sequence-structure alignment, 2.34.5.1
     examples, 2.8.3     output format, 2.18.21, 2.18.22
     functions, 2.8.10sequenceBlock, 2.18.21
     gap patching, 2.34.137, 2.34.137.11sequenceColorScheme, 2.22.23
     level, 2.8, 2.34.182sequenceLine, 2.18.22
     levels, 2.8.2sequences, 3.4
     simplification, 2.34.137.11     not in alignments, 2.33.22.23
     transfer, 2.34.137, 2.34.156.8set, 2.33.87
     type, 2.8     alternative atom, 2.33.87.18
     types, 2.8.1     area, 2.33.87.1
     variable, 2.24.12     atom, 2.33.87.3
     atoms, 2.8.8          ball label, 2.33.87.2
     functions, 2.8.10     background image, 2.33.87.4
     molecules, 2.8.6     bfactor, 2.33.87.5
     objects, 2.8.5     biological symmetry, 2.33.87.64
     output, 2.24.15     bond topology, 2.33.87.7
     residues, 2.8.7          type, 2.33.87.6
     torsions, 2.8.9          and formal charges, 2.33.87.7
     variables, 2.8.9     cartesian, 2.33.87.8
selections, 2.33.87.34     chain, 2.33.87.9
     in molecular objects, 2.8     charge, 2.33.87.10
selftether, 2.23.14.12, 5.9.4          formal, 2.33.87.11
seq_ali_project, 2.34.156.6               auto, 2.33.87.12
sequence, 2.34.172, 2.34.173, 5.8.3          mmff, 2.33.87.13
     alignment, 2.34.5.1, 2.36.1     chargemmff, 2.33.87.13
          intro, 1.4.3.3     chiral, 2.33.87.14
     analysis intro, 1.4.3          chemical, 2.33.87.15
     assembly, 2.33.43.2     color, 2.33.87.16
     belongs to alignment, 2.34.70     comment, 2.33.87.17, 2.33.87.18
     conservation, 2.34.136.7          sequence, 2.33.87.19
     distance, 2.34.137     comp_matrix, 2.33.87.20
          matrix from alignment, 2.34.90.9     current map, 2.33.87.45
     dotplot, 1.4.3.2          object, 2.33.87.48
     from alignment, 2.33.22.23     directory, 2.33.87.21
          pdb, 2.33.63.35     drestraint, 2.33.87.22
     identity, 2.36.7, 2.36.8          type, 2.33.87.23
     intro, 1.4.3     electrostatic radii, 2.33.87.79
     modification, 2.34.180     error, 2.33.87.33
     neighbor, 2.34.99.3     field, 2.33.87.34
     parray, 5.7.3.2          alignment, 2.33.87.35
     pattern, 5.7.4          map, 2.33.87.36
     position correspondence, 2.34.160.3          name, 2.33.87.37
     positional weights, 2.33.87.1     font, 2.33.87.38

     foreground, 2.33.87.40     table, 2.33.87.66
     format, 2.33.87.41     tautomer, 2.33.87.31
     grob, 2.33.87.42     terms, 2.33.87.67
          coordinates, 2.33.87.42     tether, 2.33.87.69
          label, 2.33.87.42          append, 2.33.87.70
     group, 2.33.87.63     texture, 2.33.87.32
          column, 2.33.87.24     type, 2.33.87.71
     hydrogen, 2.33.87.25          mmff, 2.33.87.77
     key, 2.33.87.43          molecule, 2.33.87.75
     label, 2.33.87.44          object, 2.33.87.74
          3d label, 2.33.87.44.4          property, 2.33.87.73
          chemical, 2.33.87.44.3          sequence, 2.33.87.76
          distance, 2.33.87.44.1          surface, 2.33.87.72
          table, 2.33.87.44.2     variable grid, 2.33.87.84
     map, 2.33.87.45     variablegrid, 2.33.87.84
     molcart, 2.33.87.46     view, 2.33.87.80
     molecular variables, 2.33.87.83     vrestraint, 2.33.87.81
     name, 2.33.87.47     vrestraintvs_var, 2.33.87.82
          sequence, 2.33.87.47.1          radii, 2.33.87.78
     object, 2.33.87.48     vwelradii, 2.33.87.79
     occupancy, 2.33.87.49     vwradii, 2.33.87.78
     plane, 2.33.87.50     window, 2.33.87.85
     pmf, 2.33.87.51     xstick, 2.33.87.86
     property, 2.33.87.52, 2.33.87.54, 2.33.87.55          radii, 2.33.87.86
          alignment, 2.33.87.55setResLabel, 2.36.80
          chemical view, 2.33.87.54setcomp_matrix, 2.33.87.20
          column, 2.33.87.53seticmff, 2.36.79
     radii graphical, 2.33.87.86setting conf properties, 2.33.87.61
     randomSeed, 2.33.87.56setvs_var, 2.33.87.83
     randomize, 2.33.87.56sf-term, 2.33.87.72
     resolution, 2.33.87.57sfWeight, 2.19.39
     selftether, 2.33.87.68sh24, 3.4
     similarity, 2.34.44.8, 2.34.136.2shadows, 2.23.5.34
     site, 2.33.87.26shell, 3.1, 5.8.5
          alignment, 2.33.87.27     functions, 2.33.40
          residue, 2.33.87.29     intro, 1.7.1
     slide, 2.33.87.30     progression, 2.33.76
     sstructure backbone, 2.33.87.59     warning message, 2.34.191
          sequence, 2.33.87.60shineStyle, 2.22.24
          to sequence, 2.33.87.60shininess, 2.19.40
     stack, 2.33.87.61show, 2.33.88, 2.33.88.39
          energy, 2.33.87.61, 2.33.92.1     alias, 2.33.88.7
     stereo, 2.33.87.58     aliases, 2.33.88.7
     swiss, 2.33.87.62     alignment, 2.33.88.8
          name, 2.33.87.62     area, 2.33.88.9
     symmetry, 2.33.87.65     atom, 2.33.88.10
          bio, 2.33.87.64          type, 2.33.88.11
          crystal, 2.33.87.63     atoms, 2.33.88.10
          group, 2.33.87.63     bond, 2.33.88.12
          to a torsion, 2.33.87.65     clash, 2.33.88.13

     column, 2.33.88.15     vrestraints, 2.33.88.49
     comp_matrix, 2.33.88.16showcomp_matrix, 2.33.88.16
     database, 2.33.88.17showing weak hydrogen bonds, 2.23.5.25
     drestraint, 2.33.88.18side chain, 2.36.90
          type, 2.33.88.19          flexibility, 2.36.90
     energy, 2.33.88.20sigma function, 2.34.44.8, 2.34.136.2
          atom, 2.33.88.21     level, 2.23.7.5
     gradient, 2.33.88.22signal recognition measure, 2.36.21
     hbond, 2.33.88.23similar chains, 2.34.137.13
          exact, 2.33.88.24similarity, 2.33.35.9, 2.33.35.10
     hbondexact, 2.33.88.24simple expressions, 2.10.1.1
     html, 2.33.88.25     string substitution, 2.34.126.2
     iarray, 2.33.88.26simplified representation, 2.23.5.16
     integer, 2.33.88.27     compound, 2.34.179
     key, 2.33.88.4     mesh structure, 2.33.15.2
     label, 2.33.88.28simulation duration, 2.19.47
     library, 2.33.88.29     temperature, 2.19.46
     link, 2.33.88.30     intro, 1.4.2
     logical, 2.33.88.31sinking number, 2.19.35
     map, 2.33.88.5site, 2.33.11.2, 5.8.6
     mol, 2.33.88.32     arrows, 2.33.87.26
     mol2, 2.33.88.33     table, 5.8.6.1
     molecule, 2.33.88.34sites, 2.33.22.26
     molecules, 2.33.88.6     by residue selection, 2.33.22.24
     object, 2.33.88.35     sequences, 5.8.6.1
     pdb, 2.33.88.36sixthe power, 2.22.6
     pharmacophore type, 2.33.88.53skin, 2.19.35, 5.8.7
     pmf, 2.33.88.37     intro, 1.4.1.2
     preferences, 2.33.88.38slide, 2.33.1.3, 2.34.144, 5.8.14
     profile, 2.33.88.39     transition time, 2.33.23.21
     residue, 2.33.88.40slides, 2.34.190
          type, 2.33.88.41slideshow, 2.33.1.3, 2.33.23.21, 2.34.144
     residuetype, 2.33.88.41sln, 5.8.8
     segment, 2.33.88.42smallest set of smallest rings, 2.34.130
     selftether, 2.33.88.1smart, 2.23.14.7
     sequence, 2.33.88.43smarts, 2.34.70.2
     shell variable, 2.33.88.3smiles, 2.23.14.7, 2.26
     site, 2.33.88.2     to chem-table element, 2.34.109
     stack, 2.33.88.44smooth alignment, 2.34.146.4
     svariable, 2.33.88.3     interpolation, 2.33.92.3
     table, 2.33.88.45     map, 2.34.146.5
          as database, 2.33.88.17     rarray, 2.34.146.1
     term, 2.33.88.46     surface, 2.36.88
     tethers, 2.33.88.47soap, 2.31
     version, 2.33.88.48soft trim, 2.34.178
     volume, 2.33.88.51solid sphere, 2.23.5.11
          map, 2.33.88.52solubility, 2.34.114
     volumemap, 2.33.88.52solvation, 2.22.25, 2.23.14.2
     vrestraint, 2.33.88.49     energy, 2.19.39, 2.22.25
          type, 2.33.88.50solvent accessible area, 2.18.23

sort, 2.33.89, 2.33.89.4     chemical, 2.33.68
     array, 2.33.89.1startup, 3.1.2.3
     arrays, 2.33.89.1static RMSD, 2.34.155
     column, 2.33.89.3     and dynamic hbonds, 2.23.5.24
          table, 2.33.89.3statistical thermodynamics, 2.34.47
     molecules, 2.33.89.5stereo, 2.23.5.52, 2.33.30, 2.33.87.58
     object, 2.33.89.4     reconstruction, 3.8.9
     stack, 2.33.89.6stereo-specific hydrogens, 2.33.22.11
     table, 2.33.89.2stereoisomer, 2.33.30
sortSeqByLength, 2.36.81stereoisomers, 2.20.16
space group, 2.33.67stick, 5.8.10
     transformations, 2.34.176store, 2.33.92
sparse atoms, 2.23.14.3     conf, 2.33.92, 2.33.92.1
spawn background job, 2.33.63.1     frame, 2.33.92.3
special values, 2.34.168     image, 2.33.63.20
specificity, 2.34.136.4     stack object, 2.33.92.2
spectral decomposition, 2.34.45     torsion type, 2.33.92
split, 2.33.90strength of hydrogen bond, 2.33.23.14
     column values, 2.33.90.5string, 5.8.11
     grob, 2.33.90.1     array, 2.34.135, 5.8.1
     group, 2.33.90.2     filtering, 2.34.178
          array, 2.33.90.3     inversion, 2.34.156.1
     molsar, 2.33.63.28     label, 2.33.23.12
     object, 2.33.90.6     matching, 2.10, 2.34.89
          to molecules, 2.33.90.6     variables, 2.21
     sequence, 2.33.90.4strings, 2.21
     table cell, 2.33.90.5strip, 2.33.94
     tree, 2.33.90.7struct, 2.34.99.2
splitting selection, 2.8.11structural alignment, 2.33.3.5, 2.34.5.2
spreadsheet, 2.33.82.44          optimization, 2.33.35.1
sprintf, 2.33.91     superposition, 2.33.3.5
sql, 2.33.79, 2.33.87.46, 2.34.50.1, 2.34.99.12, 2.34.102.5, 2.34.182.2     analysis, 3.3
sqlite, 3.5.1     comparison, 2.34.23.2
sqrt, 2.34.37     factors, 3.11.1
square matrix to element pairs, 2.34.160.5     structure, 3.11.1
ssThreshold, 2.19.41sub-alignment to selection, 2.34.128
ssWeight, 2.19.42sub-matrix, 2.34.90.2
ssbond, 5.4.5subalignment, 2.34.5.3, 5.1.1
ssearch, 2.18.17, 2.33.93submap, 2.34.86
ssearchStep, 2.19.43subroutine, 2.33.62
ssign sstructure segment, 2.33.5.2subset, 2.6
stack, 2.18.12, 2.18.13, 2.18.15, 2.22.7, 2.33.87.61, 2.33.92, 2.33.92.1, 2.34.66.6, 2.34.160.6, 5.3.12, 5.8.9substring, 2.34.89, 2.34.156, 2.34.156.1
     bin size, 2.33.14substructure, 2.33.35.9, 2.33.35.10
     cleaning, 2.33.22.17     search, 2.33.35.4
     extension, 2.33.4.2superimpose, 2.23.14, 2.33.95
     multiplication, 2.33.4.2     faq, 3.3.1
     merge, 3.7.7     how to, 3.3.1
standard chemical form, 2.33.68.4     minimize, 2.33.96
     deviation, 2.34.133support, 1.3
standardization, 2.33.22.11suppressing view changes, 2.33.23.21

     accessibility, 2.33.88.9     selected row numbers, 2.34.70
     area, 2.36.2, 5.8.15     subset, 5.9.2.2
     charge, 5.7.13     show html, 2.33.106.1
     color, 2.33.87.16targa, 5.9.3
     dot density, 2.23.5.55target coordinates, 5.9.4
     energy, 2.22.25, 2.33.87.72tautomer, 2.33.31
     mesh, 2.34.192.3tempCycle, 2.19.46
     point selection, 2.34.192tempLocal, 2.19.45
     term, 2.19.39temperature, 2.19.46
surfaceAccuracy, 2.18.23     variations in optimizer, 2.19.46
surfaceMethod, 2.22.25template docking, 3.13.2.6
surfaceTension, 2.19.44tensor product of two vectors, 2.34.90
svariable, 5.8.12terminal font, 2.37.14
     map, 2.34.160.7     window, 2.33.44
swapping protein fragments, 3.8.7terms, 2.17
swiss, 2.33.87.62     hydrogen bonding, 2.19.21
swissFields, 2.24.10test, 2.33.98
swissprot, 2.33.87.26     binary, 2.33.98.1
symmetrization of a matrix, 2.34.90.3testing if argument exists, 2.34.59
symmetry, 2.34.176tether, 2.23.14.12, 2.33.108.9, 5.9.4, 5.9.5
     faq, 3.10text, 2.34.89
     group, 2.18.2     search in tables, 2.34.56.2
     problem, 2.33.67     to script, 5.8.2
syntax highlighting, 5.8.2texture, 5.5.3
sys, 2.33.97tga, 5.9.3
system, 5.10.2then, 2.33.99
     command, 2.33.97thickness, 2.23.9.14
     copy, 2.21.26thread to template, 2.33.64.4
     file move, 2.21.28threading, 2.34.5.1
     list file, 2.21.27     letter code, 2.34.172, 2.34.173
     remove, 2.21.29thumbnails, 2.34.68
table, 2.33.22.4, 2.33.87.52, 2.33.87.53, 2.33.87.54, 2.33.89.3, 5.9.1tif, 5.9.6
     actions, 5.9.2.4time, 2.34.38, 2.34.156.2
     column, 2.34.99timeLimit, 2.19.47
          format, 2.33.87.41tolFunc, 2.19.49
          plot, 2.33.63.32tolGrad, 2.19.48
          transformations, 2.34.104topological psa, 5.7.12
     creation, 2.33.43.3torScan, 2.36.84
     display style, 5.9.1torsion rmsd comparison, 2.33.14.2
     expression, 5.9.2     scan, 2.36.84
     from matrix, 2.34.160.4torsions, 2.34.102.3
     grid view, 5.9.1     score, 2.35.2
     of atoms and distances, 2.34.160.10tpsa, 5.7.12
     operations, 5.9.2.1trajectory, 2.33.61.2, 2.33.92, 2.33.92.3, 5.6.14
     plot, 5.9.2.3     file, 2.37.17
     principal component analysis, 2.33.63.29     frame writing, 2.33.23.17
     print, 2.33.88.45     smoothing, 2.33.23.17
     row, 2.33.70.4transform, 2.33.100, 2.33.100.2
          label mark, 2.33.87.44.2     general, 2.33.100
          mark, 2.34.79     grob coordinates, 2.33.100.2

     sarray, 2.33.100.1update database, 2.33.68.5
transformation, 2.34.122, 5.9.7     speadsheet, 2.33.1.1.1
     vector, 5.9.7updates, 1.1
     and symmetry, 3.10updating atom pairs, 2.20.27
transforming points, 2.34.192.5upper case, 2.34.171
translate, 2.33.101url string parsing, 2.34.160
transparency, 2.33.87.42, 5.5.3user atom display, 2.23.5.3
     background, 2.33.108.36     commands, 2.33.82.3
     grob, 2.33.23.11     defaults, 2.33.108.42
     grobs, 2.23.5.57     environment, 3.1.2.2
tree, 2.33.63.37, 2.34.99.5     menu, 2.23.10.1
     cluster, 2.13     menus, 2.32
     delete, 2.33.22.36user-defined properties, 2.33.87.34
     label format, 2.34.99.5     solvation parameters, 2.34.7
     representatives, 2.13.1user_startup, 3.1.2.4
trim string array, 2.33.100.1     icm, 3.1.2
trimming grid map values, 2.34.178     guide, 3
true positives, 2.34.136.4v_, 2.8.1
truncate alignment, 2.33.63.34van der Waals surface, 2.23.5.56
     values, 2.34.178varLabelStyle, 2.22.27
     grob, 2.23.5.9, 2.23.5.10variable restraint, 2.33.87.81
tsShapeData, 2.23.14.12     selection, 2.8.9
     table format, 2.33.82.44vdW gap, 2.34.151
two alignments, 2.34.44.13vector, 2.34.102.6
     dimensional plot, 2.34.146.2     dot product, 2.34.187.1
     set comparison, 2.34.44.8, 2.34.136.2     length, 2.34.103
     sets, 2.34.70.10     product, 2.34.187.1
txdoc browser, 2.33.82.4     transformation, 2.34.104
type, 2.34.182.1vertex, 2.33.13.4.2
tzMethod, 2.22.26     connectivity, 2.34.90.13
tzWeight, 2.19.50vertexes, 2.33.13.4.2
uncharge functional groups, 2.33.68.2vertical alignment block, 2.33.63.34
unclip, 2.33.23.2     workspace, 2.23.8.6
underline, 2.33.87.38.1vertices, 2.33.13.4.2
undisplay, 2.33.102vicinity, 2.19.51
     graphics, 2.33.103video, 2.33.108.31
     window, 2.33.103view, 2.23.5.9, 2.23.5.10, 2.33.87.55
unfix, 2.33.104     point, 2.34.190
union, 2.34.70.10     restoration, 2.34.73
unique, 2.33.13.1, 5.10.1     transition, 2.33.87.80
     atomic order, 2.33.63.39views, 5.8.14
     column values, 2.33.43.4virtual, 5.10.3
     names, 2.34.99     arrays, 2.33.1.1.1
     new object name, 2.34.99     chemistry, 2.33.68, 2.34.102.4
     smiles, 2.33.63.39     field, 2.33.7.2
unix, 2.33.97, 5.10.2     ligand screening, 3.13, 3.13.1, 3.13.2, 3.13.3
     grep, 2.33.82.1               intro, 1.4.2.7
unlink alignments, 2.33.22.21visitsAction, 2.22.28
     sequences, 2.33.22.21vls, 3.13, 3.13.1, 3.13.2, 3.13.3
     variables, 2.33.22.21     cluster, 3.13.3.6

     intro, 1.4.2.7     database, 2.33.108.13
     job queueing, 3.13.3.6     drestraint, 2.33.108.14
     overview, 3.13.1          type, 2.33.108.15
     parallelization, 3.13.3.5     factor, 2.33.108.16
     results, 3.13.3.8     gamess, 2.33.108.17
     scores storage, 3.13.3.7     grob, 2.33.108.18
     threshold, 3.13.3.2     html, 2.33.108.19
vls_intro, 3.13.3.1     iarray, 2.33.108.3
volume, 5.10.4     image, 2.33.108.20
vrestraint, 5.10.5          alignment, 2.33.108.23
     file, 2.37.23          chemical, 2.33.108.22
     type, 5.10.6          parray, 2.33.108.21
          file, 2.37.22     index, 2.33.82.24, 2.33.108.24
vs_, 2.8.9          blast, 2.33.108.25
vs_out, 2.24.15          fasta, 2.33.108.24
vwCutoff, 2.19.52     library, 2.33.108.26
vwExpand, 2.19.53     map, 2.33.108.27
vwExpandDisplay, 2.19.54     matrix, 2.33.108.6
vwMethod, 2.22.29     model, 2.33.108.28
vwSoftMaxEnergy, 2.19.55     mol, 2.33.108.29
wait, 2.33.105     mol2, 2.33.108.30
warning, 2.23.14.3     molcart, 2.33.108.7
     message, 2.34.191     movie, 2.33.108.31
     suppression, 2.20.28     object, 2.33.108.32
water.dielectric constant, 2.19.15          parray, 2.33.108.34
waterRadius, 2.19.56          simple, 2.33.108.33
wavefront format, 2.33.63.11     pdb, 2.23.14.14, 2.33.108.35
web, 2.11, 2.33.106     png, 2.33.108.36
     table, 2.33.106.1     postscript, 2.33.108.37
webEntrezOption, 2.22.30     pov, 2.33.108.38
weighted rmsd, 2.23.14     povray, 2.33.108.38
while, 2.33.107     project, 2.33.108.2
whole string, 2.34.126.1     rarray, 2.33.108.4
window averaging, 2.34.146.1     sarray, 2.33.108.5
     layout, 2.34.156.9     sequence, 2.33.108.39
     width and height, 2.34.190     session, 2.33.108.40
windowSize, 2.18.24     several array, 2.33.108.8
     movie, 2.33.108.31     simple object, 2.33.108.33
wire, 5.10.7     stack, 2.33.108.41
wireBondSeparation, 2.19.57     system preference, 2.33.108.42
wireStyle, 2.22.31     table, 2.33.108.10
workspace, 2.33.103          mol, 2.33.108.11
write, 2.33.108          with links, 2.33.108.19
     album, 2.33.108.21     tether, 2.33.108.9
     alignment, 2.33.108.1     tethers, 2.33.108.9
     array, 2.33.108.8     trajectory, 2.33.23.17
          table, 2.33.108.8     vs_var, 2.33.108.43
     binary, 2.33.108.2writevs_var, 2.33.108.43
     blast, 2.33.108.25x-ray crystallography, 2.33.88.21
     column, 2.33.108.12xml, 2.33.82.56, 2.34.89, 5.1.6

xpdb, 2.33.82.2 
xplor format, 2.33.82.27 
xrMethod, 2.22.32 
xrWeight, 2.19.58 
xray density to rectangular energy map, 2.33.63.31 
xstick, 5.10.8 
     radii, 2.33.87.2 
xyz morphing, 3.8.8 
zega, 5.10.9 
     intro, 1.4.3.6 
|, 2.14.3 

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