ICM Manual v.3.8
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2020, Molsoft LLC
Apr 28 2020

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

Index

&, 2.14.3C, 5.3
2D labels, 2.29.55.1CCP4, 5.6.6
     to 3D, 3.16CGI, 2.11
     trees, 2.29.62.38COLOR.bg, 2.19.9
     smooth, 2.30.146.2     distanceAtom, 2.19.10
3D chemical builder, 1.4.2.8     label, 2.19.11
     font size, 2.29.23.12CONSENSUS, 2.23.1
     label, 2.29.23.12, 2.29.86.39CONSENSUSCOLOR, 2.23.2
     labels, 2.29.55.1CONSENSUS_strength, 2.19.12
     mol file, 2.32.86Cad, 2.30.23, 2.30.23.1, 2.30.23.2
     plots intro, 1.4.3.7Cad1, 2.30.23.1
     smoothing, 2.30.146.3Cadalign, 2.30.23.2
     superposition, 2.32.22Ceil, 2.30.24
     transformations, 2.29.99.2Cell, 2.30.25
     tree, 2.29.62.38Charge, 2.30.26
     chemical similarity, 2.30.136Chemical, 2.30.27
     pharmacophore comparison, 2.30.136.3Cluster, 2.30.28
3dxml, 5.5.3Collada, 5.5.3
=, 2.14.1Collection, 2.30.28.1
A, 5.1Color, 2.30.29
APF distance, 2.30.136     from gradient, 2.30.29.1
Abs, 2.30.1     image, 2.30.29.2
Acc, 2.30.2     protein, 2.30.29.3
Acos, 2.30.3Compare, 2.30.30
Acosh, 2.30.4Connolly surface, 5.8.7
Adobe, 2.21.23Consensus, 2.30.31
Align, 2.30.5Contour, 2.30.32
     sequence, 2.30.5.1Corr, 2.30.33
AlignSS, 2.31.1Cos, 2.30.34
Angle, 2.30.6Cosh, 2.30.35
Apple, 3.14.6.2Count, 2.30.36
Area, 2.30.7CubicRoot, 2.30.37
     residue contacts, 2.30.7.1D, 5.4
Asin, 2.30.8DAE, 5.5.3
Asinh, 2.30.9DE, 2.29.35.2
Ask, 2.30.10DNA Representation, 1.4.1.3
Askg, 2.30.11     alignment, 2.29.3.4
Atan, 2.30.12     melting temperature, 2.30.164
Atan2, 2.30.13     views, 1.4.1.3
Atanh, 2.30.14Date, 2.30.38
Atom, 2.30.15Deletion, 2.30.39
Augment, 2.30.16Descriptor, 2.30.40, 2.30.41
Axis, 2.30.17     numeric, 2.30.40
B, 5.2Det, 2.30.42
BPMC, 5.2.6Disgeo, 2.30.43
Bfactor, 2.30.19Distance, 2.30.44, 2.30.44.6
Blob, 2.30.18     2 alignments, 2.30.44.13
Boltzmann, 2.30.20          matrices, 2.30.44.9
Box, 2.30.21     Dayhoff, 2.30.44.11
Bracket, 2.30.22     Tanimoto, 2.30.44.7

     as_, 2.30.44.3     atomLabelShift, 2.23.5.2
          rarray, 2.30.44.4     atomValueCircles, 2.23.5.3
     atoms, 2.30.44.3     ballRadius, 2.23.5.4, 2.23.5.31
     chemical, 2.30.44.7, 2.30.44.15     ballStickRatio, 2.23.5.5
     chemset, 2.30.44.8     chainBreakLabelDisplay, 2.23.5.8
     dayhoff, 2.30.44.11     chainBreakStyle, 2.23.5.7
     hierarchical, 2.30.44.6     clashWidth, 2.23.5.6
     iarray, 2.30.44.1     clipStatic, 2.23.5.10
          alignment, 2.30.44.12     clippingPlane, 2.23.5.9
     matrix, 2.30.44.5, 2.30.44.9     cpkClipCaps, 2.23.5.11
     multiple atomic, 2.30.44.4     displayLineLabels, 2.23.5.12
     rarray, 2.30.44.2     displayMapBox, 2.23.5.13
     tether, 2.30.44.10     dnaBallRadius, 2.23.5.14
     tree, 2.30.44.14     dnaRibbonRatio, 2.23.5.15
          cluster, 2.30.44.14     dnaRibbonStyle, 2.23.5.16
     H, 5.5     dnaRibbonWidth, 2.23.5.17
     number, 2.30.44.6     dnaRibbonWorm, 2.23.5.18
EDS server, 2.32.42     dnaStickRadius, 2.23.5.19
EST-alignment, 2.29.3.4     formalChargeDisplay, 2.23.5.20
Eigen, 2.30.45     grobDotSize, 2.23.5.21
Energy, 2.30.46     grobLineWidth, 2.23.5.22
Entropy, 2.30.47     hbondAngleSharpness, 2.23.5.26
Error, 2.30.48     hbondBallPeriod, 2.23.5.27
     soap, 2.30.49     hbondBallStyle, 2.23.5.28
Exist, 2.30.50     hbondMinStrength, 2.23.5.25
     molcart, 2.30.50.1     hbondRebuild, 2.23.5.24
Existenv, 2.30.51     hbondStyle, 2.23.5.23
Exp, 2.30.53     hbondWidth, 2.23.5.29
Extension, 2.30.52     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, 2.30.91.1
     proxy, 2.23.4.3     rainbowBarStyle, 2.23.5.39
Field, 2.30.54, 2.30.54.1     resLabelDrag, 2.23.5.40
     user, 2.30.54.1     resLabelYShift, 2.23.5.41
File, 2.30.55     ribbonCylinderRadius, 2.23.5.42
Find, 2.30.56     ribbonGapDistance, 2.23.5.43
     chemical, 2.30.56.3     ribbonRatio, 2.23.5.44
          pattern, 2.30.56.3     ribbonWidth, 2.23.5.45
     in array, 2.30.56.1     ribbonWorm, 2.23.5.46
          table, 2.30.56.2     rocking, 2.23.5.47
FlexLM license info, 2.30.188     rockingRange, 2.23.5.48
Floor, 2.30.57     rockingSpeed, 2.23.5.49
Formula, 2.30.58     selectionLevel, 2.23.5.50
GRAPHICS, 2.23.5     selectionStyle, 2.23.5.51
     alignmentRainbow, 2.23.5.1     sketchAccents, 2.23.5.30

     stickRadius, 2.23.5.31, 2.23.5.53ICMFF force field, 2.32.79
     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, 2.28     stereoText, 2.23.9.11
     plot, 2.29.62.32     writeScale, 2.23.9.19
     preferences, 2.29.82.4I_out, 2.24.4
     tableRowMarkColors, 2.23.8.5Iarray, 2.30.66, 2.30.66.4, 2.30.66.5
     windowLayout, 2.23.8.6     atom numbers, 2.30.66.4
     workspaceFolderStyle, 2.23.8.9     bits to integers, 2.30.66.3
     workspaceStyle, 2.23.8.7     inverse, 2.30.66.2
     workspaceTabStyle, 2.23.8.8     residue numbers, 2.30.66.5
GaussFit, 2.30.82     reverse, 2.30.66.2
Getarg, 2.30.59     stack, 2.30.66.6
Getenv, 2.30.60Icm Options, 2.1
Gradient, 2.30.61IcmSequence, 2.30.67
Graphics, 1.4.1Image, 2.30.68
Grob, 2.30.62     collection, 3.9.2.1
Group, 2.30.63     frame by frame, 3.9.2.2
HTTP.ignoreProxyDomains, 2.23.4.5InChI, 2.30.69
     proxy, 2.23.4.4InChi, 2.30.69
Hartree-Fock, 2.29.81.21, 2.29.107.17InList, 2.30.105
Header, 2.30.64Index, 2.30.70
Histogram, 2.30.65     chemical, 2.30.70.2
     N, 5.6     compare, 2.30.70.10
ICM desktop, 2.23.8.6     element in array, 2.30.70.8
     documents, 2.29.81.4     fork, 2.30.70.1
     modules, 1.4.4     regexp, 2.30.70.4
     object, 2.32.13     string, 2.30.70.3
     residue library, 2.21.24     table label, 2.30.70.6
ICM-shell, 3.1, 5.8.5          selection, 2.30.70.5
     intro, 1.7.1     tree, 2.30.70.9
     script, 2.29.8     unique elements, 2.30.70.7

Info, 2.30.73Mod, 2.30.97
     image, 2.30.74Mol, 2.30.98
     model, 2.30.75MolPSA, 5.7.12
Insertion, 2.30.72Moment, 2.30.88
Integer, 2.30.76     of Inertia, 2.30.88
Integral, 2.30.77Money, 2.30.96
Interrupt, 2.30.78N-terminus, 2.23.14.4
Introduction, 1NMR, 2.29.60.1
JSON, 2.29.81.57NOE averaging, 2.22.6
LIBRARY, 2.23.10Name, 2.30.99
     men, 2.23.10.1     chemical, 2.30.99.6
     res, 2.23.10.2          property, 2.30.99.1
Label, 2.30.79     close sequence, 2.30.99.3
Laplacian, 2.30.80     conf, 2.30.99.7
Latent, 2.30.187.3     image, 2.30.99.11
LatentVector, 2.30.187.3     molcart, 2.30.99.12
Length, 2.30.81     object parray, 2.30.99.10
LinearFit, 2.30.83     sequence, 2.30.99.8
LinearModel, 2.30.84     soap, 2.30.99.2
Log, 2.30.85     string, 2.30.99.4
LogP, 2.30.114     tree, 2.30.99.5
LogS, 2.30.114Namex, 2.30.100
M_out, 2.24.5     image, 2.30.100.2
Mac, 3.14.6.2     sequence, 2.30.100.1
Map, 2.30.86Newick tree format, 2.30.156.4
Markush structures, 2.29.52Next, 2.30.101, 2.30.101.1
Mass, 2.30.87     covalent neighbors, 2.30.101.1
Match, 2.30.89Nof, 2.30.102
Mathews, 2.30.136.4     chemical, 2.30.102.2
Matrix, 2.30.90     distance, 2.30.102.3
     alignment, 2.30.90.9     latent, 2.30.102.6
     boundary, 2.30.90.10     library, 2.30.102.4
     color, 2.30.90.4     molcart, 2.30.102.5
     grob connectivity, 2.30.90.13     soap, 2.30.102.7
     histogram, 2.30.90.12     tree, 2.30.102.1
     new, 2.30.90.1Norm, 2.30.103
     residue areas, 2.30.90.8Normalize, 2.30.104
          comparison, 2.30.90.5NotInList, 2.30.105
     stack, 2.30.90.11     R, 5.7
     sub, 2.30.90.2OBJECT, 2.23.11
     symmetric, 2.30.90.3Obj, 2.30.106
     table, 2.30.90.6Occupancy, 2.30.107
     tensor, 2.30.90.7PBS, 3.13.3.6
Max, 2.30.91PLOT, 2.23.12
     image graphic, 2.30.91.1     Yratio, 2.23.12.9
MaxHKL, 2.30.92     box, 2.23.12.1
Mean, 2.30.94     color, 2.23.12.2
Median, 2.30.93     font, 2.23.12.3
Method, 2.22.13     fontSize, 2.23.12.4
Min, 2.30.95     gridLineWidth, 2.23.12.5

     lineWidth, 2.23.12.6     simple, 2.30.126.2
     logo, 2.23.12.10Res, 2.30.127, 2.30.128
     markSize, 2.23.12.7Resali, 2.30.128
     numberOffset, 2.23.12.8Resolution, 2.30.129
     orientation, 2.23.12.11Rfactor, 2.30.131
     rainbowStyle, 2.23.12.14Rfree, 2.30.132
     seriesLabels, 2.23.12.12Ring, 2.30.130
PLS, 2.30.102.6Rmsd, 2.30.133
     error, 2.30.136.4     of subset, 2.23.14
     models, 2.30.136.4Rot, 2.30.134
Parray, 2.30.109S, 5.8
Parray-object, 2.30.109SAR analysis, 2.29.62.27, 2.29.62.28, 2.29.89.2, 2.29.89.3
Path, 2.30.108SC, 2.29.35.2
Pattern, 2.30.110SEQUENCE.restoreOrigNames, 2.23.12.15
Pi, 2.30.111SITE, 2.23.13
Polar Surface Area, 5.7.12     defSelect, 2.23.13.2
Potential, 2.30.112     labelOffset, 2.23.13.3
Power, 2.30.113     labelStyle, 2.23.13.4
Predict, 2.30.114     labelWrap, 2.23.13.5
Probability, 2.30.115     showSeqSkip, 2.23.13.6
Profile, 2.30.116     wrapComment, 2.23.13.7
Property, 2.30.117SLN notation, 2.30.156.10
Putarg, 2.30.118SMARTS, 2.26, 2.29.10, 2.30.102.2
Putenv, 2.30.119SOAP, 2.30.99.2, 2.30.102.7, 2.30.182.1
R-groups, 2.29.52     request message, 2.30.152
REBEL, 3.7.2SSSR, 2.30.130
     faq, 3.7.2S_out, 2.24.8
     file, 2.29.52S_proteinTags, 2.24.9
RNA topology, 2.23.5.16Sarray, 2.30.135
R_2out, 2.24.7     index, 2.30.135.1
R_out, 2.24.6Score, 2.30.136
Radius, 2.30.120     alignment, 2.30.136.8
Random, 2.30.121     apf, 2.30.136.3
     string, 2.30.121.1     chemset, 2.30.136.2
Rarray, 2.30.122     conservation, 2.30.136.7
     reverse, 2.30.122.2     model, 2.30.136.4
     sequence projection, 2.30.122.1     overlap, 2.30.136.1
     alignment projection, 2.30.122.3     predictions, 2.30.136.5
          strength, 2.30.122.5     sequence, 2.30.136.6
     property assignment, 2.30.122.4Scripting Tutorials, 1.8
RarrayAlignment, 2.30.122.5Select, 2.30.137
Rarrayinverse, 2.30.122.2     break, 2.30.137.1
Real, 2.30.123          alignment, 2.30.137.14
Reference, 2.30.125          atom property, 2.30.137.7
     Guide, 2          nmembers, 2.30.137.4
Remainder, 2.30.124          string, 2.30.137.9
Replace, 2.30.126     expand, 2.30.137.6
     chemical, 2.30.126.4     fix, 2.30.137.2
     exact, 2.30.126.1     graphical, 2.30.137.5
     regexp, 2.30.126.3     neighbors, 2.30.137.3

Select_by_sequence, 2.30.137.13     membrane, 2.23.14.2
Select_by_text, 2.30.137.9     minSphereCubeSize, 2.23.14.3
Select_lists, 2.30.137.12     pdbChargeNterm, 2.23.14.4
Select_patching, 2.30.137.11     pdbReadNmrModels, 2.23.14.5
Select_projection, 2.30.137.8     rebelPatchSize, 2.18.5, 2.23.14.6
Sequence, 2.30.138     smilesXyzSeparator, 2.23.14.7
     array, 2.30.138.2     superimposeMaxDeviation, 2.23.14.10
Sequence(dna reverse), 2.30.138.1     superimposeMaxIterations, 2.23.14.8
Shannon, 2.30.47     superimposeMinAtomFraction, 2.23.14.9
Shuffle, 2.30.139     tsShape, 2.23.14.12
Sign, 2.30.140     tsWeight, 2.23.14.13
Simulations, 1.4.2     writePdbRenameRes, 2.23.14.14
Sin, 2.30.141Table, 2.30.160
Sinh, 2.30.142     alignment numbers, 2.30.160.3
Site, 2.30.143     distance, 2.30.160.10
Slide, 2.30.144     matrix, 2.30.160.4
Smiles, 2.30.145     model, 2.30.160.8
Smooth, 2.18.24, 2.30.146, 2.30.146.1, 2.30.146.3          chem, 2.30.160.9
     matrix, 2.30.146.2     pairs, 2.30.160.5
Smoothrs, 2.30.146.3     plot, 2.30.160.7
SoapMessage, 2.30.152     stack, 2.30.160.6
SolveQuadratic, 2.30.147     url_decoder, 2.30.160.1
SolveQubic, 2.30.148Table(alignment), 2.30.160.2
Sort, 2.30.153Table(stack), 2.30.160.6
Sphere, 2.23.14.3, 2.30.151Tan, 2.30.161
Split, 2.30.154Tanh, 2.30.162
     chemical, 2.30.154.4Tanimoto, 2.30.66.3
     multisep, 2.30.154.3     distance, 2.29.62.37
     regexp, 2.30.154.2          matrix, 2.30.44.7
     tree, 2.30.154.1Temperature, 2.30.164
Sql, 2.30.149Tensor, 2.30.163
Sqrt, 2.30.150Time, 2.30.165
Srmsd, 2.30.155Tointeger, 2.30.166
Sstructure, 2.30.157Tolower, 2.30.167
String, 2.30.156, 2.30.156.8Toreal, 2.30.168
     alternative, 2.30.156.7Torsion, 2.30.169
     date, 2.30.156.2Tostring, 2.30.170
     mol, 2.30.156.3Toupper, 2.30.171
     selection, 2.30.156.8ToxScore, 2.31.2
     slide gui, 2.30.156.9Tr123, 2.30.172
     substring, 2.30.156.1Tr321, 2.30.173
     chemical formula, 2.30.156.10Trace, 2.30.174
Sum, 2.30.158Trans, 2.30.175
     chemical, 2.30.158.1Transform, 2.30.176
     image, 2.30.158.2Transpose, 2.30.177
Swissprot, 2.29.107.24Trim, 2.30.178
Symgroup, 2.30.159     chemical, 2.30.179
T, 5.9     sequence, 2.30.180
TOOLS, 2.23.14Turn, 2.30.181
     edsDir, 2.23.14.1Type, 2.30.182

     soap, 2.30.182.1accessMethod, 2.22.2
     Z, 5.10accessible residues, 3.3.6
Unique, 2.30.183     surface, 2.29.62.14, 5.8.15
Unix, 2.30.184accessing sections, 2.29.107.24
Uppsala, 2.32.42accuracy, 2.30.136.4
     server, 2.32.43acidity constant, 2.29.86.11, 2.29.86.12
V_, 2.8.1activate fog, 2.29.23.24
Value, 2.30.185     alignment, 2.29.86.40
     soap, 2.30.186     document, 2.29.86.40
Vector, 2.30.16, 2.30.187, 2.30.187.1, 2.30.187.3     tab, 2.29.86.40
     symmetry transformation, 2.30.187.2     table, 5.9.2.4
Vectorproduct, 2.30.187.1add, 2.29.1
Vectorsymmetrytransformation, 2.30.187.2     column, 2.29.1.1
Version, 2.30.188          function, 2.29.1.1.1
View, 2.30.190     matrix, 2.29.1.2
Volume, 2.30.189     slide, 2.29.1.3
WEBAUTOLINK, 2.23.16     table, 2.29.1.4
WEBLINK, 2.23.15          row, 2.29.1.4
Warning, 2.30.191addBfactor, 2.19.1
Wavefront format, 2.29.81.22adding atoms to non-ICM objects, 2.29.7.1
XML, 2.12     columns to table, 2.29.1.1
Xyz, 2.30.192     hydrogens, 2.32.13
     axes, 2.30.192.8     in place, 2.14.4
     chemical match, 2.30.192.6     to slideshow, 2.29.1.3
     fract, 2.30.192.4admet selection, 3.13.3.4
     mesh, 2.30.192.3advanced chemical search, 3.6
     points, 2.30.192.1     operations, 2.14.6
     rings, 2.30.192.2     ops, 2.14.6
     transformed xyz, 2.30.192.5ahfs, 2.30.44.6
     vector2matrix, 2.30.192.7ali_seq_project, 2.30.156.5
Z-shift, 2.19.35alias, 2.29.2
ZEGA, 5.10.9align, 2.29.3
     intro, 1.4.3.6     3D, 2.29.3.5
_NAME, 2.29.86.47          faq, 3.3.2
_chemBatch, 3.1.2.5          heavy, 2.29.3.6
_chemSuper, 3.15          how to, 3.3.2
_confGen, 3.16     chemical, 2.29.85.1
_dockScan, 3.13.2.5     fragments, 2.29.3.4
_macro, 2.33.1     intro, 1.4.3.3
     file, 2.33.1     number, 2.29.3.2
_startup, 3.1.2.3          chemical, 2.29.3.1
     file, 2.33.2     res numbers, 2.29.3.2
     icm, 2.33.2     sequence, 2.29.3.3
a_, 2.8.1     sequences, 2.29.3.3
abbr, 1.6alignMethod, 2.22.3
abbreviations, 1.6alignMinCoverage, 2.19.2
absolute to cell x y z, 2.30.192.4alignMinMethod, 2.19.2
accFunction, 2.24.2alignOldStatWeight, 2.19.3
acceptor, 3.6.1alignTwoSequences, 2.32.1
access large sdf file, 2.29.81.24aligned residues, 2.30.128

     as table, 2.30.160.2appending, 2.29.1.1
     block length, 2.18.22     an element, 2.14.4
          secondary structure, 2.31.1     menu items, 2.23.10.1
     cleaning, 2.30.146.4     representations to a slide, 2.29.23.21
     color by property, 2.29.86.34     rows to matrix, 2.29.1.2
     coloring, 2.21.1area under curve, 2.32.21
     conservation, 2.32.8arguments, 2.29.61
     distance, 2.30.137.13arithmetic operations, 2.14.2
     editor, 2.4arithmetics, 2.14
     extraction, 2.30.5aromatic planes, 2.32.4
     gap format, 5.1.1.1array, 2.29.69.4, 5.1.6, 5.7.3.1
     intro, 1.4.3.4     assignment, 2.14.1
     projection, 2.30.156, 2.30.156.5, 2.30.156.6     derivative, 2.30.146.1
     score, 2.30.136.7     overlap, 2.30.136.1
     sequence reordering, 2.30.5     parray, 2.29.22.31
     strength, 2.30.122.5     size, 2.30.102
     structural, 2.29.3.5, 2.30.5     subset, 2.6
     to sequence transfer, 2.30.122.1arrow from selection, 2.32.36
          text conversion, 2.30.156.4     length, 2.29.86.26
     weighted, 2.30.5as2_out, 2.24.14
     gapExtension, 2.19.18as_, 2.8.8
     gapOpen, 2.19.19as_graph, 2.23.5.50, 2.23.5.51, 2.30.137.5
alignment_as_text, 2.30.156.4as_out, 2.24.13
aliphatic amines, 2.29.67.2assign, 2.29.5
all, 5.1.2     residue, 2.29.6.1
     torsions table, 3.3.11     ring conformation to template, 2.29.63.4
alpha, 2.23.5.57, 2.29.86.42, 5.1.3     sstructure, 2.29.5.1
     channel, 2.23.9.10          segment, 2.18.20, 2.29.5.2
alternative flag, 2.29.86.18assignment, 2.14.1
amber, 5.1.4atc code, 2.30.44.6
amino acid, 2.21.24, 2.30.172, 2.30.173atom, 2.29.13.1, 5.1.7
          colors, 2.30.29.3     centers within, 2.30.151
          labels, 2.29.3.2     code file, 2.33.4
and, 2.14.3     coordinates, 2.30.192.1
angle rotation, 2.32.84     flickering, 2.29.86.3
angles, 2.30.102.3     label font, 2.33.15
angular hbond dependence, 2.23.5.26     labels, 2.29.86.2
animated story, 5.8.14     name, 2.29.3.1, 2.30.79
animation, 2.29.23.5, 2.29.23.6, 3.9     pairs, 2.29.86.68, 2.29.86.69, 2.30.160.10
annotation, 2.29.22.26, 2.29.86.26, 2.29.86.27     proximity to surface, 2.29.87.9
apf, 3.15     selection by number, 2.30.66.4
append, 5.1.5     type, 2.30.182
     a tables, 2.29.1.4     user field, 2.30.54.1
     column, 2.29.4.3atomLabelStyle, 2.22.4
     command, 2.29.4atomSingleStyle, 2.22.5
     sequence, 2.29.4.1atomic contributions, 2.29.87.20, 2.29.87.21
          to group, 2.29.4.1     coordinate transfer, 2.29.86.3
     stack, 2.29.4.2     property fields, 3.15
     tables, 2.29.50     solvation contributions, 2.30.7
          by shared column, 2.29.4.3     in residue, 2.30.63

     selecting, 2.8.8brightness, 2.23.5.33
     translate, 2.29.86.3build, 2.29.7
attenuation by occupancy, 2.29.62.25     atom, 2.29.7.1
auc enrichment, 2.32.21     column, 2.29.7.2
auto saving log, 2.22.11     faq, 3.8.1
autoSavePeriod, 2.18.1     from string, 2.29.7.8
avi, 2.29.107.31     helix, 3.10.5
axis, 5.1.8     how to, 3.8.1
axisLength, 2.19.4     hydrogen, 2.29.7.9
background, 2.30.29.2     loop, 2.29.7.6
     color, 2.19.9     model, 2.29.7.5, 2.29.107.9
ball, 2.29.86.2, 5.2.2     molcart, 2.29.7.10
base, 5.2.1     sequence, 2.29.7.3
     pair diagram, 2.23.5.16     smiles, 2.29.7.7
basis set, 2.29.81.21, 2.29.107.17     string, 2.29.7.8
batch chemical processing, 3.1.2.5     tautomer, 2.29.7.4
     docking, 3.13.2.5built-in functions, 5.5.5
beta, 5.2.3     plot, 2.29.86.53
bfactor circles, 2.23.5.3     atoms, 2.29.14
biased probability monte carlo, 2.29.68     contact surface, 2.29.14
binary file table of contents, 2.29.81.2     molecule, 2.29.13.1
     files, 2.29.107.2     number of bonds, 2.30.137.3
     string, 5.2.4     variables, 2.29.14
     key, 2.29.86.43cage, 2.32.4
binding energy, 3.7.4calcArea, 2.32.2
     pocket finding, 3.4.2calcBindingEnergy, 2.32.3
     pockets, 2.29.89.1calcDihedralAngle, 2.32.4
     side comparison, 2.32.8calcEnergyStrain, 2.32.20
     site analysis, 3.4.2calcEnsembleAver, 2.32.5
biological symmetry, 2.29.86.9calcMaps, 2.32.6
     vector, 2.30.66.3calcPairSeqIdsFromAli, 2.32.7
     to integers compression, 2.30.66.3calcPepHelicity, 2.32.9
blast, 2.29.107.25calcProtUnfoldingEnergy, 2.32.10
     files, 2.29.107.25calcRmsd, 2.32.11
blast-formatted database, 2.29.35.3, 2.29.107.25calcRoc, 2.32.21
blending, 2.29.107.31calcSeqContent, 2.32.12
     images, 2.30.158.2calcSeqSimilarity, 2.32.8
blob, 5.2.4calculate phases, 3.11.2
bold, 2.29.86.38.1call, 2.29.8
bond angle bending, 2.33.5canonical form, 2.30.45
     errors, 2.29.87.12carboxylic acid, 2.29.67.2
     stretching, 2.33.6cartesian cooridnates, 2.30.192
     to protein, 2.29.69.3cartridge, 3.5
     width, 2.23.9.14cavities, 2.29.89.1
bonded atoms, 2.30.101.1cavity, 5.3.1
born radii, 2.29.87.9     analysis, 3.3.13
boundary element, 5.2.5ccp4 maps, 2.29.81.27
          matrix, 2.30.90.10cd, 2.29.86.21
box, 2.30.21cell axis vectors, 2.30.192.8
break, 2.29.6     specific icm commands, 5.9.2.4

cgi programming with icm, 2.11     text format, 5.6.11
chain breaks, 2.23.5.7, 2.23.5.8, 2.30.137.1     topological descriptors, 2.30.40
     symbol, 2.29.86.9     view, 2.29.86.54
change atom position, 2.29.86.3chemistry, 2.25, 2.30.27
     sequence position in multiple alignment, 2.29.69.7chiral isomer generation, 2.29.30
     unix directory, 2.29.86.21chirality, 2.20.16, 2.29.30
changing local stick radii, 2.29.86.86choosing ligands, 3.13.1.2
     surface dot size, 2.23.5.54chroma, 2.30.90.4
channel, 2.23.14.2cif, 2.29.81.48
charge, 2.23.14.4, 5.3.2circular permutation of coordinates, 2.29.66
     compounds, 2.29.67.2clamp values to range, 2.30.178
     prediction, 2.29.86.11, 2.29.86.12clashThreshold, 2.19.5
     state, 2.29.29clashes, 2.29.62.16
     change, 2.29.86.10     labels, 2.30.166
chem formula, 2.30.156.10classification, 2.30.44.6
chemSuper3D, 2.32.22clear, 2.29.10
chemical, 2.23.14.7, 2.25, 2.29.35.9, 2.30.69     graphical selection, 2.29.10
     2D drawings, 2.29.62.9     screen, 2.29.10
     SMARTS search, 2.29.35.5click and lock, 5.9.2.4
     atom annotation, 2.29.22.20clipping plane, 2.23.5.9, 2.23.5.10, 2.23.5.11, 2.29.69.6, 5.3.3
     database, 3.5closer than threshold, 2.30.44.9
     decomposition, 2.29.62.27, 2.29.89.2, 2.29.89.3closest sequence, 2.30.99.3
     descriptors, 2.30.41, 5.7.12     value, 2.30.56.1
     distance, 2.30.44.8, 2.30.136.2, 2.30.136.3cluster, 2.30.154.1
     diversity, 3.14.6.4     center, 2.30.70.9
     drawing, 2.23.9.14     centers, 2.13.1
          quality, 2.23.9.15     selection, 2.30.70.9
     fingerprints, 2.9     tree, 2.30.99.5
     formula, 2.30.156.10          size, 2.30.102.1
     fragment counting, 2.30.102.2clustering, 2.13, 2.29.62.37, 2.29.62.38, 2.29.89.7
     keys, 2.29.62.21clusters, 2.13, 2.13.1
     match coordinates, 2.30.192.6cnMethodAverage, 2.22.6
     matching, 2.29.35.4, 2.29.81.49, 2.29.81.50, 2.30.133, 2.30.155cnWeight, 2.19.6
     models, 2.30.99.1code, 2.30.44.6
     modification, 2.29.65, 2.29.67, 2.32.37coil, 5.3.4
     name, 2.30.99.6collection, 2.12, 5.3.6
     normalization, 2.29.67color, 2.23.5.33, 2.29.11
          rules, 2.29.67.4     accessibility, 2.29.13
     pattern, 2.26, 2.29.85.1     background, 2.29.13.2
          search, 2.30.56.3          example, 3.2.7
     reaction product generation, 2.29.62.33          accessibility, 3.2.11
     search, 2.29.35.10, 2.29.85.1, 2.30.102.2          alignment, 2.29.13.3
     similarity, 3.5          atom contributions, 2.29.12
     simplification, 2.30.178          bfactor, 3.2.9
     spreadsheet, 2.29.12, 2.29.81.48, 2.29.81.49, 2.29.81.50, 2.29.86.47, 2.29.107.11          charge, 3.2.12
     structure from smiles, 2.29.86.7          electrostatic potential, 2.18.5
     substructure, 2.29.35.4          hydrophobicity, 3.2.10
          mask, 2.29.62.21          pharmacophore, 2.29.12
     superposition, 2.22.7, 2.30.133, 3.15          potential, 2.32.25
     table, 2.25          shape depth, 2.29.13

     choice, 2.19.9compareMethod, 2.22.7
     file, 2.33.15comparing two sarrays, 2.30.105
     grob, 2.29.13.4comparison, 2.30.70.10
          by atom selection, 2.29.13.4.3     operations, 2.14.5
               atoms, 2.23.7.1complete view, 2.30.144
          map, 2.29.13.4.4compound accessibilities, 3.14.4.1
          matrix, 2.29.13.4.2     array, 2.25
          potential, 2.29.13.4.5     property prediction, 2.29.51.2
          unique, 2.29.13.4.1compress, 2.29.15
     label, 2.29.13.5     alignment, 2.29.15.1
     map, 2.29.13.6     binary, 2.29.15.4
          by value, 2.29.23.16     conf, 2.29.15.3
     molecule, 2.29.13.1     grob, 2.29.15.2
     names, 2.30.29     in place, 2.29.15.4
     object, 2.29.11.2     objects, 2.29.15
     preference, 2.19.10     stack, 2.29.15.3
     specification, 2.29.11.1compressed table view, 2.29.86.24
     surface by conservation, 2.29.13.3conditional buttons, 5.5.5
     table, 2.30.29.3     string, 2.30.156.7
     volume, 2.29.13.7conf, 2.29.86.61, 2.29.107.41, 2.30.160.6, 5.3.12, 5.8.9
column, 5.3.5     data, 2.30.160.6
     correlation, 2.29.88.3confgen, 3.16
     function, 2.29.7.2configuration, 2.33.14
     names, 2.29.82.1, 2.29.85.2     file, 2.29.107.42
     of grobs, 2.30.109     memory usage, 2.18.7
     selection, 2.30.99conformation comparison, 2.22.7
combinatorial compounds, 2.30.27conformational ensemble, 2.29.7.5.2
     libraries, 2.29.62.33, 2.30.102.4     generator, 2.29.63.1, 3.16
     PDB, 2.32.92     interpolation, 2.29.23.6
     transformations, 3.10.4     stack, 2.29.107.41, 5.3.12, 5.8.9
combining plots, 2.29.62.32          compression, 2.29.15.3
     receptor and ligand stacks, 2.29.4.2          file, 2.33.7
command, 2.30.99.4, 5.3.10     transition, 2.32.38
     line editing, 2.2conformer storage, 2.29.60.5, 2.29.91.2
          help, 2.29.45conformers, 3.16
          options, 2.1connect, 2.29.16
     word list, 3.1.5     chains with alignments, 2.29.54
commands, 2.22.11, 5.1.1     molcart, 2.29.16.1
communication protocols, 2.27consensus, 2.19.7
comp, 2.30.105     coloring, 2.19.12, 2.23.2
comp_matrix, 2.29.86.20, 2.29.87.16, 5.3.11     definitions, 2.23.1
compare, 2.18.12, 2.18.15, 2.29.14consensusStrength, 2.19.7
     angles, 2.29.14.2conservation, 2.30.122.5, 2.30.136.7
     atom, 2.29.14.1constant, 2.5
     by rmsd without superposition, 2.29.14.1constants, 2.5
     chemical tables, 2.29.35.10contact areas, 2.30.90
     patch only, 2.29.14.3continue, 2.29.17
     rmsd, 2.29.14.1contour lines, 2.30.32
     surface, 2.29.14.3     surfaces, 2.23.7.5
     variables, 2.29.14.2contouring density, 2.29.62.14

conversion, 5.1.6     symmetry transformation, 3.10.2
     to real array, 2.30.168          transformations, 2.30.176
convert, 2.29.18, 2.29.18.2, 3.13.2crystallographic cell, 2.29.66
     3D to chemical, 2.30.27     occupancy, 2.30.107
     3D/0D to 2D, 2.29.62.9     symmetry intro, 1.4.2.4
     ICM object to PDB, 2.29.93crystallography, 2.30.129
     and reroot, 2.29.18.4csv format, 2.29.81.44
     chemical 3D, 2.32.82csym, 1.4.2.4
               and optmimize geometry, 2.32.83cube, 2.23.14.2
     comp, 2.29.18.1current, 5.3.9
     comparison, 2.29.18.1     map, 5.3.7
     fragments, 2.29.18.2     object, 5.3.8
     mol, 2.29.18.3     working directory, 2.30.108
     object 3D and optmimize geometry, 2.32.85cursor action, 5.9.2.4
          macro, 2.32.13custom alignment color, 2.23.5.1
     pdb, 3.8.2     field, 2.29.86.51
     to 3D, 2.29.86.8     interaction, 2.29.87.37
          ICM object, 2.32.86     menu, 2.28, 2.29.81.3
          iarray, 2.30.166customization, 3.1.2
          icm-object, 2.29.18     environment, 2.28
          integer, 2.30.166     and paste chemicals, 2.23.9.14, 2.23.9.15
convert2Dto3D, 2.32.85cyclic temperature protocol, 2.19.46
convert3Dto3D, 2.32.86cylinder, 2.23.14.2
convertObject, 2.32.13cz32, 4.5
converting a chemical, 2.29.18.3data visualization, 2.29.62.38
          pdb-chemical, 3.13.2database, 5.4.1
     alignment to table, 2.30.160.2     browser, 2.29.60.3
     chemicals, 3.13.2.3     connection, 2.29.16.1
     table columns into matrix, 2.30.90.6     file, 3.5.1
     to, 2.30.123     import, 2.29.62.26
cool, 2.32.40date, 2.29.21, 2.30.156.2
     pictures, 2.23.5.30     array, 2.29.21
cooling schedule, 2.19.46dcMethod, 2.22.8
coordinate frame, 2.19.4, 2.29.23.4dcWeight, 2.19.8
coordinates, 2.23.14.7decomposition, 2.29.62.27, 2.29.89.2, 2.29.89.3
copy, 2.29.19defCell, 2.24.1
     chemical image, 2.23.9.15defSymGroup, 2.18.2
     file, 2.21.26default atom colors, 2.29.86.16
     site, 2.29.86.28     color of label, 2.19.11
correlation matrix, 2.30.163     parameters, 2.22.1
covalent bound count, 2.30.137.3     value, 5.8.2
     neighbors, 2.30.101.1define axis, 3.10.3
covalently attached molecule, 2.30.101.1defining space box, 2.30.21
cpk, 2.19.35, 5.3.13dehtml, 2.30.126.3
create a covalent bond, 2.29.62.2del, 2.29.22.9
     pharmacophore, 2.32.87delete, 2.29.22
creating a local patch object, 2.29.18.2     3D graphics panel, 2.29.102
credits, 4.5     alias, 2.29.22.2
crypt, 2.29.20     array element, 2.29.22.6
crystal axis vectors, 2.30.16          index, 2.29.22.6

     atom, 2.29.22.7delphi, 2.32.25
     bond, 2.29.22.14density correlation, 2.19.8, 3.11.3
     boundary, 2.29.22.15     fitting, 2.22.8
     chemical, 2.29.22.37     in unit cell, 2.29.62.23
          fragment, 2.29.22.37densityCutoff, 2.19.13
          selection, 2.29.22.37dependent columns, 2.29.1.1.1
     class, 2.29.22depth cueing, 2.29.13.7, 5.4.2
     column table, 2.29.22.16depth-cueing, 2.19.17
     conf, 2.29.22.17desolvation, 2.22.25
     directory, 2.29.22.8detecting bad covalent geometry, 2.29.87.12
     disulfide bond, 2.29.22.27     proximity, 2.30.44.9
     drestraint, 2.29.22.18dialog generation, 2.30.11
     element, 2.29.22.31     in html documents, 2.29.44
     file, 2.29.22.9          tables, 2.29.44
     from array, 2.29.22.6     scripting, 2.30.11
     hydrogen, 2.29.22.11dielConst, 2.19.14
     label, 2.29.22.19, 2.29.22.20dielConstExtern, 2.19.15
          chemical, 2.29.22.20dielectric constant, 2.19.14
     link, 2.29.22.21diff, 2.30.105
     map, 2.29.22.22dihedral, 2.32.4
     molcart, 2.29.22.3     angle, 2.29.62.19
     molecule, 2.29.22.13          calculation, 3.3.10
     object, 2.29.22.12directory, 2.29.22.8, 2.29.62.5, 2.30.135
     parray, 2.29.22.36display, 2.29.23
          element, 2.29.22.36     GUI window, 2.29.23.26
     peptide bond, 2.29.22.28     box, 2.29.23.7
     plot, 2.29.22.4     clash, 2.19.5, 2.29.23.8
     salts, 2.29.67.3     contact, 2.29.62.16
     selection, 2.29.22.5     drestraint, 2.29.23.9
     selftether, 2.29.22.34     field, 2.23.5.3
     sequence, 2.29.22.23     from script, 2.29.23.3
     session, 2.29.22.10     gradient, 2.29.23.10
     shell object, 2.29.22.1     grob, 2.29.23.11
     site, 2.29.22.24          label, 2.29.23.12
          alignment, 2.29.22.26     gui, 2.29.23.26
     sstructure, 2.29.22.25     hbond, 2.29.23.13
     stack, 2.29.22.29     label, 2.29.23.15
          object, 2.29.22.30     map, 2.23.5.13, 2.29.23.16
     system, 2.29.22.9     model, 2.29.23.1
     table, 2.29.22.32     new, 2.29.23.2
          rows, 2.29.22.32     off-screen, 2.29.23.3
     term, 2.29.22.33     offscreen, 2.29.23.3
     tether, 2.29.22.35     origin, 2.29.23.4
     tree, 2.29.22.36     ribbon, 2.29.23.18
     variable, 2.29.22.6     rotate, 2.29.23.5
     views, 2.29.22     site, 2.29.23.19
     backbone, 2.30.137.1     skin, 2.29.23.20
     restraint, 2.29.22.18     slide, 2.29.23.21
deleting, 2.29.22.26     stack, 2.29.23.6
     sites by number, 2.29.22.24     string, 2.29.23.22

          area, 2.23.5.3dsPropertySkin, 2.32.19
     tethers, 2.29.23.23dsPrositePdb, 2.32.24
     trajectory, 2.29.23.17dsRebel, 2.18.5, 2.23.14.6, 2.32.25
     volume, 2.29.23.24dsSeqPdbOutput, 2.32.26
     window, 2.3, 2.29.23.25dsSkinLabel, 2.32.27
distance, 2.23.5.24, 2.30.41, 5.4.3dsStackConf, 2.32.29
     averaging, 2.22.6dsVarLabels, 2.32.30
     contact-based, 2.30.23, 2.30.23.1dsXyz, 2.32.32
     geometry, 5.4.4dump database, 2.29.107.7
     matrix, 2.30.160.5, 2.32.7dynamic gui, 5.5.5
          between stack conformations, 2.30.90.11ecepp, 5.5.1
     restraint, 5.4.6edit, 2.29.24
          file, 2.33.9     files, 2.23.14.1
          type file, 2.33.8eigen value factorization, 2.30.45
     restraints, 2.29.86.22eigendecomposition of a matrix, 2.30.45
distances, 2.30.102.3eigenvalues, 2.30.45
distribution, 1.3eigenvectors, 2.30.45
     comparison, 2.30.136electro intro, 1.4.2.9
disulfide bond, 5.4.5electroMethod, 2.22.9
diverse subset, 3.14.6.4     density, 2.23.7.5, 2.29.86.36, 2.29.87.21, 2.32.42, 2.32.43
dividing chemical into individual molecules, 2.30.154.4          around selection, 2.19.25
dna to protein sequence translation, 2.30.175.1          map generation, 2.19.1
     translate, 2.30.175.1          maps, 2.23.14.1
dockScan, 3.13.2.5electrostatic boundary matrix, 2.30.90.10
docking, 2.32.89     coloring, 2.23.14.6
     intro, 3.13.2.1     isopotential surfaces, 2.29.62.13
     result viewing, 2.32.28     potential, 2.29.13.4.5
     simple models, 3.14.3     solvation, 3.7.2
     timing, 3.13.1.3     surface, 2.32.25
     with template, 3.13.2.6     troubleshooting, 5.7.13
documents, 5.5.8electrostatics, 2.23.14.6
dollar separated file, 2.29.81.44     intro, 1.4.2.9
dominant color, 2.30.29.2ellipsoid, 2.30.163
donor, 3.6.1elseif, 2.29.25
     plot intro, 1.4.3.2empty model, 2.30.109
dots, 2.29.75endfor, 2.29.26
dotted surface, 2.23.5.56endif, 2.29.27
double click action, 5.9.2.4endmacro, 2.29.28
drestraint, 2.29.87.18, 5.4.6endwhile, 2.29.33
     generate from structure, 2.29.62.7energetics, 3.7
     global weight, 2.19.6     function, 2.23.14.3
     set, 2.29.86.22     profile, 2.32.84
     type, 5.4.7     terms, 2.17
drop, 2.19.16ensemble, 2.29.60.1, 2.29.91.1
drug, 2.12     average, 3.7.5
ds3D, 2.32.31entropy of alignment, 2.30.136.7
dsCellBox, 2.32.15     atom, 2.29.18.4
dsChem, 2.32.17enumerate, 2.29.29, 2.29.30, 2.29.31, 2.29.32
dsCustom, 2.32.18     charge, 2.29.29
dsPocket, 2.32.28     chiral, 2.29.30

     tautomer, 2.29.31fasta, 2.23.12.15, 5.5.2
enumeration, 2.30.27     format, 2.29.107.1
eps files, 2.21.23feature table, 5.8.6.1
equipotential surface, 2.30.32     in sequences, 2.29.86.26
error SOAP services, 2.30.49ffMethod, 2.22.12
     ignoring, 2.21.25field, 2.29.86.35
error/warning bits cleanup, 2.29.10     name, 2.30.99.2
errorAction, 2.22.10file, 2.29.107.24
     vrestraint vs_var, 2.29.86.82     exists, 2.30.50
evalSidechainFlex, 2.32.90     list, 2.30.59
evol tree intro, 1.4.3.5     length, 2.30.55
evolutionary tree intro, 1.4.3.5     object origin, 2.30.55
exact, 2.29.35.9, 2.29.35.10     permissions, 2.30.55
     match, 2.30.126.1     time modified, 2.30.55
example scripts, 3.14     type, 2.30.55
excel, 2.29.81.44files, 2.33
exit, 2.29.34filling volume, 2.23.5.11
exitSeslogStyle, 2.22.11filter, 2.29.35.10, 2.29.60.3
expanding substructure match, 2.29.86.70     functions, 5.5.4
export, 2.29.107.7filtering table rows, 5.5.4
     animation, 2.29.107.31find, 2.29.35
     pdb, 2.23.14.14     alignment, 2.29.35.1
exporting sdf, 2.29.107.11     and replace a chemical pattern, 2.29.67.1
expression shortcuts, 2.10.1.2               chemical fragment, 2.29.67
     tags, 2.24.9     chemical, 2.29.35.5
     comparison, 2.14.5          pattern, 2.29.67
     arithmetics, 2.14.2          substructure, 2.30.70.2
     assignment, 2.14.1     database, 2.19.2, 2.29.35.2
     comparison, 2.14.5          fast, 2.29.35.3
     logical, 2.14.3     family of commands, 2.29.35
extending to bonded hydrogens, 2.30.137.6     in sarray, 2.30.70.8
               terminal atoms, 2.30.137.6     molcart, 2.29.35.9, 3.5
external process, 2.29.62.1     molecule, 2.29.35.4
extracting from Markush, 2.29.52     motifs, 2.24.9
     icm script arguments, 2.30.59     pattern, 2.29.35.8
     stack from object, 2.29.60.5     pdb, 2.29.35.6
ez25, 3.7     pharmacophore, 2.29.35.11
factor, 5.8.13     prosite, 2.29.35.7
false negatives, 2.30.136.4     scaffold, 2.30.179
family, 2.29.86.38.1     table, 2.29.35.10
faq, 1.3findFuncMin, 2.32.33, 2.32.34
     cheminformatics, 3.14.6findFuncZero, 2.32.35
     chemsuper, 3.14.5findSymNeighbors, 2.32.16
     mac gui preferences, 3.14.6.2find_related_sequences, 2.32.33
     molcart dump, 3.14.6.3finding long covalent bonds, 2.30.137.1
          query, 3.14.6.1fingerprint, 2.30.41
     multiple chem overlay, 3.14.5.1fingerprints, 2.9
     residue table, 3.14.4.1     to density, 2.22.8
fast Fourier transform, 2.29.62.24fix, 2.29.36
     sequence search, 2.29.35.3fixed branches, 2.30.137.2

flexible superimpose, 2.32.50graph matching, 2.30.133
flow control, 2.15graphical box, 2.29.23.7
fog, 2.19.17, 2.29.13.7, 2.29.23.24, 5.4.2     row selection, 2.30.70.5
     color, 2.19.17     selection, 2.30.137.5
fogStart, 2.19.17graphics, 2.19.9, 2.29.86.4, 2.30.188, 3.2, 5.3.3
fold search, 5.8.4     card, 2.23.5.52
foldbank.db, 2.33.3     controls, 2.3, 2.33.15, 5.4.2
folding procedure, 3.14.1     exists, 2.30.50
font, 2.29.55.1     intro, 1.4.1, 1.4.1.4
     size, 2.29.86.38.1, 2.33.14     learning, 3.2.1
     sizes, 3.14.6.2     attributes, 2.19.4
     specification, 2.29.86.38.1     fogStart, 2.19.17
for, 2.29.37     view vector, 2.29.86.80
fork, 2.29.38, 2.30.70.1graphviz, 2.30.160.7
formal charge, 2.23.5.20, 2.29.86.12, 5.3.2greedy matching, 2.10.1.4
formatdb, 2.29.107.25grid energy, 2.29.87.21
fprintf, 2.29.39     potentials, 2.29.62.25
fractional coordinates, 2.30.192.4grob, 5.5.3
     to abs coordinates, 2.30.16     coloring, 2.29.13
fragmented molecule, 2.29.18.2     files, 2.33.10
frame, 2.29.91, 2.29.107.31     inside-out flip, 2.29.86.42
fullscreen, 2.29.86.85     normal directions, 2.29.86.42
function, 2.29.40, 2.29.61     vertex, 2.23.5.21
     columns, 2.29.1.1.1     translate, 2.29.100
functions, 5.1.1group, 2.29.43
     selecting in objects, 2.8.10     by column, 2.29.43.4
gamess, 5.5.6     column, 2.29.43.4
     expansion, 2.30.146.4     rename of table columns, 2.29.82.1
gapExtension, 2.19.18     replacement, 2.29.65
gapFunction, 2.24.3     select of table columns, 2.29.85.2
gapOpen, 2.19.19     sequence, 2.29.43.1
gaussian averaging, 2.30.146.2          unique, 2.29.43.2
gcMethod, 2.22.13     table, 2.29.43.3
genbank, 2.23.12.15grouping table by a column, 2.29.86.24
generalized arrays, 5.1.6gui, 2.29.44, 5.9.2.4
generate intermediate conformers, 2.32.38     exists, 2.30.50
generating movie images, 3.9.2.1     functions, 5.5.5
genomics, 1.4.3.1     panels, 2.29.102
     clustering, 2.29.43.2     programming, 2.28, 2.29.44, 2.29.86.24
     intro, 1.4.3.1gvim text editor, 5.8.2
geometry optimization, 2.29.63.1gzip files, 2.29.15.4
     started, 1.7hash, 2.12, 5.3.6
getting data from outside, 2.27     table, 5.3.6
     started, 1.7haze, 2.19.17
global, 2.29.41hb, 2.19.21
glossary, 5hbCutoff, 2.19.21
go, 2.30.44.6hbond, 2.23.5.25, 2.23.5.26, 2.29.22.6, 5.5.7
goto, 2.29.42     color, 2.29.23.14
     term, 2.19.20, 2.29.86.73     display, 2.23.5.27, 2.23.5.28
gpWeights, 2.19.20     energy, 2.29.23.14

     show, 2.29.87.23hydrophobicity 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, 2.29.1.1iarray, 2.29.22.6, 2.30.56.1, 2.30.66.2, 2.30.70.8, 5.6.1
helical axis, 2.32.36     making, 2.30.66.1
     cylinders, 2.23.5.42icb files, 5.8.14
helicity, 3.7.6     GUI, 2.29.86.40
     content calculation, 3.7.6     algorithms, 4.3
help, 2.29.45, 2.29.45.1, 2.29.45.2     application refs, 4.4
     browser, 2.29.45.1          literature, 4.3
     commands, 2.29.45.3     archive, 2.29.81.2
     functions, 2.29.45.4     arguments, 2.30.59
     getting, 3.1.1     binary, 2.30.108
     word, 2.29.45.2     branching, 2.15.2
     getting, 3.1.1     commands, 2.29
heterogenous environment, 2.23.14.2     controls, 2.15
hidden blocks, 5.1.1.1     flags, 2.1
     display, 2.29.23.3     functions, 2.30
     hydrogens, 2.23.5.32     graphics, 3.2
     stack in object, 2.29.91.2     history, 1.2
hierarchical, 2.13     jumps, 2.15.3
highEnergyAction, 2.22.14     learning, 3.1.4
his-tags, 2.30.180     loops, 2.15.1
histogram, 2.29.62.32     macros, 2.32
     2D, 2.30.90     main refs, 4.2
history, 2.29.46, 2.29.107.40     menus, 2.23.10.1
     delete, 2.29.22.10     method literature, 4.4
     of ICM, 1.2     molecules, 2.16
homodel, 2.32.41     object file, 2.33.18
homology modeling, 1.4.2.2, 2.29.7.5, 2.29.86.68, 2.29.86.69, 2.31.1, 3.14.4     preferences, 2.22.1
          faq, 3.14.4     session, 2.22.11
          intro, 1.4.2.2     shell, 3.1
     output, 2.29.7.5.3          functions, 2.31
     steps, 2.29.7.5.1     support, 1.3
     to export a molcart table, 3.14.6.3     table, 2.23
html, 2.11, 2.29.44, 2.30.99.4, 5.5.8     ali, 2.33.31
     document order, 2.29.86.40     all, 2.33.32
     tag removal, 2.30.126.3     bbt, 2.33.5
html-formatted text, 5.5.8     bst, 2.33.6
html5, 2.11     cfg, 2.33.14
hue, 2.30.90.4     clr, 2.33.15
hydration, 2.23.14.2, 2.30.7     cmp, 2.33.33
     parameters, 2.33.13     cn, 2.33.9
hydrogen bond, 2.23.5.25, 2.23.5.26, 2.29.62.17, 5.5.7     cnf, 2.33.7
     bonding parameters, 2.33.12     cnt, 2.33.8
          cutoff, 2.19.21     cod, 2.33.4
     bonds, 2.30.102.3     col, 2.33.24
     display, 2.23.5.32     gro, 2.33.10
     placement, 2.29.86.25     gui, 2.28

     hdt, 2.33.13          entry, 2.30.135.1
     htm, 2.33.11          sdf-file path, 2.30.108
     iar, 2.33.35indices of labeled table rows, 2.30.70.6
     lps, 2.29.7.5.2          selected table rows, 2.30.70.5
     map, 2.33.16infinity, 2.30.168
     mat, 2.33.37info, 2.29.48
     ob, 2.33.18     molcart, 2.29.48.1
     pdb, 2.33.28inner join, 2.29.50
     prf, 2.33.34insert rows, 2.29.1.4
     rar, 2.33.38integer, 5.6.2
     res, 2.33.20     array, 2.30.66, 5.6.1
     rs, 2.33.23     output, 2.18.4
     rst, 2.33.22     shell variables, 2.18
     sar, 2.33.36intensity, 2.30.90.4
     se, 2.33.30interaction cutoff, 2.20.27
     seq, 2.33.29     lists, 2.20.27, 2.23.14.3
     tab, 2.33.25interactive docking, 1.4.2.8
     tot, 2.33.26interatomic distance, 2.19.10, 2.29.62.16, 2.30.151
     trj, 2.33.17     potential, 2.29.86.51, 2.29.87.37
     var, 2.33.21interface comparison, 2.29.14.3
     vwt, 2.33.27     residues, 3.3.5
icmCavityFinder, 2.32.14     torsions, 3.3.7
icmMacroShape, 2.32.88     view, 2.32.28
icmPmfProfile, 2.32.23intermolecular bond, 2.29.69.3
icmPocketFinder, 2.32.89internal coordinate file, 2.33.21
icmscript, 2.29.81.4     coordinates, 2.8.9
     arguments, 2.30.59     positional restraints, 5.9.4
if, 2.29.47interplanar angle, 2.32.4
ignoring swiss secondary structure, 2.24.10interpolate, 2.30.29.1
illegal smiles, 2.30.70.2interpolation, 2.30.29.1
image, 3.2.6interruptAction, 2.22.15
     annotation, 3.2.5inverting array order, 2.30.66.2, 2.30.122.2
     center, 3.2.8italic, 2.29.86.38.1
     format, 5.9.3iterative overlay, 2.29.94
     high quality, 3.2.2     superposition, 2.23.14, 2.29.95
     parray, 5.7.3.3javascript, 2.11
     resolution, 3.2.2join, 2.29.50
     rotation, 3.2.3     tables, 2.29.50
implicit continuous solvation, 2.33.13keep, 2.29.49
     solvation, 2.29.86.72kernel models quality, 2.30.136.4
imposing tether, 2.29.86.68, 2.29.86.69     mapping, 2.33.15
     place, 2.14.4kmz, 5.5.3
          ops, 2.14.4l_antiAlias, 2.20.1
incidence, 2.30.90.13l_autoLink, 2.20.2
increasing the number of shell variables, 2.33.14l_bpmc, 2.20.3
increment charge, 2.29.86.10l_breakRibbon, 2.20.4
index expressions, 2.6l_bufferedOutput, 2.20.5
     in array, 2.30.70.4l_bug, 2.20.6
     substring, 2.30.70.3l_caseSensitivity, 2.20.7
     table, 2.29.107.24l_commands, 2.20.8

l_easyRotate, 2.20.10     group, 2.29.52
l_info, 2.20.11     internal variables of molecular object, 2.29.53
l_minRedraw, 2.20.12     ms2ali, 2.29.54
l_neutralAcids, 2.20.13     sequences to 3D objects, 2.29.54
l_out, 2.20.14     to alignment, 2.29.54
l_print, 2.20.15     variable, 2.29.53
l_racemicMC, 2.20.16     variables, 2.29.53
l_readMolArom, 2.20.17linked alignment, 2.30.99
l_showAccessibility, 2.20.18     sequence, 2.30.99
l_showMC, 2.20.19linux shell, 2.29.96, 5.10.2
l_showMinSteps, 2.20.20list, 2.29.55
l_showResCodeInSelection, 2.20.21     binary, 2.29.56
l_showSites, 2.20.23     database, 2.29.57
l_showSpecialChar, 2.20.22     directory, 2.29.58
l_showSstructure, 2.20.24     font, 2.29.55.1
l_showTerms, 2.20.26     html documents, 2.30.99
l_showWater, 2.20.25     molcart, 2.29.59
l_updateLists, 2.20.27          database, 2.29.59
l_warn, 2.20.28     of files, 2.30.135
l_wrapLine, 2.20.29     updates, 2.29.63
l_writeStartObjMC, 2.20.30listUpdateThreshold, 2.19.23
l_xrUseHydrogen, 2.20.31literature, 4.1
label, 2.29.23.22, 5.6.3load, 2.29.60
     fonts, 2.33.15     conf, 2.29.60.1
large text, 2.29.81.40     frame, 2.29.60.2
latent, 2.30.102.6     molcart, 2.29.60.3
learn, 2.29.51, 2.30.109     object, 2.29.60.6
     atom, 2.29.51.1     solution, 2.29.60.4
     chemical, 2.29.51.2     stack object, 2.29.60.5
left join, 2.29.50loadEDS, 2.32.42
     triangle of a matrix, 2.30.90.3loadEDSweb, 2.32.43
library to replacement groups, 2.29.62.27, 2.29.89.2, 2.29.89.3local, 3.5.1
ligand based screening, 3.15logarithm, 2.30.85
     binding, 2.32.28logical, 5.6.4
     dock faq, 3.13.2     operations, 2.14.3
     docking, 3.13, 3.13.1, 3.13.2     variables, 2.20
          intro, 1.4.2.6logical_ops, 2.14.3
     editing, 1.4.2.8logicals, 2.20
     editor, 2.32.37long axes, 2.30.163
     fit, 3.13loop database rebuilding, 2.29.107.28
     setting, 3.13.2     interrupt, 2.19.47
     view, 2.23.5.31     library, 2.29.7.5.2
light, 2.23.5.34     modeling, 1.4.2.3
lightness, 2.30.90.4          intro, 1.4.2.3
limits, 2.33.14     search, 2.29.7.5.2
line thickness, 2.23.12.5     resolution shape, 2.32.88
          in 2D chemicals, 2.23.9.14lower case, 2.30.167
lineWidth, 2.19.22ma29, 3.11
linear chemical notation, 2.26macro, 2.29.61, 5.6.5
     regression, 2.30.84macro_def, 5.6.5

     concepts, 3.10.1makeIndexSwiss, 2.32.45
make, 2.29.62makePdbFromStereo, 2.32.46
     3d label, 2.29.62.15makePharma, 2.32.87
     angle, 2.29.62.18makeSimpleDockObj, 2.32.47
     background, 2.29.62.1makeSimpleModel, 2.32.48
     blast index, 2.29.107.25making predictive models, 2.29.51
     bond, 2.29.62.2manual style, 1.5
          chain, 2.29.62.3map, 2.19.25, 2.23.5.13, 2.23.6.1, 5.6.6
          multi, 2.29.62.3     aa property to sequence, 2.30.122.1
     boundary, 2.29.62.4     averaging, 2.30.146.5
     directory, 2.29.62.5     calculation, 2.29.62.24
     distance, 2.29.62.16     conversion, 2.29.62.31
     disulfide bond, 2.29.62.6     file, 2.33.16
     drestraint, 2.29.62.7     fitting, 2.22.8
     factor, 2.29.62.8     format, 5.6.6
     flat, 2.29.62.9     mean value, 2.30.94
          chem_array, 2.29.62.9     min value, 2.30.95
     grob, 2.32.36     name, 2.30.86
          from image, 2.29.62.11     operations, 5.6.6
               matrix, 2.29.62.12     transformations, 2.30.146.5
          image, 2.29.62.11     trimming, 2.30.22
          map, 2.29.62.10     value sigma, 2.30.133
          matrix, 2.29.62.12          on atoms, 2.29.86.36
          potential, 2.29.62.13     contouring, 2.29.62.14
          skin, 2.29.62.14mapAtomMargin, 2.19.25
     hbond, 2.29.62.17mapSigmaLevel, 2.19.24
     image, 2.29.62.20mapping chemical equivalences, 2.30.70
     index fasta, 2.29.81.24, 2.29.107.24     properties to sequence, 2.30.122.4
     key, 2.29.62.21     and factors, 3.11
     map, 2.29.62.22margin, 2.23.6.1
          cell, 2.29.62.23mass-spectrometry functions, 2.29.30, 2.29.31, 2.29.32
          factor, 2.29.62.24matching chemicals, 2.30.70.2
          potential, 2.29.62.25     hydrogens, 2.29.86.70
          xray, 2.29.62.31matrix, 5.6.7
     molcart, 2.29.62.26     derivatives, 2.30.80
     molsar, 2.29.62.27     new, 2.30.90.1
     pca, 2.29.62.29     plot, 2.30.32
     peptide bond, 2.29.62.30     map value, 2.30.91
     plot, 2.29.62.32maxColorPotential, 2.18.5, 2.32.25
     reaction, 2.29.62.33maxMemory, 2.18.7
     sequence, 2.29.62.35, 2.29.62.36     movie, 3.9.2
          alignment, 2.29.62.34mcBell, 2.19.26
          from alignment, 2.29.62.34mcJump, 2.19.27
          random, 2.29.62.36mcShake, 2.19.28
     torsion, 2.29.62.19mcStep, 2.19.29
     tree, 2.29.62.37mean force, 2.29.86.51, 2.29.87.37
          object, 2.29.62.38median value, 2.30.93
     unique, 2.29.62.39membrane, 2.23.14.2
makeAxisArrow, 2.32.36memorizing positions, 3.2.4
makeIndexChemDb, 2.32.44menu, 2.29.64

merge PDB, 2.32.92     and reroot, 2.29.18.4
     arrays to table, 2.29.43.3     chem, 2.29.67
     continuation lines, 2.29.81.39          charge, 2.29.67.2
     objects, 2.29.69.2          delete salt, 2.29.67.3
     parts of molecule, 2.29.69.3          normalize, 2.29.67.4
     pdb, 3.4.4     chemical column, 2.29.67.3
     sarray into string, 2.30.158          find replace, 2.29.67.1
     stacks, 3.7.7     molcart, 2.29.67.5
     tables, 2.29.4.3, 2.29.50     rotate, 2.29.66
merge2, 3.8.7modifyGroupSmiles, 2.32.37
mergePdb, 2.32.92modules, 1.4.4
     several chemical, 2.30.158.1mol, 2.29.81.49, 2.29.81.50, 2.29.107.11, 2.29.107.24, 5.6.11
merging into one molecule, 2.29.69.3     file, 2.30.156.3
mesh, 2.30.109, 2.30.189     to icm, 2.29.18.3
     point radius, 2.23.5.21     translation, 3.2.4
     score, 3.13.3.3mol-file to chem-table element, 2.30.109
mfMethod, 2.22.16mol-format, 2.23.14.7
mfWeight, 2.19.30mol2, 5.6.12
mimel, 5.6.8molcart, 2.29.16.1, 3.5
mimelDepth, 2.19.31     connection options, 3.5.2
mimelMolDensity, 2.19.32molecular, 2.30.58, 5.7.3.1
minNumGrad, 2.29.63     arrays, 5.7.3
minTetherWindow, 2.18.8     manipulations, 3.8
minimization exit criteria, 2.29.63     modifications, 3.8.5
minimize, 2.18.10, 2.29.63     object, 5.7.1
     cartesian, 2.29.63.1     objects, 2.16
     loop, 2.29.63.2     surface, 2.29.87.9, 5.8.7
     stack, 2.29.63.3     views, 1.4.1.1
     tether, 2.18.8, 2.29.63.4     volume, 2.30.114
     drop, 2.19.16molecule, 2.7
minimizeMethod, 2.22.17     create, 3.8.4
missing bonds, 2.29.69.3     properties, 2.29.86.34
     loop, 2.23.5.7, 2.23.5.8     rotation, 3.2.3
     residues, 2.30.54.1     translation, 3.2.3, 3.2.4
     triangles, 2.30.189     create, 1.7.2
mkUniqPdbSequences, 2.32.49     intro, 1.7.2, 2.7
mm26, 3.8     sort/reorder, 2.29.88.5
mmcif, 5.6.10     selecting, 2.8.6
mmff, 5.6.9molt, 3.5.1
     type, 2.30.182monte carlo, 2.29.68
     show atom types, 2.29.87.11montecarlo, 2.18.11, 2.18.13, 2.18.14, 2.18.15, 2.18.19, 2.22.7, 2.29.68
mnSolutions, 2.18.9     local, 2.18.16
mncalls, 2.18.10     trajectory, 2.29.23.17
mncallsMC, 2.18.11moprphing, 2.32.38
mnconf, 2.18.12more, 5.6.13
mnhighEnergy, 2.18.13morph, 2.29.23.6
mnreject, 2.18.14     to tether target, 2.32.38
mnvisits, 2.18.15morph2tz, 2.32.38
model reliability, 2.32.23morphing, 2.29.23.6, 2.29.86.68, 2.29.86.69, 2.29.91.3
modify, 2.29.65mouse controls, 2.3

move, 2.29.69neighbors, 2.30.151
     alignment sequence, 2.29.69.7nested script, 5.8.2
     atoms, 2.29.86.3     real array, 2.30.122
     bonding, 2.29.69.3nice, 2.32.39
     column, 2.29.69.5     image, 3.2.2
     element, 2.29.69.4non-redundant, 3.4.3
     file, 2.21.28, 2.29.82.3normal distribution, 2.30.121
     fragments together, 2.29.69.3normalize chemicals, 2.29.67.4
     molecule, 2.29.69.1     defined, 2.30.168
     ms_molecule, 2.29.69.1nota, 1.5
     multiple molecules, 2.29.69.2notational conventions, 1.5
     object, 2.29.69.2nproc, 2.29.38
     plane, 2.29.69.6nucleotides, 2.21.24
     sequence, 2.29.69.7number, 2.18.18
     table column, 2.29.69.5     of dots, 2.23.5.55
movie, 2.29.91.3          elements, 2.30.102
     images by frame, 3.9.2.2          hydrogen bonds, 2.29.87.23
     molecular simulation, 3.9.2          molecules in objects, 2.30.137.4
     rotate view, 3.9.1          occurrences, 2.30.102
     zooming, 3.9.1          residues in molecules, 2.30.137.4
moving selection to another object, 2.30.137.8          van der Waals contacts, 2.29.87.13
mpeg, 2.29.107.31     transfer from sequence, 2.29.3.2
ms_, 2.8.6nvis, 2.30.66.6
multi center drestraint, 2.22.6object, 2.29.13.1, 5.7.1
multi-part molecule, 2.29.18.2     in table, 2.30.109
multicore, 2.30.70.1     parray, 5.7.3.1
multiline input, 2.29.81.5     properties, 2.29.86.34
multiple NMR models, 2.23.14.5     stack, 5.8.9
     alignment, 2.29.3.3     to chemarray, 2.30.27
          to pairwise similarities, 2.32.7     user fields, 2.30.54.1
     conformation storage, 5.8.9     assign comment, 2.29.86.17
     conformations, 2.29.60.1, 2.29.91.1     source file, 2.30.55
     mol as text, 2.30.156.3     translate, 2.29.100
     object file, 2.29.81.2     merge, 3.8.6
     sequence alignment intro, 1.4.3.4     selecting, 2.8.5
     smiles file format, 2.29.81.46obsolete, 2.19.54
multiprocessor, 2.29.38occlusion shading, 2.29.13
mutate residue, 2.29.65octanol transfer, 2.30.114
mutating residue, 3.8.5off, 2.29.81.22
mute, 5.6.15     format, 5.5.3
mysql, 2.29.16.1oligonucleotide melting, 2.30.164
nLocalDeformVar, 2.18.16on-line help, 2.29.45.1, 2.29.45.2
nProc, 2.18.18     third, 2.30.37
nSsearchStep, 2.18.17only, 5.7.2
name, 2.30.79ontology, 2.30.44.6
     atom fields, 2.29.86.34openGL window, 2.29.102
naming compounds, 2.29.86.47operating system, 2.29.22.9, 2.29.96, 2.30.188, 5.10.2
nearest sequence, 2.30.95optimal chemical superposition, 3.14.5.1
neato, 2.30.160.7optimization, 2.29.68
neighbor joining, 2.29.62.38     Hbond, 2.32.91

optimizeHbonds, 2.32.91     folding, 1.4.2.1
or, 2.14.3          intro, 1.4.2.1
order, 2.29.3.1, 2.29.69.7personal 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, 2.29.87.21     object faq, 3.6.1
output, 2.18.3pharmacophore, 2.29.12, 3.5, 5.7.8
outside penalty, 2.23.6.1     faq, 3.6
overlap, 2.30.70.10     grid type definitions, 2.29.86.73
     by atom pairs, 2.29.94     object, 3.6.1
          chemical substructure, 2.32.22     objects, 3.6
overview, 1.4pharmacophores, 3.6
pK shift, 3.7.3     psi plot, 2.32.58
pKa, 2.29.22.20, 2.29.86.11, 2.29.86.12pipe, 2.29.81.43
     model, 2.29.86.12placeLigand, 2.32.50
packing density, 3.3.8planar angle, 2.29.62.18
pair-distances, 2.29.22.6plot, 2.29.71
pairdistance parray, 2.23.5.24     3D 2Dfunction, 3.12.3
pairwise interactions, 2.29.86.51          shape, 3.12.4
panel layout, 2.23.8.6     area, 2.29.72
paragraphs, 2.29.107.24     grid line width, 2.23.12.5
parallel, 2.18.18     histogram, 3.12.2
     computing, 2.30.70.1     how to, 3.12
     processing, 2.29.38     simple, 3.12.1
parallelization, 2.30.70.1plot2DSeq, 2.32.51
parameter list file, 3.14.6.2plotBestEnergies, 2.32.54
parray, 2.29.22.6, 5.7.3plotCluster, 2.32.56
parrayTo3D, 2.32.83plotFlexibility, 2.32.55
parrayToMol, 2.32.82plotMatrix, 2.32.57
parse SOAP message, 2.30.186plotRama, 2.32.58
parsing, 2.30.89plotRose, 2.32.59
     web pages, 2.29.81.47plotSeqDotMatrix, 2.32.52
partial least squares, 2.29.51plotSeqDotMatrix2, 2.32.53
     slide display, 2.29.23.21plotSeqProperty, 2.32.60
     sum, 2.30.77     3d, 1.4.3.7
passing arguments, 5.8.2plotting van der Waals, 3.7.1
     by reference, 2.29.61          faq, 3.7.1
pattern, 5.7.4pls, 2.29.51
     search, 2.29.35.2     column contributions, 2.30.160.8, 2.30.160.9
pause, 2.29.70     model, 2.30.160.8, 2.30.160.9
pdb, 5.6.10, 5.7.6     weights, 2.30.160.8, 2.30.160.9
     file creation time, 2.30.38pmf, 2.22.16
     files, 2.33.28     residue profile, 2.32.23
     format, 2.29.81.48pmf-file, 2.33.19
     merge, 3.4.4pmffile, 2.33.19
     sequence generation, 3.4.3png, 2.29.107.36, 5.7.5
pdbDirStyle, 2.22.18pocket, 2.32.28, 2.32.89, 3.13.1.1
peptide, 5.7.7point coordinates, 2.30.192.1
     docking, 3.12.5     size, 2.23.5.21

polar hydrogens, 2.23.5.32     grid docking, 3.14.2
     surface area, 2.30.114     health, 2.32.58
polarization charge, 3.7.2, 5.7.13     topology, 2.23.5.42
positional constraint, 2.23.14.12psa, 5.7.12
postscript, 2.21.23purple box, 2.30.21
potential surface, 2.23.14.6quadratic equation, 2.30.147
          coloring, 5.7.13quantum mechanics, 2.29.81.21, 2.29.107.17
pov-ray, 2.29.107.38qubic equation, 2.30.148
pow, 2.30.37query, 3.14.6.1
precision, 2.30.136.4     molcart, 2.29.78
predict, 2.29.73question mark operator, 2.30.156.7
predictSeq, 2.32.61quit, 2.29.79
prediction model, 2.30.84     property transfer via alignment, 2.30.122.3
     quality, 2.30.136r_2out, 2.19.34
     score, 2.30.136r_out, 2.19.33
predictive models, 2.29.51.2radii.electrostatic, 2.30.120
preference, 2.22     van der Waals, 2.30.120
     system, 2.22.1rainbow, 2.30.29.1
preferences, 3.1.2.3ramachandran faq, 3.3.3
prepSwiss, 2.32.62     how to, 3.3.3
previous atom, 2.30.101.1random array, 2.30.121
principal axes, 2.30.163     order, 2.30.139
     component analysis, 3.3.9     sequence, 2.29.62.36
     inertia moments, 2.30.88randomSeed, 2.18.19
print, 2.29.74randomize, 2.18.19, 2.29.80
     bar, 2.29.75     angles, 2.29.80.1
     image, 2.29.77     coordinates, 2.29.80
     to string, 2.29.90     torsions, 2.29.80
printMatrix, 2.32.63rarray, 2.29.22.6, 2.30.56.1, 2.30.70.8, 2.30.122.2, 5.7.11
printPostScript, 2.32.64     properties, 2.30.122.4
printTorsions, 2.32.65rdBlastOutput, 2.32.68
printf, 2.29.76rdSeqTab, 2.32.69
problem, 3.14.6.2reaction, 2.29.62.33
processors, 2.18.18     group file, 2.29.52
profile, 5.7.9read, 2.29.81, 2.29.81.56, 2.29.81.57
program overview, 1.4     FILTER, 2.29.81.6
progress bar, 2.29.75     alignment, 2.29.81.12
progression, 2.29.75     all, 2.29.81.7
project setup, 3.13.2.2     binary, 2.29.81.2
projected alignment, 2.30.99.3     blob, 2.29.81.38
projecting surface charge, 3.7.2     color, 2.29.81.13
property, 2.29.86.52, 2.29.86.53, 2.29.86.54     column, 2.29.81.51
     grids, 2.19.20     comp_matrix, 2.29.81.14
     map, 2.29.86.73     conf, 2.29.81.15
     superposition, 2.29.86.73     csd, 2.29.81.16
prosite, 5.7.10     csv, 2.29.81.44
     pattern, 5.7.4     database, 2.29.81.17
protein docking, 2.30.192.3     drestraint, 2.29.81.18
          intro, 1.4.2.5          type, 2.29.81.19
     engineering, 2.24.9     entries from database, 2.29.81.8

     file by chunk, 2.29.81.40     vrestraint, 2.29.81.54
     from file, 2.29.81.1          type, 2.29.81.55
          string, 2.29.81.5     with filter, 2.29.81.6
     fromstring, 2.29.81.5     xml, 2.29.81.56
     ftp http, 2.29.81.9readMolNames, 2.24.11
     gamess, 2.29.81.21readcomp_matrix, 2.29.81.14
     grob, 2.29.81.22reading external tool output, 2.29.62.1
     gui, 2.29.81.3     from standard input, 2.29.81.43
     html, 2.29.81.4     pdb from ftp, 2.21.18
          file, 2.29.81.4               web, 2.21.19
     iarray, 2.29.81.23     restraint, 2.29.81.54
     index, 2.29.81.24real, 5.7.14
          table, 2.29.81.8     array, 5.7.11
     json, 2.29.81.57     shell variables, 2.19
     library, 2.29.81.25     space refinement, 2.29.62.31
          mmff, 2.29.81.26reals, 2.19
     librarymmff, 2.29.81.26rebel, 2.18.5, 2.23.14.6, 5.7.13
     map, 2.29.81.27rebuild molcart index, 2.29.7.10
     matrix, 2.29.81.28recalculate dependent values, 2.29.7.2
     menu file, 2.29.81.3     values, 2.29.1.1.1
     mol, 2.20.13, 2.29.81.8, 2.29.81.29receptor, 3.13.1.1
     mol2, 2.29.81.8, 2.29.81.30     preparation, 3.13.1.1
     object, 2.29.81.32redefine hydrogen coordinates, 2.29.86.25
          parray, 2.29.81.32.1references, 4
     pdb, 2.23.14.4, 2.23.14.5, 2.29.81.2, 2.29.81.33refineModel, 2.32.66
          sequence, 2.29.81.34reflections, 2.23.5.33
     profile, 2.29.81.35refresh view, 2.29.23.2
     prosite, 2.29.81.36refs, 4.1
     rarray, 2.29.81.37regexp, 2.10, 2.30.89
     sarray, 2.29.81.39, 2.29.81.40     back references, 2.10.1.3
     sequence, 2.29.81.8, 2.29.81.41     syntax, 2.10.1
          database, 2.29.81.41.1regression, 2.29.51
     smiles, 2.29.81.46regul, 2.32.67
     stack, 2.29.81.42regular expression, 2.10, 2.30.70.4, 2.30.89
     string, 2.29.81.43          filter, 2.29.81.1
     table, 2.29.81.44     expression, 2.30.126.3
          chunk, 2.29.81.45regularization, 2.18.8, 2.29.63.4, 5.7.15
          csv, 2.29.81.44     procedure, 3.8.3
          html, 2.29.81.47rejectAction, 2.22.19
          mmcif, 2.29.81.48relational database, 2.30.149
          mol, 2.29.81.50relative accessible area of atoms, 2.22.2
          mol2, 2.29.81.49release notes, 1.1
     text, 2.29.81.40remarkObj, 2.32.70
     trajectory, 2.29.81.31remove columns, 2.29.22.16
          and save a fragment, 2.29.81.31.1     expression tags, 2.30.180
          write, 2.29.81.31.1     file, 2.29.22.9
     unix, 2.29.81.10     trailing blanks, 2.30.178
          cat, 2.29.81.11removing html tags, 2.29.81.47
     variable, 2.29.81.52     outliers, 2.30.178
     view, 2.29.81.53rename, 2.29.3.1, 2.29.82

     column table, 2.29.82.1restraining molecules to shapes, 2.23.14.12
     file, 2.29.82.3restraints, 2.17, 2.29.86.68, 2.29.86.69
     molcart, 2.29.82.2     torsion, 2.29.86.81
     system, 2.29.82.3return, 2.29.83
renaming, 2.23.12.15reverse complement, 2.30.138.1
reorder, 2.29.69.7     lighting, 2.29.86.42
     alignment sequences, 2.29.107.1     normals, 2.29.86.42
     array, 2.30.139reversing order, 2.30.66.2
     columns by function, 2.29.88.3rgb, 2.30.90.4, 5.7.17
     objects, 2.29.88.4     matrix, 2.30.29
replace matching array element, 2.30.126.1ribbon, 5.7.18
     without interpretation, 2.30.126.2     bullets, 2.23.5.7
replacing scaffold in a library, 2.29.67.1     diagram, 2.23.5.42, 2.23.5.43
reproducible randomness, 2.18.19ribbonColorStyle, 2.22.21
reroot, 2.29.18.4ribbonStyle, 2.22.22
     selections, 3.3.6right join, 2.29.50
resLabelShift, 2.19.35rigid chemical superposition, 2.29.94
resLabelStyle, 2.22.20ring, 2.30.130
reserved names, 2.24     center coordinates, 2.30.192.2
residue, 2.29.13.1, 5.7.16     sampling, 3.16
     accumulators, 2.30.63     templates, 2.29.86.8
     alignment, 2.29.86.68, 2.29.86.69rm, 2.29.22.9
     conservation, 2.30.122.5rocking, 2.29.23.5
     contact area matrix, 2.30.90.8root mean square deviation, 2.30.136.4
          areas, 2.30.7.1roots, 2.30.147, 2.30.148
     field, 2.29.86.34rotate, 2.29.84
     gap, 2.23.5.7, 2.23.5.8     grob, 2.29.84.2
     label, 2.19.35, 2.29.3.2     object, 2.29.84.1
     library file, 2.33.20     view, 2.29.84.3
     name, 2.30.79rotation, 2.29.23.5
          translation, 2.23.14.14     angle, 2.30.17
     number, 2.30.66.5rounding, 2.30.122
          table, 2.30.160.3     a real, 2.30.156
     property averaging, 2.30.146.3     output, 2.29.87.45
          calculation, 2.30.63rsWeight, 2.19.36
     proximity, 2.30.90.8rs_, 2.8.7
     ranges, 2.8.11ruler, 2.19.10
     selection, 2.20.21     script, 2.29.8
          as string, 2.30.156.8running a docking job, 3.13.2.5
          function, 2.30.127     dock job, 3.13.2.4
     table, 3.14.4.1     script from html, 5.8.2
     tethering, 2.29.86.68, 2.29.86.69s-s bond, 5.4.5
     user field, 2.30.54.1s_alignment_rainbow, 2.21.1
residue_selections, 2.8.11s_blastdbDir, 2.21.2
     selecting, 2.8.7s_editor, 2.21.3
resizing, 2.30.68s_entryDelimiter, 2.21.4
resorting nodes edges, 2.30.160.7s_errorFormat, 2.21.5
restore, 3.14.6.2s_fieldDelimiter, 2.21.6
     defaults, 2.29.82.4s_helpEngine, 2.21.7
     preference, 2.29.82.4s_icmPrompt, 2.21.10

s_imageViewer, 2.21.11search for chemical pattern, 2.30.56.3
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, 2.29.35.8
s_lib, 2.21.14searchObjSegment, 2.32.73
s_logDir, 2.21.15searchPatternDb, 2.32.71
s_out, 2.21.16searchPatternPdb, 2.32.72
s_pdbDir, 2.21.17searchSeqDb, 2.32.74
s_pdbDirFtp, 2.21.18searchSeqFullPdb, 2.32.76
s_pdbDirWeb, 2.21.19searchSeqPdb, 2.32.75
s_printCommand, 2.21.21searchSeqProsite, 2.32.77
s_projectDir, 2.21.20searchSeqSwiss, 2.32.78
s_prositeDat, 2.21.22searches and alignments, 3.4
s_psViewer, 2.21.23second moments, 2.30.163
s_reslib, 2.21.24secondary structure derivation from 3D, 2.29.5.1
s_skipMessages, 2.21.25          schematic, 2.23.5.42
s_sysCp, 2.21.26segMinLength, 2.18.20
s_sysLs, 2.21.27segment, 5.8.4
s_sysMv, 2.21.28select, 2.29.85
s_sysRm, 2.21.29     atoms by number of bonded atoms, 2.30.137.3
s_tempDir, 2.21.30          of the fixed torsions, 2.30.137.2
s_translateString, 2.21.31     based on alignment, 2.30.137.14
s_userDir, 2.21.32          bfactor, 2.30.137.7
s_usrlib, 2.21.33          center of mass, 2.30.137.15
s_webEntrezLink, 2.21.34          coordinates, 2.30.137.7
s_webViewer, 2.21.35          iarray, 2.30.137
s_xpdbDir, 2.21.36          length, 2.30.137.13
sa23, 3.3          occupancy, 2.30.137.7
sampling grid, 2.30.192.3          user field, 2.30.137.7
sarray, 2.29.22.6, 5.8.1     chemical, 2.29.85.1
     transformation in place, 2.29.99.1     column table, 2.29.85.2
save preferences, 2.29.107.42     lines, 2.29.81.1
     print, 3.2.6     tether partners, 2.30.137.12
     sdf file, 2.29.107.11     vw partners, 2.30.137.12
saving graphics to album, 2.29.62.20selectMinGrad, 2.19.37
     image, 2.29.107.36selectSphereRadius, 2.19.38
scaffold, 2.30.178selected stack conformations, 2.29.22.17
scaffolds, 2.29.52selecting by b-factor, 2.30.137
scoring, 3.13.1.4               y z, 2.30.137
screen X, 2.30.190     columns, 5.9.1
     coordinates, 2.30.190     from clusters, 3.14.6.4
script, 2.30.99.4, 5.8.2     neighboring elements, 2.30.101
     file name, 2.30.55     residues, 3.3.6
     inside ICM, 5.8.2     saving, 2.30.66.4
     name, 5.8.2selection, 2.8, 2.30.137, 2.30.137.6
     image generation, 2.29.23.3     elements, 2.8.4
scripting molecular movements, 3.2.4     examples, 2.8.3
sdf, 2.23.14.7, 2.29.107.24, 5.6.11     functions, 2.8.10
     file, 2.29.81.49, 2.29.81.50, 2.29.86.47, 2.29.107.11, 2.30.156.3, 5.7.3     gap patching, 2.30.137, 2.30.137.11
     to chem-table, 2.30.109     level, 2.8, 2.30.182

     simplification, 2.30.137.11     not in alignments, 2.29.22.23
     transfer, 2.30.137, 2.30.156.8set, 2.29.86
     type, 2.8     alternative atom, 2.29.86.18
     types, 2.8.1     area, 2.29.86.1
     variable, 2.24.12     atom, 2.29.86.3
     atoms, 2.8.8          ball label, 2.29.86.2
     functions, 2.8.10     background image, 2.29.86.4
     molecules, 2.8.6     bfactor, 2.29.86.5
     objects, 2.8.5     biological symmetry, 2.29.86.64
     output, 2.24.15     bond topology, 2.29.86.7
     residues, 2.8.7          type, 2.29.86.6
     torsions, 2.8.9          and formal charges, 2.29.86.7
     variables, 2.8.9     cartesian, 2.29.86.8
selections, 2.29.86.34     chain, 2.29.86.9
     in molecular objects, 2.8     charge, 2.29.86.10
selftether, 2.23.14.12, 5.9.4          formal, 2.29.86.11
seq_ali_project, 2.30.156.6               auto, 2.29.86.12
sequence, 2.30.172, 2.30.173, 5.8.3          mmff, 2.29.86.13
     alignment, 2.30.5.1, 2.32.1     chargemmff, 2.29.86.13
          intro, 1.4.3.3     chiral, 2.29.86.14
     analysis intro, 1.4.3          chemical, 2.29.86.15
     assembly, 2.29.43.2     color, 2.29.86.16
     belongs to alignment, 2.30.70     comment, 2.29.86.17, 2.29.86.18
     conservation, 2.30.136.7          sequence, 2.29.86.19
     distance, 2.30.137     comp_matrix, 2.29.86.20
          matrix from alignment, 2.30.90.9     current map, 2.29.86.45
     dotplot, 1.4.3.2          object, 2.29.86.48
     from alignment, 2.29.22.23     directory, 2.29.86.21
          pdb, 2.29.62.35     drestraint, 2.29.86.22
     identity, 2.32.7, 2.32.8          type, 2.29.86.23
     intro, 1.4.3     electrostatic radii, 2.29.86.79
     modification, 2.30.180     error, 2.29.86.33
     neighbor, 2.30.99.3     field, 2.29.86.34
     parray, 5.7.3.2          alignment, 2.29.86.35
     pattern, 5.7.4          map, 2.29.86.36
     position correspondence, 2.30.160.3          name, 2.29.86.37
     positional weights, 2.29.86.1     font, 2.29.86.38
     redundancy removal, 2.29.43.2          grob, 2.29.86.39
     search, 2.29.35.2     foreground, 2.29.86.40
     selection, 2.29.22.23     format, 2.29.86.41
     structure alignment, 2.31.1     grob, 2.29.86.42
     to alignment transfer, 2.30.122.3          coordinates, 2.29.86.42
     type, 5.8.3          label, 2.29.86.42
sequence-alignment mapping, 2.30.156.5, 2.30.156.6     group, 2.29.86.63
sequence-structure alignment, 2.30.5.1          column, 2.29.86.24
     output format, 2.18.21, 2.18.22     hydrogen, 2.29.86.25
sequenceBlock, 2.18.21     key, 2.29.86.43
sequenceColorScheme, 2.22.23     label, 2.29.86.44
sequenceLine, 2.18.22          3d label, 2.29.86.44.4
sequences, 3.4          chemical, 2.29.86.44.3

          table, 2.29.86.44.2     variable grid, 2.29.86.84
     map, 2.29.86.45     variablegrid, 2.29.86.84
     molcart, 2.29.86.46     view, 2.29.86.80
     molecular variables, 2.29.86.83     vrestraint, 2.29.86.81
     name, 2.29.86.47     vrestraintvs_var, 2.29.86.82
          sequence, 2.29.86.47.1          radii, 2.29.86.78
     object, 2.29.86.48     vwelradii, 2.29.86.79
     occupancy, 2.29.86.49     vwradii, 2.29.86.78
     plane, 2.29.86.50     window, 2.29.86.85
     pmf, 2.29.86.51     xstick, 2.29.86.86
     property, 2.29.86.52, 2.29.86.54, 2.29.86.55          radii, 2.29.86.86
          alignment, 2.29.86.55setResLabel, 2.32.80
          chemical view, 2.29.86.54setcomp_matrix, 2.29.86.20
          column, 2.29.86.53seticmff, 2.32.79
     radii graphical, 2.29.86.86setting conf properties, 2.29.86.61
     randomSeed, 2.29.86.56setvs_var, 2.29.86.83
     randomize, 2.29.86.56sf-term, 2.29.86.72
     resolution, 2.29.86.57sfWeight, 2.19.39
     selftether, 2.29.86.68sh24, 3.4
     similarity, 2.30.44.8, 2.30.136.2shadows, 2.23.5.34
     site, 2.29.86.26shell, 3.1, 5.8.5
          alignment, 2.29.86.27     functions, 2.29.40
          residue, 2.29.86.29     intro, 1.7.1
     slide, 2.29.86.30     progression, 2.29.75
     sstructure backbone, 2.29.86.59     warning message, 2.30.191
          sequence, 2.29.86.60shineStyle, 2.22.24
          to sequence, 2.29.86.60shininess, 2.19.40
     stack, 2.29.86.61show, 2.29.87, 2.29.87.39
          energy, 2.29.86.61, 2.29.91.1     alias, 2.29.87.7
     stereo, 2.29.86.58     aliases, 2.29.87.7
     swiss, 2.29.86.62     alignment, 2.29.87.8
          name, 2.29.86.62     area, 2.29.87.9
     symmetry, 2.29.86.65     atom, 2.29.87.10
          bio, 2.29.86.64          type, 2.29.87.11
          crystal, 2.29.86.63     atoms, 2.29.87.10
          group, 2.29.86.63     bond, 2.29.87.12
          to a torsion, 2.29.86.65     clash, 2.29.87.13
     table, 2.29.86.66     color, 2.29.87.14
     tautomer, 2.29.86.31     column, 2.29.87.15
     terms, 2.29.86.67     comp_matrix, 2.29.87.16
     tether, 2.29.86.69     database, 2.29.87.17
          append, 2.29.86.70     drestraint, 2.29.87.18
     texture, 2.29.86.32          type, 2.29.87.19
     type, 2.29.86.71     energy, 2.29.87.20
          mmff, 2.29.86.77          atom, 2.29.87.21
          molecule, 2.29.86.75     gradient, 2.29.87.22
          object, 2.29.86.74     hbond, 2.29.87.23
          property, 2.29.86.73          exact, 2.29.87.24
          sequence, 2.29.86.76     hbondexact, 2.29.87.24
          surface, 2.29.86.72     html, 2.29.87.25

     integer, 2.29.87.27     compound, 2.30.179
     key, 2.29.87.4     mesh structure, 2.29.15.2
     label, 2.29.87.28simulation duration, 2.19.47
     library, 2.29.87.29     temperature, 2.19.46
     link, 2.29.87.30     intro, 1.4.2
     logical, 2.29.87.31sinking number, 2.19.35
     map, 2.29.87.5site, 2.29.11.2, 5.8.6
     mol, 2.29.87.32     arrows, 2.29.86.26
     mol2, 2.29.87.33     table, 5.8.6.1
     molecule, 2.29.87.34sites, 2.29.22.26
     molecules, 2.29.87.6     by residue selection, 2.29.22.24
     object, 2.29.87.35     sequences, 5.8.6.1
     pdb, 2.29.87.36sixthe power, 2.22.6
     pharmacophore type, 2.29.87.53skin, 2.19.35, 5.8.7
     pmf, 2.29.87.37     intro, 1.4.1.2
     preferences, 2.29.87.38slide, 2.29.1.3, 2.30.144, 5.8.14
     profile, 2.29.87.39     transition time, 2.29.23.21
     residue, 2.29.87.40slides, 2.30.190
          type, 2.29.87.41slideshow, 2.29.1.3, 2.29.23.21, 2.30.144
     residuetype, 2.29.87.41sln, 5.8.8
     segment, 2.29.87.42smallest set of smallest rings, 2.30.130
     selftether, 2.29.87.1smart, 2.23.14.7
     sequence, 2.29.87.43smarts, 2.30.70.2
     shell variable, 2.29.87.3smiles, 2.23.14.7, 2.26
     site, 2.29.87.2     to chem-table element, 2.30.109
     stack, 2.29.87.44smooth alignment, 2.30.146.4
     svariable, 2.29.87.3     interpolation, 2.29.91.3
     table, 2.29.87.45     map, 2.30.146.5
          as database, 2.29.87.17     rarray, 2.30.146.1
     term, 2.29.87.46     surface, 2.32.88
     tethers, 2.29.87.47soap, 2.27
     version, 2.29.87.48soft trim, 2.30.178
     volume, 2.29.87.51solid sphere, 2.23.5.11
          map, 2.29.87.52solubility, 2.30.114
     volumemap, 2.29.87.52solvation, 2.22.25, 2.23.14.2
     vrestraint, 2.29.87.49     energy, 2.19.39, 2.22.25
          type, 2.29.87.50solvent accessible area, 2.18.23
     vrestraints, 2.29.87.49          surface, 2.23.5.55, 2.23.5.56, 2.29.87.9
showcomp_matrix, 2.29.87.16sort, 2.29.88, 2.29.88.4
showing weak hydrogen bonds, 2.23.5.25     array, 2.29.88.1
side chain, 2.32.90     arrays, 2.29.88.1
          flexibility, 2.32.90     column, 2.29.88.3
sigma function, 2.30.44.8, 2.30.136.2          table, 2.29.88.3
     level, 2.23.7.5     molecules, 2.29.88.5
signal recognition measure, 2.32.21     object, 2.29.88.4
similar chains, 2.30.137.13     stack, 2.29.88.6
similarity, 2.29.35.9, 2.29.35.10     table, 2.29.88.2
simple expressions, 2.10.1.1sortSeqByLength, 2.32.81
     string substitution, 2.30.126.2space group, 2.29.66
simplified representation, 2.23.5.16     transformations, 2.30.176

spawn background job, 2.29.62.1     frame, 2.29.91.3
special values, 2.30.168     image, 2.29.62.20
specificity, 2.30.136.4     stack object, 2.29.91.2
spectral decomposition, 2.30.45     torsion type, 2.29.91
split, 2.29.89strength of hydrogen bond, 2.29.23.14
     column values, 2.29.89.5string, 5.8.11
     grob, 2.29.89.1     array, 2.30.135, 5.8.1
     group, 2.29.89.2     filtering, 2.30.178
          array, 2.29.89.3     inversion, 2.30.156.1
     molsar, 2.29.62.28     label, 2.29.23.12
     object, 2.29.89.6     matching, 2.10, 2.30.89
          to molecules, 2.29.89.6     variables, 2.21
     sequence, 2.29.89.4strings, 2.21
     table cell, 2.29.89.5strip, 2.29.93
     tree, 2.29.89.7struct, 2.30.99.2
splitting selection, 2.8.11structural alignment, 2.29.3.5, 2.30.5.2
spreadsheet, 2.29.81.44          optimization, 2.29.35.1
sprintf, 2.29.90     superposition, 2.29.3.5
sql, 2.29.78, 2.29.86.46, 2.30.50.1, 2.30.99.12, 2.30.102.5, 2.30.182.2     analysis, 3.3
sqlite, 3.5.1     comparison, 2.30.23.2
sqrt, 2.30.37     factors, 3.11.1
square matrix to element pairs, 2.30.160.5     structure, 3.11.1
ssThreshold, 2.19.41sub-alignment to selection, 2.30.128
ssWeight, 2.19.42sub-matrix, 2.30.90.2
ssbond, 5.4.5subalignment, 2.30.5.3, 5.1.1
ssearch, 2.18.17, 2.29.92submap, 2.30.86
ssearchStep, 2.19.43subroutine, 2.29.61
ssign sstructure segment, 2.29.5.2subset, 2.6
stack, 2.18.12, 2.18.13, 2.18.15, 2.22.7, 2.29.86.61, 2.29.91, 2.29.91.1, 2.30.66.6, 2.30.160.6, 5.3.12, 5.8.9substring, 2.30.89, 2.30.156, 2.30.156.1
     bin size, 2.29.14substructure, 2.29.35.9, 2.29.35.10
     cleaning, 2.29.22.17     search, 2.29.35.4
     extension, 2.29.4.2superimpose, 2.23.14, 2.29.94
     multiplication, 2.29.4.2     faq, 3.3.1
     merge, 3.7.7     how to, 3.3.1
standard chemical form, 2.29.67.4     minimize, 2.29.95
     deviation, 2.30.133support, 1.3
standardization, 2.29.22.11suppressing view changes, 2.29.23.21
     chemical, 2.29.67surface, 2.19.35, 2.30.109, 5.8.15
startup, 3.1.2.3     accessibility, 2.29.87.9
static RMSD, 2.30.155     area, 2.32.2, 5.8.15
     and dynamic hbonds, 2.23.5.24     charge, 5.7.13
statistical thermodynamics, 2.30.47     color, 2.29.86.16
stereo, 2.23.5.52, 2.29.30, 2.29.86.58     dot density, 2.23.5.55
     reconstruction, 3.8.9     energy, 2.22.25, 2.29.86.72
stereo-specific hydrogens, 2.29.22.11     mesh, 2.30.192.3
stereoisomer, 2.29.30     point selection, 2.30.192
stereoisomers, 2.20.16     term, 2.19.39
stick, 5.8.10surfaceAccuracy, 2.18.23
store, 2.29.91surfaceMethod, 2.22.25
     conf, 2.29.91, 2.29.91.1surfaceTension, 2.19.44

     map, 2.30.160.7     window, 2.29.44
swapping protein fragments, 3.8.7terms, 2.17
swiss, 2.29.86.62     hydrogen bonding, 2.19.21
swissFields, 2.24.10test, 2.29.97
swissprot, 2.29.86.26     binary, 2.29.97.1
symmetrization of a matrix, 2.30.90.3testing if argument exists, 2.30.59
symmetry, 2.30.176tether, 2.23.14.12, 2.29.107.9, 5.9.4, 5.9.5
     faq, 3.10text, 2.30.89
     group, 2.18.2     search in tables, 2.30.56.2
     problem, 2.29.66     to script, 5.8.2
syntax highlighting, 5.8.2texture, 5.5.3
sys, 2.29.96tga, 5.9.3
system, 5.10.2then, 2.29.98
     command, 2.29.96thickness, 2.23.9.14
     copy, 2.21.26thread to template, 2.29.63.4
     file move, 2.21.28threading, 2.30.5.1
     list file, 2.21.27     letter code, 2.30.172, 2.30.173
     remove, 2.21.29thumbnails, 2.30.68
table, 2.29.22.4, 2.29.86.52, 2.29.86.53, 2.29.86.54, 2.29.88.3, 5.9.1tif, 5.9.6
     actions, 5.9.2.4time, 2.30.38, 2.30.156.2
     column, 2.30.99timeLimit, 2.19.47
          format, 2.29.86.41tolFunc, 2.19.49
          plot, 2.29.62.32tolGrad, 2.19.48
          transformations, 2.30.104topological psa, 5.7.12
     creation, 2.29.43.3torScan, 2.32.84
     display style, 5.9.1torsion rmsd comparison, 2.29.14.2
     expression, 5.9.2     scan, 2.32.84
     from matrix, 2.30.160.4torsions, 2.30.102.3
     grid view, 5.9.1     score, 2.31.2
     of atoms and distances, 2.30.160.10tpsa, 5.7.12
     operations, 5.9.2.1trajectory, 2.29.60.2, 2.29.91, 2.29.91.3, 5.6.14
     plot, 5.9.2.3     file, 2.33.17
     principal component analysis, 2.29.62.29     frame writing, 2.29.23.17
     print, 2.29.87.45     smoothing, 2.29.23.17
     row, 2.29.69.4transform, 2.29.99, 2.29.99.2
          label mark, 2.29.86.44.2     general, 2.29.99
          mark, 2.30.79     grob coordinates, 2.29.99.2
     selected row numbers, 2.30.70     molecules, 2.29.99.2
     subset, 5.9.2.2     sarray, 2.29.99.1
     show html, 2.29.105.1transformation, 2.30.122, 5.9.7
targa, 5.9.3     vector, 5.9.7
target coordinates, 5.9.4     and symmetry, 3.10
tautomer, 2.29.31transforming points, 2.30.192.5
tempCycle, 2.19.46translate, 2.29.100
tempLocal, 2.19.45transparency, 2.29.86.42, 5.5.3
temperature, 2.19.46     background, 2.29.107.36
     variations in optimizer, 2.19.46     grob, 2.29.23.11
template docking, 3.13.2.6     grobs, 2.23.5.57
tensor product of two vectors, 2.30.90tree, 2.29.62.37, 2.30.99.5
terminal font, 2.33.14     cluster, 2.13

     label format, 2.30.99.5     solvation parameters, 2.30.7
     representatives, 2.13.1user_startup, 3.1.2.4
trim string array, 2.29.99.1     icm, 3.1.2
trimming grid map values, 2.30.178     guide, 3
true positives, 2.30.136.4v_, 2.8.1
truncate alignment, 2.29.62.34van der Waals surface, 2.23.5.56
     values, 2.30.178varLabelStyle, 2.22.27
     grob, 2.23.5.9, 2.23.5.10variable restraint, 2.29.86.81
tsShapeData, 2.23.14.12     selection, 2.8.9
     table format, 2.29.81.44vdW gap, 2.30.151
two alignments, 2.30.44.13vector, 2.30.102.6
     dimensional plot, 2.30.146.2     dot product, 2.30.187.1
     set comparison, 2.30.44.8, 2.30.136.2     length, 2.30.103
     sets, 2.30.70.10     product, 2.30.187.1
txdoc browser, 2.29.81.4     transformation, 2.30.104
type, 2.30.182.1vertex, 2.29.13.4.2
tzMethod, 2.22.26     connectivity, 2.30.90.13
tzWeight, 2.19.50vertexes, 2.29.13.4.2
uncharge functional groups, 2.29.67.2vertical alignment block, 2.29.62.34
unclip, 2.29.23.2     workspace, 2.23.8.6
underline, 2.29.86.38.1vertices, 2.29.13.4.2
undisplay, 2.29.101vicinity, 2.19.51
     graphics, 2.29.102video, 2.29.107.31
     window, 2.29.102view, 2.23.5.9, 2.23.5.10, 2.29.86.55
unfix, 2.29.103     point, 2.30.190
union, 2.30.70.10     restoration, 2.30.73
unique, 2.29.13.1, 5.10.1     transition, 2.29.86.80
     atomic order, 2.29.62.39views, 5.8.14
     column values, 2.29.43.4virtual, 5.10.3
     names, 2.30.99     arrays, 2.29.1.1.1
     new object name, 2.30.99     chemistry, 2.29.67, 2.30.102.4
     smiles, 2.29.62.39     field, 2.29.7.2
unix, 2.29.96, 5.10.2     ligand screening, 3.13, 3.13.1, 3.13.2, 3.13.3
     grep, 2.29.81.1               intro, 1.4.2.7
unlink alignments, 2.29.22.21visitsAction, 2.22.28
     sequences, 2.29.22.21vls, 3.13, 3.13.1, 3.13.2, 3.13.3
     variables, 2.29.22.21     cluster, 3.13.3.6
update database, 2.29.67.5     faq, 3.13.3
     speadsheet, 2.29.1.1.1     intro, 1.4.2.7
updates, 1.1     job queueing, 3.13.3.6
updating atom pairs, 2.20.27     overview, 3.13.1
upper case, 2.30.171     parallelization, 3.13.3.5
url string parsing, 2.30.160     results, 3.13.3.8
user atom display, 2.23.5.3     scores storage, 3.13.3.7
     commands, 2.29.81.3     threshold, 3.13.3.2
     defaults, 2.29.107.42vls_intro, 3.13.3.1
     environment, 3.1.2.2volume, 5.10.4
     menu, 2.23.10.1vrestraint, 5.10.5
     menus, 2.28     file, 2.33.23
user-defined properties, 2.29.86.34     type, 5.10.6

vs_, 2.8.9          blast, 2.29.107.25
vs_out, 2.24.15          fasta, 2.29.107.24
vwCutoff, 2.19.52     library, 2.29.107.26
vwExpand, 2.19.53     map, 2.29.107.27
vwExpandDisplay, 2.19.54     matrix, 2.29.107.6
vwMethod, 2.22.29     model, 2.29.107.28
vwSoftMaxEnergy, 2.19.55     mol, 2.29.107.29
wait, 2.29.104     mol2, 2.29.107.30
warning, 2.23.14.3     molcart, 2.29.107.7
     message, 2.30.191     movie, 2.29.107.31
     suppression, 2.20.28     object, 2.29.107.32
water.dielectric constant, 2.19.15          parray, 2.29.107.34
waterRadius, 2.19.56          simple, 2.29.107.33
wavefront format, 2.29.62.11     pdb, 2.23.14.14, 2.29.107.35
web, 2.11, 2.29.105     png, 2.29.107.36
     table, 2.29.105.1     postscript, 2.29.107.37
webEntrezOption, 2.22.30     pov, 2.29.107.38
weighted rmsd, 2.23.14     povray, 2.29.107.38
while, 2.29.106     project, 2.29.107.2
whole string, 2.30.126.1     rarray, 2.29.107.4
window averaging, 2.30.146.1     sarray, 2.29.107.5
     layout, 2.30.156.9     sequence, 2.29.107.39
     width and height, 2.30.190     session, 2.29.107.40
windowSize, 2.18.24     several array, 2.29.107.8
     movie, 2.29.107.31     simple object, 2.29.107.33
wire, 5.10.7     stack, 2.29.107.41
wireBondSeparation, 2.19.57     system preference, 2.29.107.42
wireStyle, 2.22.31     table, 2.29.107.10
workspace, 2.29.102          mol, 2.29.107.11
write, 2.29.107          with links, 2.29.107.19
     album, 2.29.107.21     tether, 2.29.107.9
     alignment, 2.29.107.1     tethers, 2.29.107.9
     array, 2.29.107.8     trajectory, 2.29.23.17
          table, 2.29.107.8     vs_var, 2.29.107.43
     binary, 2.29.107.2writevs_var, 2.29.107.43
     blast, 2.29.107.25x-ray crystallography, 2.29.87.21
     column, 2.29.107.12xml, 2.29.81.56, 2.30.89, 5.1.6
     database, 2.29.107.13     drugbank example, 2.12
     drestraint, 2.29.107.14xpdb, 2.29.81.2
          type, 2.29.107.15xplor format, 2.29.81.27
     factor, 2.29.107.16xrMethod, 2.22.32
     gamess, 2.29.107.17xrWeight, 2.19.58
     grob, 2.29.107.18xray density to rectangular energy map, 2.29.62.31
     html, 2.29.107.19xstick, 5.10.8
     iarray, 2.29.107.3     radii, 2.29.86.2
     image, 2.29.107.20xyz morphing, 3.8.8
          alignment, 2.29.107.23zega, 5.10.9
          chemical, 2.29.107.22     intro, 1.4.3.6
          parray, 2.29.107.21|, 2.14.3
     index, 2.29.81.24, 2.29.107.24 

Copyright© 1989-2020, Molsoft,LLC - All Rights Reserved. Copyright© 1989-2020, Molsoft,LLC - All Rights Reserved. This document contains proprietary and confidential information of Molsoft, LLC. The content of this document may not be disclosed to third parties, copied or duplicated in any form, in whole or in part, without the prior written permission from Molsoft, LLC.