ICM Manual v.3.8
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2018, Molsoft LLC
Apr 11 2018

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

Index

&, 2.14.3C, 5.3
2D labels, 2.29.55.1CCP4, 5.6.6
     to 3D, 3.16CGI, 2.11
     trees, 2.29.62.38COLOR.bg, 2.19.9
     smooth, 2.30.144.2     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, 2.30.144.3Cadalign, 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, 2.30.134Chemical, 2.30.27
     pharmacophore comparison, 2.30.134.3Cluster, 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, 2.30.134     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, 2.30.162
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, 2.30.90.1
     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, 2.30.186     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, 2.23.5.53ICMHOME, 3.1.2.1
     surfaceDotDensity, 2.23.5.55     shell variable, 3.1.2.1
     surfaceDotSize, 2.23.5.54IMAGE, 2.23.9
     surfaceProbeRadius, 2.23.5.56     bondLength2D, 2.23.9.15
     transparency, 2.23.5.57     color, 2.23.9.8
     wormRadius, 2.23.5.58     compress, 2.23.9.9
GRID, 2.23.6     gammaCorrection, 2.23.9.7
     gcghExteriorPenalty, 2.23.6.1     generateAlpha, 2.23.9.10
     gpGaussianRadius, 2.23.6.6     lineWidth, 2.23.9.3
     margin, 2.23.6.2     lineWidth2D, 2.23.9.14
     maxEl, 2.23.6.3     orientation, 2.23.9.16
     maxVw, 2.23.6.5     paperSize, 2.23.9.17
     minEl, 2.23.6.4     previewResolution, 2.23.9.13
GROB, 2.23.7     previewer, 2.23.9.12
     arrowRadius, 2.23.7.3     printerDPI, 2.23.9.2
     atomSphereRadius, 2.23.7.1     quality, 2.23.9.1
     contourSigmaIncrement, 2.23.7.5     rgb2bw, 2.23.9.18
     relArrowHead, 2.23.7.4     scale, 2.23.9.4
     relArrowSize, 2.23.7.2     stereoAngle, 2.23.9.6
GUI, 2.23.8     stereoBase, 2.23.9.5
     defaults, 3.14.6.2     stereoText, 2.23.9.11
     dialog, 2.28     writeScale, 2.23.9.19
     plot, 2.29.62.32I_out, 2.24.4
     preferences, 2.29.82.4Iarray, 2.30.66, 2.30.66.4, 2.30.66.5
     tableRowMarkColors, 2.23.8.5     atom numbers, 2.30.66.4
     windowLayout, 2.23.8.6     bits to integers, 2.30.66.3
     workspaceFolderStyle, 2.23.8.9     inverse, 2.30.66.2
     workspaceStyle, 2.23.8.7     residue numbers, 2.30.66.5
     workspaceTabStyle, 2.23.8.8     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, 2.30.103
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
ICMFF force field, 2.32.79Indexx, 2.30.71

     image, 2.30.74MolPSA, 5.7.12
     model, 2.30.75Moment, 2.30.87
Insertion, 2.30.72     of Inertia, 2.30.87
Integer, 2.30.76Money, 2.30.94
Integral, 2.30.77NMR, 2.29.60.1
Interrupt, 2.30.78NOE averaging, 2.22.6
Introduction, 1Name, 2.30.97
JSON, 2.29.81.57     chemical, 2.30.97.6
LIBRARY, 2.23.10          property, 2.30.97.1
     men, 2.23.10.1     close sequence, 2.30.97.3
     res, 2.23.10.2     conf, 2.30.97.7
Label, 2.30.79     image, 2.30.97.11
Laplacian, 2.30.80     molcart, 2.30.97.12
Latent, 2.30.185.3     object parray, 2.30.97.10
LatentVector, 2.30.185.3     sequence, 2.30.97.8
Length, 2.30.81     soap, 2.30.97.2
LinearFit, 2.30.82     string, 2.30.97.4
LinearModel, 2.30.83     tree, 2.30.97.5
Log, 2.30.84Namex, 2.30.98
LogP, 2.30.112     image, 2.30.98.2
LogS, 2.30.112     sequence, 2.30.98.1
M_out, 2.24.5Newick tree format, 2.30.154.4
Mac, 3.14.6.2Next, 2.30.99, 2.30.99.1
Map, 2.30.85     covalent neighbors, 2.30.99.1
Markush structures, 2.29.52Nof, 2.30.100
Mass, 2.30.86     chemical, 2.30.100.2
Match, 2.30.88     distance, 2.30.100.3
Mathews, 2.30.134.4     latent, 2.30.100.6
Matrix, 2.30.89     library, 2.30.100.4
     alignment, 2.30.89.9     molcart, 2.30.100.5
     boundary, 2.30.89.10     soap, 2.30.100.7
     color, 2.30.89.4     tree, 2.30.100.1
     grob connectivity, 2.30.89.13Norm, 2.30.101
     histogram, 2.30.89.12Normalize, 2.30.102
     new, 2.30.89.1NotInList, 2.30.103
     residue areas, 2.30.89.8     R, 5.7
          comparison, 2.30.89.5OBJECT, 2.23.11
     stack, 2.30.89.11Obj, 2.30.104
     sub, 2.30.89.2Occupancy, 2.30.105
     symmetric, 2.30.89.3PBS, 3.13.3.6
     table, 2.30.89.6PLOT, 2.23.12
     tensor, 2.30.89.7     Yratio, 2.23.12.9
Max, 2.30.90     box, 2.23.12.1
     image graphic, 2.30.90.1     color, 2.23.12.2
MaxHKL, 2.30.91     font, 2.23.12.3
Mean, 2.30.92     fontSize, 2.23.12.4
Method, 2.22.13     gridLineWidth, 2.23.12.5
Min, 2.30.93     labelFont, 2.23.12.13
Mod, 2.30.95     lineWidth, 2.23.12.6
Mol, 2.30.96     logo, 2.23.12.10

     numberOffset, 2.23.12.8Resolution, 2.30.127
     orientation, 2.23.12.11Rfactor, 2.30.129
     rainbowStyle, 2.23.12.14Rfree, 2.30.130
     seriesLabels, 2.23.12.12Ring, 2.30.128
PLS, 2.30.100.6Rmsd, 2.30.131
     error, 2.30.134.4     of subset, 2.23.14
     models, 2.30.134.4Rot, 2.30.132
Parray, 2.30.107S, 5.8
Parray-object, 2.30.107SAR analysis, 2.29.62.27, 2.29.62.28, 2.29.89.2, 2.29.89.3
Path, 2.30.106SC, 2.29.35.2
Pattern, 2.30.108SEQUENCE.restoreOrigNames, 2.23.12.15
Pi, 2.30.109SITE, 2.23.13
Polar Surface Area, 5.7.12     defSelect, 2.23.13.2
Potential, 2.30.110     labelOffset, 2.23.13.3
Power, 2.30.111     labelStyle, 2.23.13.4
Predict, 2.30.112     labelWrap, 2.23.13.5
Probability, 2.30.113     showSeqSkip, 2.23.13.6
Profile, 2.30.114     wrapComment, 2.23.13.7
Property, 2.30.115SLN notation, 2.30.154.10
Putarg, 2.30.116SMARTS, 2.26, 2.29.10, 2.30.100.2
Putenv, 2.30.117SOAP, 2.30.97.2, 2.30.100.7, 2.30.180.1
R-groups, 2.29.52     request message, 2.30.150
REBEL, 3.7.2SSSR, 2.30.128
     faq, 3.7.2S_out, 2.24.8
     file, 2.29.52S_proteinTags, 2.24.9
RNA topology, 2.23.5.16Sarray, 2.30.133
R_2out, 2.24.7     index, 2.30.133.1
R_out, 2.24.6Score, 2.30.134
Radius, 2.30.118     alignment, 2.30.134.8
Random, 2.30.119     apf, 2.30.134.3
     string, 2.30.119.1     chemset, 2.30.134.2
Rarray, 2.30.120     conservation, 2.30.134.7
     reverse, 2.30.120.2     model, 2.30.134.4
     sequence projection, 2.30.120.1     overlap, 2.30.134.1
     alignment projection, 2.30.120.3     predictions, 2.30.134.5
          strength, 2.30.120.5     sequence, 2.30.134.6
     property assignment, 2.30.120.4Scripting Tutorials, 1.8
RarrayAlignment, 2.30.120.5Select, 2.30.135
Rarrayinverse, 2.30.120.2     break, 2.30.135.1
Real, 2.30.121          alignment, 2.30.135.14
Reference, 2.30.123          atom property, 2.30.135.7
     Guide, 2          nmembers, 2.30.135.4
Remainder, 2.30.122          string, 2.30.135.9
Replace, 2.30.124     expand, 2.30.135.6
     chemical, 2.30.124.4     fix, 2.30.135.2
     exact, 2.30.124.1     graphical, 2.30.135.5
     regexp, 2.30.124.3     neighbors, 2.30.135.3
     simple, 2.30.124.2Select_by atom numbers, 2.30.135.10
Res, 2.30.125, 2.30.126Select_by_sequence, 2.30.135.13
Resali, 2.30.126Select_by_text, 2.30.135.9

Select_patching, 2.30.135.11     rebelPatchSize, 2.18.5, 2.23.14.5
Select_projection, 2.30.135.8     smilesXyzSeparator, 2.23.14.6
Sequence, 2.30.136     superimposeMaxDeviation, 2.23.14.9
     array, 2.30.136.2     superimposeMaxIterations, 2.23.14.7
Sequence(dna reverse), 2.30.136.1     superimposeMinAtomFraction, 2.23.14.8
Shannon, 2.30.47     tsShape, 2.23.14.11
Shuffle, 2.30.137     tsWeight, 2.23.14.12
Sign, 2.30.138     writePdbRenameRes, 2.23.14.13
Simulations, 1.4.2Table, 2.30.158
Sin, 2.30.139     alignment numbers, 2.30.158.3
Sinh, 2.30.140     distance, 2.30.158.10
Site, 2.30.141     matrix, 2.30.158.4
Slide, 2.30.142     model, 2.30.158.8
Smiles, 2.30.143          chem, 2.30.158.9
Smooth, 2.18.24, 2.30.144, 2.30.144.1, 2.30.144.3     pairs, 2.30.158.5
     matrix, 2.30.144.2     plot, 2.30.158.7
Smoothrs, 2.30.144.3     stack, 2.30.158.6
SoapMessage, 2.30.150     url_decoder, 2.30.158.1
SolveQuadratic, 2.30.145Table(alignment), 2.30.158.2
SolveQubic, 2.30.146Table(stack), 2.30.158.6
Sort, 2.30.151Tan, 2.30.159
Sphere, 2.23.14.3, 2.30.149Tanh, 2.30.160
Split, 2.30.152Tanimoto, 2.30.66.3
     chemical, 2.30.152.4     distance, 2.29.62.37
     multisep, 2.30.152.3          matrix, 2.30.44.7
     regexp, 2.30.152.2Temperature, 2.30.162
     tree, 2.30.152.1Tensor, 2.30.161
Sql, 2.30.147Time, 2.30.163
Sqrt, 2.30.148Tointeger, 2.30.164
Srmsd, 2.30.153Tolower, 2.30.165
Sstructure, 2.30.155Toreal, 2.30.166
String, 2.30.154, 2.30.154.8Torsion, 2.30.167
     alternative, 2.30.154.7Tostring, 2.30.168
     date, 2.30.154.2Toupper, 2.30.169
     mol, 2.30.154.3ToxScore, 2.31.2
     selection, 2.30.154.8Tr123, 2.30.170
     slide gui, 2.30.154.9Tr321, 2.30.171
     substring, 2.30.154.1Trace, 2.30.172
     chemical formula, 2.30.154.10Trans, 2.30.173
Sum, 2.30.156Transform, 2.30.174
     chemical, 2.30.156.1Transpose, 2.30.175
     image, 2.30.156.2Trim, 2.30.176
Swissprot, 2.29.107.24     chemical, 2.30.177
Symgroup, 2.30.157     sequence, 2.30.178
T, 5.9Turn, 2.30.179
TOOLS, 2.23.14Type, 2.30.180
     edsDir, 2.23.14.1     molcart, 2.30.180.2
     membrane, 2.23.14.2     soap, 2.30.180.1
     minSphereCubeSize, 2.23.14.3     Z, 5.10
     pdbReadNmrModels, 2.23.14.4Unique, 2.30.181

Uppsala, 2.32.42acidity constant, 2.29.86.11, 2.29.86.12
     server, 2.32.43activate fog, 2.29.23.24
V_, 2.8.1     alignment, 2.29.86.40
Value, 2.30.183     document, 2.29.86.40
     soap, 2.30.184     tab, 2.29.86.40
Vector, 2.30.16, 2.30.185, 2.30.185.1, 2.30.185.3     table, 5.9.2.4
     symmetry transformation, 2.30.185.2add, 2.29.1
Vectorproduct, 2.30.185.1     column, 2.29.1.1
Vectorsymmetrytransformation, 2.30.185.2          function, 2.29.1.1.1
Version, 2.30.186     matrix, 2.29.1.2
View, 2.30.188     slide, 2.29.1.3
Volume, 2.30.187     table, 2.29.1.4
WEBAUTOLINK, 2.23.16          row, 2.29.1.4
WEBLINK, 2.23.15addBfactor, 2.19.1
Warning, 2.30.189adding atoms to non-ICM objects, 2.29.7.1
Wavefront format, 2.29.81.22     columns to table, 2.29.1.1
XML, 2.12     hydrogens, 2.32.13
Xyz, 2.30.190     in place, 2.14.4
     axes, 2.30.190.7     to slideshow, 2.29.1.3
     chemical match, 2.30.190.5admet selection, 3.13.3.4
     fract, 2.30.190.3advanced chemical search, 3.6
     mesh, 2.30.190.2     operations, 2.14.6
     points, 2.30.190.1     ops, 2.14.6
     transformed xyz, 2.30.190.4ahfs, 2.30.44.6
     vector2matrix, 2.30.190.6ali_seq_project, 2.30.154.5
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, 2.30.190.3alignMinMethod, 2.19.2
accFunction, 2.24.2alignOldStatWeight, 2.19.3
acceptor, 3.6.1alignTwoSequences, 2.32.1
access large sdf file, 2.29.81.24aligned residues, 2.30.126
accessMethod, 2.22.2alignment, 2.29.22.26, 2.29.86.27, 2.29.86.35, 2.29.86.55, 5.1.1
accessible residues, 3.3.6     as table, 2.30.158.2
     surface, 2.29.62.14, 5.8.15     block length, 2.18.22
accessing sections, 2.29.107.24          secondary structure, 2.31.1
accuracy, 2.30.134.4     cleaning, 2.30.144.4

     coloring, 2.21.1area under curve, 2.32.21
     conservation, 2.32.8arguments, 2.29.61
     distance, 2.30.135.13arithmetic 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, 2.30.154, 2.30.154.5, 2.30.154.6     derivative, 2.30.144.1
     score, 2.30.134.7     overlap, 2.30.134.1
     sequence reordering, 2.30.5     parray, 2.29.22.31
     strength, 2.30.120.5     size, 2.30.100
     structural, 2.29.3.5, 2.30.5     subset, 2.6
     to sequence transfer, 2.30.120.1arrow from selection, 2.32.36
          text conversion, 2.30.154.4     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, 2.30.135.5
alignment_as_text, 2.30.154.4as_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, 2.30.170, 2.30.171atom, 2.29.13.1, 5.1.7
          colors, 2.30.29.3     centers within, 2.30.149
          labels, 2.29.3.2     code file, 2.33.4
and, 2.14.3     coordinates, 2.30.190.1
angle rotation, 2.32.84     flickering, 2.29.86.3
angles, 2.30.100.3     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, 2.30.158.10
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, 2.30.180
     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
appending, 2.29.1.1     alternative position, 2.29.86.18
     an element, 2.14.4     selecting, 2.8.8
     menu items, 2.23.10.1     translate, 2.29.86.3
     representations to a slide, 2.29.23.21attenuation by occupancy, 2.29.62.25
     rows to matrix, 2.29.1.2auc enrichment, 2.32.21

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, 2.30.135.3
     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, 2.30.156.2calcSeqSimilarity, 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, 2.30.190
     to protein, 2.29.69.3cartridge, 3.5
     width, 2.23.9.14cavities, 2.29.89.1
bonded atoms, 2.30.99.1cavity, 5.3.1
born radii, 2.29.87.9     analysis, 3.3.13
boundary element, 5.2.5ccp4 maps, 2.29.81.27
          matrix, 2.30.89.10cd, 2.29.86.21
box, 2.30.21cell axis vectors, 2.30.190.7
break, 2.29.6     specific icm commands, 5.9.2.4
brightness, 2.23.5.33center, 2.13.1, 2.29.9
build, 2.29.7cgi programming with icm, 2.11
     atom, 2.29.7.1chain breaks, 2.23.5.7, 2.23.5.8, 2.30.135.1
     column, 2.29.7.2     symbol, 2.29.86.9
     faq, 3.8.1change atom position, 2.29.86.3

     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, 2.30.89.4
channel, 2.23.14.2cif, 2.29.81.48
charge, 5.3.2circular permutation of coordinates, 2.29.66
     compounds, 2.29.67.2clamp values to range, 2.30.176
     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, 2.30.164
chem formula, 2.30.154.10classification, 2.30.44.6
chemSuper3D, 2.32.22clear, 2.29.10
chemical, 2.23.14.6, 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, 2.30.97.3
     descriptors, 2.30.41, 5.7.12     value, 2.30.56.1
     distance, 2.30.44.8, 2.30.134.2, 2.30.134.3cluster, 2.30.152.1
     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, 2.30.97.5
     formula, 2.30.154.10          size, 2.30.100.1
     fragment counting, 2.30.100.2clustering, 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, 2.30.190.5cnMethodAverage, 2.22.6
     matching, 2.29.35.4, 2.29.81.49, 2.29.81.50, 2.30.131, 2.30.153cnWeight, 2.19.6
     models, 2.30.97.1code, 2.30.44.6
     modification, 2.29.65, 2.29.67, 2.32.37coil, 5.3.4
     name, 2.30.97.6collection, 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, 2.30.100.2          alignment, 2.29.13.3
     similarity, 3.5          atom contributions, 2.29.12
     simplification, 2.30.176          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, 2.30.131, 3.15          potential, 2.32.25
     table, 2.25          shape depth, 2.29.13
     text format, 5.6.11     chemical, 2.29.12, 2.29.85.1
     topological descriptors, 2.30.40     choice, 2.19.9
     view, 2.29.86.54     file, 2.33.15
chemistry, 2.25, 2.30.27     grob, 2.29.13.4
chiral isomer generation, 2.29.30          by atom selection, 2.29.13.4.3

          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, 2.30.154.7
     volume, 2.29.13.7conf, 2.29.86.61, 2.29.107.41, 2.30.158.6, 5.3.12, 5.8.9
column, 5.3.5     data, 2.30.158.6
     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, 2.30.107     memory usage, 2.18.7
     selection, 2.30.97conformation comparison, 2.22.7
combinatorial compounds, 2.30.27conformational ensemble, 2.29.7.5.2
     libraries, 2.29.62.33, 2.30.100.4     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, 2.30.97.4, 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, 2.30.103     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, 2.30.120.5, 2.30.134.7
     atom, 2.29.14.1constant, 2.5
     by rmsd without superposition, 2.29.14.1constants, 2.5
     chemical tables, 2.29.35.10contact areas, 2.30.89
     patch only, 2.29.14.3continue, 2.29.17
     rmsd, 2.29.14.1contour lines, 2.30.32
     surface, 2.29.14.3     surfaces, 2.23.7.5
     variables, 2.29.14.2contouring density, 2.29.62.14
compareMethod, 2.22.7contrast, 2.23.5.33
comparing two sarrays, 2.30.103conversion, 5.1.6
comparison, 2.30.70.10     to real array, 2.30.166
     operations, 2.14.5convert, 2.29.18, 2.29.18.2, 3.13.2
complete view, 2.30.142     3D to chemical, 2.30.27

     ICM object to PDB, 2.29.93crystallography, 2.30.127
     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, 2.30.106
     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, 2.30.164customization, 3.1.2
          icm-object, 2.29.18     environment, 2.28
          integer, 2.30.164     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, 2.30.158.2     browser, 2.29.60.3
     chemicals, 3.13.2.3     connection, 2.29.16.1
     table columns into matrix, 2.30.89.6     file, 3.5.1
     to, 2.30.121     import, 2.29.62.26
cool, 2.32.40date, 2.29.21, 2.30.154.2
     pictures, 2.23.5.30     array, 2.29.21
cooling schedule, 2.19.46dcMethod, 2.22.8
coordinate frame, 2.19.4, 2.29.23.4dcWeight, 2.19.8
coordinates, 2.23.14.6decomposition, 2.29.62.27, 2.29.89.2, 2.29.89.3
copy, 2.29.19defCell, 2.24.1
     chemical image, 2.23.9.15defSymGroup, 2.18.2
     file, 2.21.26default atom colors, 2.29.86.16
     site, 2.29.86.28     color of label, 2.19.11
correlation matrix, 2.30.161     parameters, 2.22.1
covalent bound count, 2.30.135.3     value, 5.8.2
     neighbors, 2.30.99.1define axis, 3.10.3
covalently attached molecule, 2.30.99.1defining space box, 2.30.21
cpk, 2.19.35, 5.3.13dehtml, 2.30.124.3
create a covalent bond, 2.29.62.2del, 2.29.22.9
     pharmacophore, 2.32.87delete, 2.29.22
creating a local patch object, 2.29.18.2     3D graphics panel, 2.29.102
credits, 4.5     alias, 2.29.22.2
crypt, 2.29.20     array element, 2.29.22.6
crystal axis vectors, 2.30.16          index, 2.29.22.6
     symmetry transformation, 3.10.2          selection, 2.29.22.1
          transformations, 2.30.174     atom, 2.29.22.7
crystallographic cell, 2.29.66     bond, 2.29.22.14
     occupancy, 2.30.105     boundary, 2.29.22.15
     symmetry intro, 1.4.2.4     chemical, 2.29.22.37

          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, 2.30.103
     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, 2.30.133
     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, 2.30.135.1     skin, 2.29.23.20
     restraint, 2.29.22.18     slide, 2.29.23.21
deleting, 2.29.22.26     stack, 2.29.23.6
     sites by number, 2.29.22.24     string, 2.29.23.22
delphi, 2.32.25     surface, 2.29.23.20
density correlation, 2.19.8, 3.11.3          area, 2.23.5.3
     fitting, 2.22.8     tethers, 2.29.23.23
     in unit cell, 2.29.62.23     trajectory, 2.29.23.17
densityCutoff, 2.19.13     volume, 2.29.23.24

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, 2.30.158.5, 2.32.7dynamic gui, 5.5.5
          between stack conformations, 2.30.89.11ecepp, 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, 2.30.100.3eigenvalues, 2.30.45
distribution, 1.3eigenvectors, 2.30.45
     comparison, 2.30.134electro 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, 2.30.152.4          around selection, 2.19.25
dna to protein sequence translation, 2.30.173.1          map generation, 2.19.1
     translate, 2.30.173.1          maps, 2.23.14.1
dockScan, 3.13.2.5electrostatic boundary matrix, 2.30.89.10
docking, 2.32.89     coloring, 2.23.14.5
     intro, 3.13.2.1     isopotential surfaces, 2.29.62.13
     result viewing, 2.32.28     potential, 2.29.13.4.5
     simple models, 3.14.3     solvation, 3.7.2
     timing, 3.13.1.3     surface, 2.32.25
     with template, 3.13.2.6     troubleshooting, 5.7.13
documents, 5.5.8electrostatics, 2.23.14.5
dollar separated file, 2.29.81.44     intro, 1.4.2.9
dominant color, 2.30.29.2ellipsoid, 2.30.161
donor, 3.6.1elseif, 2.29.25
     plot intro, 1.4.3.2empty model, 2.30.107
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, 2.30.134.7
dsCellBox, 2.32.15     atom, 2.29.18.4
dsChem, 2.32.17enumerate, 2.29.29, 2.29.30, 2.29.31, 2.29.32
dsCustom, 2.32.18     charge, 2.29.29
dsPocket, 2.32.28     chiral, 2.29.30
dsPropertySkin, 2.32.19     library, 2.29.32
dsPrositePdb, 2.32.24     tautomer, 2.29.31
dsRebel, 2.18.5, 2.23.14.5, 2.32.25enumeration, 2.30.27
dsSeqPdbOutput, 2.32.26eps files, 2.21.23
dsSkinLabel, 2.32.27equipotential surface, 2.30.32

     ignoring, 2.21.25field, 2.29.86.35
error/warning bits cleanup, 2.29.10     name, 2.30.97.2
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, 2.30.124.1     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, 2.23.14.13     alignment, 2.29.35.1
exporting sdf, 2.29.107.11     and replace a chemical pattern, 2.29.67.1
expression shortcuts, 2.10.1.2               chemical fragment, 2.29.67
     tags, 2.24.9     chemical, 2.29.35.5
     comparison, 2.14.5          pattern, 2.29.67
     arithmetics, 2.14.2          substructure, 2.30.70.2
     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, 2.30.135.6     in sarray, 2.30.70.8
               terminal atoms, 2.30.135.6     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, 2.30.134.4     scaffold, 2.30.177
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, 2.30.135.1
          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, 2.30.135.2
fasta, 2.23.12.15, 5.5.2flattening 3D molecule, 2.32.17
     format, 2.29.107.1flexible superimpose, 2.32.50
feature table, 5.8.6.1flow control, 2.15
     in sequences, 2.29.86.26fog, 2.19.17, 2.29.13.7, 2.29.23.24, 5.4.2
ffMethod, 2.22.12     color, 2.19.17

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, 2.30.158.7
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, 2.30.190.3grob, 5.5.3
     to abs coordinates, 2.30.16     coloring, 2.29.13
fragmented molecule, 2.29.18.2     files, 2.33.10
frame, 2.29.91, 2.29.107.31     inside-out flip, 2.29.86.42
fullscreen, 2.29.86.85     normal directions, 2.29.86.42
function, 2.29.40, 2.29.61     vertex, 2.23.5.21
     columns, 2.29.1.1.1     translate, 2.29.100
functions, 5.1.1group, 2.29.43
     selecting in objects, 2.8.10     by column, 2.29.43.4
gamess, 5.5.6     column, 2.29.43.4
     expansion, 2.30.144.4     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, 2.30.144.2          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
graph matching, 2.30.131     list, 2.30.158.10
graphical box, 2.29.23.7     show, 2.29.87.23
     row selection, 2.30.70.5hbondMinStrength, 2.23.5.25
     selection, 2.30.135.5     faq, 3.3.4
graphics, 2.19.9, 2.29.86.4, 2.30.186, 3.2, 5.3.3     how to, 3.3.4

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, 2.30.106
     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, 2.30.178     loops, 2.15.1
histogram, 2.29.62.32     macros, 2.32
     2D, 2.30.89     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, 2.30.97.4, 5.5.8     ali, 2.33.31
     document order, 2.29.86.40     all, 2.33.32
     tag removal, 2.30.124.3     bbt, 2.33.5
html-formatted text, 5.5.8     bst, 2.33.6
html5, 2.11     cfg, 2.33.14
hue, 2.30.89.4     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, 2.30.100.3     col, 2.33.24
     display, 2.23.5.32     gro, 2.33.10
     placement, 2.29.86.25     gui, 2.28
hydrophobicity profile, 3.3.12     hbt, 2.33.12
iSee, 5.8.14     hdt, 2.33.13
i_2out, 2.18.4     htm, 2.33.11
i_out, 2.18.3     iar, 2.33.35
iarray, 2.29.22.6, 2.30.56.1, 2.30.66.2, 2.30.70.8, 5.6.1     lps, 2.29.7.5.2

     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, 2.30.89.4
     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, 2.30.149
     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, 2.30.120.2
     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, 2.30.134.4
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, 2.30.89.13l_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
          entry, 2.30.133.1l_confirm, 2.20.9
          sdf-file path, 2.30.106l_easyRotate, 2.20.10
indices of labeled table rows, 2.30.70.6l_info, 2.20.11
          selected table rows, 2.30.70.5l_minRedraw, 2.20.12
infinity, 2.30.166l_neutralAcids, 2.20.13

l_print, 2.20.15     variable, 2.29.53
l_racemicMC, 2.20.16     variables, 2.29.53
l_readMolArom, 2.20.17linked alignment, 2.30.97
l_showAccessibility, 2.20.18     sequence, 2.30.97
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, 2.30.97
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, 2.30.133
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, 2.30.100.6     molcart, 2.29.60.3
learn, 2.29.51, 2.30.107     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, 2.30.89.3loadEDSweb, 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, 2.30.84
     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, 2.30.161
     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, 2.30.89.4          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, 2.30.165
lineWidth, 2.19.22ma29, 3.11
linear chemical notation, 2.26macro, 2.29.61, 5.6.5
     regression, 2.30.83macro_def, 5.6.5
     group, 2.29.52main ICM references, 4.2
     internal variables of molecular object, 2.29.53     concepts, 3.10.1
     ms2ali, 2.29.54make, 2.29.62
     sequences to 3D objects, 2.29.54     3d label, 2.29.62.15
     to alignment, 2.29.54     angle, 2.29.62.18

     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, 2.30.120.1
     boundary, 2.29.62.4     averaging, 2.30.144.5
     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, 2.30.92
          chem_array, 2.29.62.9     min value, 2.30.93
     grob, 2.32.36     name, 2.30.85
          from image, 2.29.62.11     operations, 5.6.6
               matrix, 2.29.62.12     transformations, 2.30.144.5
          image, 2.29.62.11     trimming, 2.30.22
          map, 2.29.62.10     value sigma, 2.30.131
          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, 2.30.120.4
     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, 2.30.89.1
     pca, 2.29.62.29     plot, 2.30.32
     peptide bond, 2.29.62.30     map value, 2.30.90
     plot, 2.29.62.32maxColorPotential, 2.18.5, 2.32.25
     reaction, 2.29.62.33maxMemory, 2.18.7
     sequence, 2.29.62.35, 2.29.62.36     movie, 3.9.2
          alignment, 2.29.62.34mcBell, 2.19.26
          from alignment, 2.29.62.34mcJump, 2.19.27
          random, 2.29.62.36mcShake, 2.19.28
     torsion, 2.29.62.19mcStep, 2.19.29
     tree, 2.29.62.37mean force, 2.29.86.51, 2.29.87.37
          object, 2.29.62.38membrane, 2.23.14.2
     unique, 2.29.62.39memorizing positions, 3.2.4
makeAxisArrow, 2.32.36menu, 2.29.64
makeIndexChemDb, 2.32.44     script, 3.1.3
makeIndexSwiss, 2.32.45merge PDB, 2.32.92
makePdbFromStereo, 2.32.46     arrays to table, 2.29.43.3
makePharma, 2.32.87     continuation lines, 2.29.81.39
makeSimpleDockObj, 2.32.47     objects, 2.29.69.2
makeSimpleModel, 2.32.48     parts of molecule, 2.29.69.3

     sarray into string, 2.30.156          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, 2.30.156.1mol, 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, 2.30.154.3
mesh, 2.30.107, 2.30.187     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, 2.30.107
mfMethod, 2.22.16mol-format, 2.23.14.6
mfWeight, 2.19.30mol2, 5.6.12
mimel, 5.6.8molcart, 2.29.16.1, 3.5
mimelDepth, 2.19.31     connection options, 3.5.2
mimelMolDensity, 2.19.32molecular, 2.30.58, 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, 2.30.112
     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, 2.30.187     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, 2.30.180monte 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
     and reroot, 2.29.18.4     file, 2.29.107.31
     chem, 2.29.67move, 2.29.69
          charge, 2.29.67.2     alignment sequence, 2.29.69.7
          delete salt, 2.29.67.3     atoms, 2.29.86.3
          normalize, 2.29.67.4     bonding, 2.29.69.3
     chemical column, 2.29.67.3     column, 2.29.69.5

     file, 2.21.28, 2.29.82.3normal distribution, 2.30.119
     fragments together, 2.29.69.3normalize chemicals, 2.29.67.4
     molecule, 2.29.69.1     defined, 2.30.166
     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, 2.30.100
     images by frame, 3.9.2.2          hydrogen bonds, 2.29.87.23
     molecular simulation, 3.9.2          molecules in objects, 2.30.135.4
     rotate view, 3.9.1          occurrences, 2.30.100
     zooming, 3.9.1          residues in molecules, 2.30.135.4
moving selection to another object, 2.30.135.8          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, 2.30.107
multicore, 2.30.70.1     parray, 5.7.3.1
multiline input, 2.29.81.5     properties, 2.29.86.34
multiple NMR models, 2.23.14.4     stack, 5.8.9
     alignment, 2.29.3.3     to chemarray, 2.30.27
          to pairwise similarities, 2.32.7     user fields, 2.30.54.1
     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, 2.30.154.3     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, 2.30.112
mutating residue, 3.8.5off, 2.29.81.22
mute, 5.6.15     format, 5.5.3
mysql, 2.29.16.1oligonucleotide melting, 2.30.162
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, 2.30.186, 5.10.2
nearest sequence, 2.30.93optimal chemical superposition, 3.14.5.1
neato, 2.30.158.7optimization, 2.29.68
neighbor joining, 2.29.62.38     Hbond, 2.32.91
neighbors, 2.30.149     hydrogen bond, 2.32.91
nested script, 5.8.2optimizeHbonds, 2.32.91
     real array, 2.30.120or, 2.14.3
nice, 2.32.39order, 2.29.3.1, 2.29.69.7
     image, 3.2.2original sequence names, 2.23.12.15
non-redundant, 3.4.3os_, 2.8.5

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, 2.30.184plotRama, 2.32.58
parsing, 2.30.88plotRose, 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, 2.30.158.8, 2.30.158.9
pause, 2.29.70     model, 2.30.158.8, 2.30.158.9
pdb, 5.6.10, 5.7.6     weights, 2.30.158.8, 2.30.158.9
     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, 2.30.190.1
     docking, 3.12.5     size, 2.23.5.21
     folding, 1.4.2.1pointer array, 5.7.3
          intro, 1.4.2.1polar hydrogens, 2.23.5.32
personal gui controls, 3.1.2     surface area, 2.30.112
     setup, 3.1.2polarization charge, 3.7.2, 5.7.13
ph30, 3.12positional constraint, 2.23.14.11
ph4, 5.7.8postscript, 2.21.23

          coloring, 5.7.13quantum mechanics, 2.29.81.21, 2.29.107.17
pov-ray, 2.29.107.38qubic equation, 2.30.146
pow, 2.30.37query, 3.14.6.1
precision, 2.30.134.4     molcart, 2.29.78
predict, 2.29.73question mark operator, 2.30.154.7
predictSeq, 2.32.61quit, 2.29.79
prediction model, 2.30.83     property transfer via alignment, 2.30.120.3
     quality, 2.30.134r_2out, 2.19.34
     score, 2.30.134r_out, 2.19.33
predictive models, 2.29.51.2radii.electrostatic, 2.30.118
preference, 2.22     van der Waals, 2.30.118
     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, 2.30.99.1random array, 2.30.119
principal axes, 2.30.161     order, 2.30.137
     component analysis, 3.3.9     sequence, 2.29.62.36
     inertia moments, 2.30.87randomSeed, 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, 2.30.120.2, 5.7.11
printPostScript, 2.32.64     properties, 2.30.120.4
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, 2.30.97.3     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, 2.30.190.2     drestraint, 2.29.81.18
          intro, 1.4.2.5          type, 2.29.81.19
     engineering, 2.24.9     entries from database, 2.29.81.8
     grid docking, 3.14.2     factor, 2.29.81.20
     health, 2.32.58     file by chunk, 2.29.81.40
     topology, 2.23.5.42     from file, 2.29.81.1
psa, 5.7.12          string, 2.29.81.5
purple box, 2.30.21     fromstring, 2.29.81.5
quadratic equation, 2.30.145     ftp http, 2.29.81.9

     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, 2.23.14.5, 5.7.13
     map, 2.29.81.27rebuild molcart index, 2.29.7.10
     matrix, 2.29.81.28recalculate dependent values, 2.29.7.2
     menu file, 2.29.81.3     values, 2.29.1.1.1
     mol, 2.20.13, 2.29.81.8, 2.29.81.29receptor, 3.13.1.1
     mol2, 2.29.81.8, 2.29.81.30     preparation, 3.13.1.1
     object, 2.29.81.32redefine hydrogen coordinates, 2.29.86.25
          parray, 2.29.81.32.1references, 4
     pdb, 2.23.14.4, 2.29.81.2, 2.29.81.33refineModel, 2.32.66
          sequence, 2.29.81.34reflections, 2.23.5.33
     profile, 2.29.81.35refresh view, 2.29.23.2
     prosite, 2.29.81.36refs, 4.1
     rarray, 2.29.81.37regexp, 2.10, 2.30.88
     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, 2.30.88
     string, 2.29.81.43          filter, 2.29.81.1
     table, 2.29.81.44     expression, 2.30.124.3
          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, 2.30.147
          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, 2.30.178
          write, 2.29.81.31.1     file, 2.29.22.9
     unix, 2.29.81.10     trailing blanks, 2.30.176
          cat, 2.29.81.11removing html tags, 2.29.81.47
     variable, 2.29.81.52     outliers, 2.30.176
     view, 2.29.81.53rename, 2.29.3.1, 2.29.82
     vrestraint, 2.29.81.54     chemicals, 2.29.86.47
          type, 2.29.81.55     column table, 2.29.82.1
     with filter, 2.29.81.6     file, 2.29.82.3
     xml, 2.29.81.56     molcart, 2.29.82.2
readMolNames, 2.24.11     system, 2.29.82.3
readcomp_matrix, 2.29.81.14renaming, 2.23.12.15

     alignment sequences, 2.29.107.1     normals, 2.29.86.42
     array, 2.30.137reversing order, 2.30.66.2
     columns by function, 2.29.88.3rgb, 2.30.89.4, 5.7.17
     objects, 2.29.88.4     matrix, 2.30.29
replace matching array element, 2.30.124.1ribbon, 5.7.18
     without interpretation, 2.30.124.2     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, 2.30.128
reserved names, 2.24     sampling, 3.16
residue, 2.29.13.1, 5.7.16     templates, 2.29.86.8
     accumulators, 2.30.63rm, 2.29.22.9
     alignment, 2.29.86.68, 2.29.86.69rocking, 2.29.23.5
     conservation, 2.30.120.5root mean square deviation, 2.30.134.4
     contact area matrix, 2.30.89.8roots, 2.30.145, 2.30.146
          areas, 2.30.7.1rotate, 2.29.84
     field, 2.29.86.34     grob, 2.29.84.2
     gap, 2.23.5.7, 2.23.5.8     object, 2.29.84.1
     label, 2.19.35, 2.29.3.2     view, 2.29.84.3
     library file, 2.33.20rotation, 2.29.23.5
     name, 2.30.79     angle, 2.30.17
          translation, 2.23.14.13rounding, 2.30.120
     number, 2.30.66.5     a real, 2.30.154
          table, 2.30.158.3     output, 2.29.87.45
     property averaging, 2.30.144.3rsWeight, 2.19.36
          calculation, 2.30.63rs_, 2.8.7
     proximity, 2.30.89.8ruler, 2.19.10
     ranges, 2.8.11     script, 2.29.8
     selection, 2.20.21running a docking job, 3.13.2.5
          as string, 2.30.154.8     dock job, 3.13.2.4
          function, 2.30.125     script from html, 5.8.2
     table, 3.14.4.1s-s bond, 5.4.5
     tethering, 2.29.86.68, 2.29.86.69s_alignment_rainbow, 2.21.1
     user field, 2.30.54.1s_blastdbDir, 2.21.2
residue_selections, 2.8.11s_editor, 2.21.3
     selecting, 2.8.7s_entryDelimiter, 2.21.4
resizing, 2.30.68s_errorFormat, 2.21.5
resorting nodes edges, 2.30.158.7s_fieldDelimiter, 2.21.6
restore, 3.14.6.2s_helpEngine, 2.21.7
     defaults, 2.29.82.4s_icmPrompt, 2.21.10
     preference, 2.29.82.4s_icmhome, 2.21.8, 3.1.2.1
restraining molecules to shapes, 2.23.14.11s_imageViewer, 2.21.11
restraints, 2.17, 2.29.86.68, 2.29.86.69s_inxDir, 2.21.9
     torsion, 2.29.86.81s_javaCodeBase, 2.21.12
return, 2.29.83s_labelHeader, 2.21.13
reverse complement, 2.30.136.1s_lib, 2.21.14
     lighting, 2.29.86.42s_logDir, 2.21.15

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, 2.30.161
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, 2.30.135.3
s_tempDir, 2.21.30          of the fixed torsions, 2.30.135.2
s_translateString, 2.21.31     based on alignment, 2.30.135.14
s_userDir, 2.21.32          bfactor, 2.30.135.7
s_usrlib, 2.21.33          center of mass, 2.30.135.15
s_webEntrezLink, 2.21.34          coordinates, 2.30.135.7
s_webViewer, 2.21.35          iarray, 2.30.135
s_xpdbDir, 2.21.36          length, 2.30.135.13
sa23, 3.3          occupancy, 2.30.135.7
sampling grid, 2.30.190.2          user field, 2.30.135.7
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, 2.30.135.12
     sdf file, 2.29.107.11     vw partners, 2.30.135.12
saving graphics to album, 2.29.62.20selectMinGrad, 2.19.37
     image, 2.29.107.36selectSphereRadius, 2.19.38
scaffold, 2.30.176selected stack conformations, 2.29.22.17
scaffolds, 2.29.52selecting by b-factor, 2.30.135
scoring, 3.13.1.4               y z, 2.30.135
screen X, 2.30.188     columns, 5.9.1
     coordinates, 2.30.188     from clusters, 3.14.6.4
script, 2.30.97.4, 5.8.2     neighboring elements, 2.30.99
     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, 2.30.135, 2.30.135.6
     image generation, 2.29.23.3     elements, 2.8.4
scripting molecular movements, 3.2.4     examples, 2.8.3
sdf, 2.23.14.6, 2.29.107.24, 5.6.11     functions, 2.8.10
     file, 2.29.81.49, 2.29.81.50, 2.29.86.47, 2.29.107.11, 2.30.154.3, 5.7.3     gap patching, 2.30.135, 2.30.135.11
     to chem-table, 2.30.107     level, 2.8, 2.30.180
search for chemical pattern, 2.30.56.3     levels, 2.8.2
     pdb headers, 3.4.5     simplification, 2.30.135.11
     prosite, 3.4.1     transfer, 2.30.135, 2.30.154.8
     sequence pattern, 2.29.35.8     type, 2.8
searchObjSegment, 2.32.73     types, 2.8.1
searchPatternDb, 2.32.71     variable, 2.24.12
searchPatternPdb, 2.32.72     atoms, 2.8.8

     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, 2.23.14.11, 5.9.4          formal, 2.29.86.11
seq_ali_project, 2.30.154.6               auto, 2.29.86.12
sequence, 2.30.170, 2.30.171, 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, 2.30.134.7          sequence, 2.29.86.19
     distance, 2.30.135     comp_matrix, 2.29.86.20
          matrix from alignment, 2.30.89.9     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, 2.30.178     error, 2.29.86.33
     neighbor, 2.30.97.3     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, 2.30.158.3          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, 2.30.120.3          coordinates, 2.29.86.42
     type, 5.8.3          label, 2.29.86.42
sequence-alignment mapping, 2.30.154.5, 2.30.154.6     group, 2.29.86.63
sequence-structure alignment, 2.30.5.1          column, 2.29.86.24
     output format, 2.18.21, 2.18.22     hydrogen, 2.29.86.25
sequenceBlock, 2.18.21     key, 2.29.86.43
sequenceColorScheme, 2.22.23     label, 2.29.86.44
sequenceLine, 2.18.22          3d label, 2.29.86.44.4
sequences, 3.4          chemical, 2.29.86.44.3
     not in alignments, 2.29.22.23          distance, 2.29.86.44.1
set, 2.29.86          table, 2.29.86.44.2
     alternative atom, 2.29.86.18     map, 2.29.86.45
     area, 2.29.86.1     molcart, 2.29.86.46
     atom, 2.29.86.3     molecular variables, 2.29.86.83
          ball label, 2.29.86.2     name, 2.29.86.47
     background image, 2.29.86.4          sequence, 2.29.86.47.1

     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, 2.30.134.2shadows, 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, 2.30.189
          sequence, 2.29.86.60shineStyle, 2.22.24
          to sequence, 2.29.86.60shininess, 2.19.40
     stack, 2.29.86.61show, 2.29.87, 2.29.87.39
          energy, 2.29.86.61, 2.29.91.1     alias, 2.29.87.7
     stereo, 2.29.86.58     aliases, 2.29.87.7
     swiss, 2.29.86.62     alignment, 2.29.87.8
          name, 2.29.86.62     area, 2.29.87.9
     symmetry, 2.29.86.65     atom, 2.29.87.10
          bio, 2.29.86.64          type, 2.29.87.11
          crystal, 2.29.86.63     atoms, 2.29.87.10
          group, 2.29.86.63     bond, 2.29.87.12
          to a torsion, 2.29.86.65     clash, 2.29.87.13
     table, 2.29.86.66     color, 2.29.87.14
     tautomer, 2.29.86.31     column, 2.29.87.15
     terms, 2.29.86.67     comp_matrix, 2.29.87.16
     tether, 2.29.86.69     database, 2.29.87.17
          append, 2.29.86.70     drestraint, 2.29.87.18
     texture, 2.29.86.32          type, 2.29.87.19
     type, 2.29.86.71     energy, 2.29.87.20
          mmff, 2.29.86.77          atom, 2.29.87.21
          molecule, 2.29.86.75     gradient, 2.29.87.22
          object, 2.29.86.74     hbond, 2.29.87.23
          property, 2.29.86.73          exact, 2.29.87.24
          sequence, 2.29.86.76     hbondexact, 2.29.87.24
          surface, 2.29.86.72     html, 2.29.87.25
     variable grid, 2.29.86.84     iarray, 2.29.87.26
     variablegrid, 2.29.86.84     integer, 2.29.87.27
     view, 2.29.86.80     key, 2.29.87.4
     vrestraint, 2.29.86.81     label, 2.29.87.28
     vrestraintvs_var, 2.29.86.82     library, 2.29.87.29
          radii, 2.29.86.78     link, 2.29.87.30
     vwelradii, 2.29.86.79     logical, 2.29.87.31

     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, 2.30.142, 5.8.14
     profile, 2.29.87.39     transition time, 2.29.23.21
     residue, 2.29.87.40slides, 2.30.188
          type, 2.29.87.41slideshow, 2.29.1.3, 2.29.23.21, 2.30.142
     residuetype, 2.29.87.41sln, 5.8.8
     segment, 2.29.87.42smallest set of smallest rings, 2.30.128
     selftether, 2.29.87.1smart, 2.23.14.6
     sequence, 2.29.87.43smarts, 2.30.70.2
     shell variable, 2.29.87.3smiles, 2.23.14.6, 2.26
     site, 2.29.87.2     to chem-table element, 2.30.107
     stack, 2.29.87.44smooth alignment, 2.30.144.4
     svariable, 2.29.87.3     interpolation, 2.29.91.3
     table, 2.29.87.45     map, 2.30.144.5
          as database, 2.29.87.17     rarray, 2.30.144.1
     term, 2.29.87.46     surface, 2.32.88
     tethers, 2.29.87.47soap, 2.27
     version, 2.29.87.48soft trim, 2.30.176
     volume, 2.29.87.51solid sphere, 2.23.5.11
          map, 2.29.87.52solubility, 2.30.112
     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, 2.30.134.2          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, 2.30.135.13     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, 2.30.124.2space group, 2.29.66
simplified representation, 2.23.5.16     transformations, 2.30.174
     compound, 2.30.177sparse atoms, 2.23.14.3
     mesh structure, 2.29.15.2spawn background job, 2.29.62.1
simulation duration, 2.19.47special values, 2.30.166
     temperature, 2.19.46specificity, 2.30.134.4
     intro, 1.4.2spectral decomposition, 2.30.45
sinking number, 2.19.35split, 2.29.89
site, 2.29.11.2, 5.8.6     column values, 2.29.89.5

     group, 2.29.89.2     filtering, 2.30.176
          array, 2.29.89.3     inversion, 2.30.154.1
     molsar, 2.29.62.28     label, 2.29.23.12
     object, 2.29.89.6     matching, 2.10, 2.30.88
          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, 2.30.97.2
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, 2.30.97.12, 2.30.100.5, 2.30.180.2     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, 2.30.158.5     structure, 3.11.1
ssThreshold, 2.19.41sub-alignment to selection, 2.30.126
ssWeight, 2.19.42sub-matrix, 2.30.89.2
ssbond, 5.4.5subalignment, 2.30.5.3, 5.1.1
ssearch, 2.18.17, 2.29.92submap, 2.30.85
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, 2.30.158.6, 5.3.12, 5.8.9substring, 2.30.88, 2.30.154, 2.30.154.1
     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, 2.30.131support, 1.3
standardization, 2.29.22.11suppressing view changes, 2.29.23.21
     chemical, 2.29.67surface, 2.19.35, 2.30.107, 5.8.15
startup, 3.1.2.3     accessibility, 2.29.87.9
static RMSD, 2.30.153     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, 2.30.190.2
stereoisomer, 2.29.30     point selection, 2.30.190
stereoisomers, 2.20.16     term, 2.19.39
stick, 5.8.10surfaceAccuracy, 2.18.23
store, 2.29.91surfaceMethod, 2.22.25
     conf, 2.29.91, 2.29.91.1surfaceTension, 2.19.44
     frame, 2.29.91.3svariable, 5.8.12
     image, 2.29.62.20     map, 2.30.158.7
     stack object, 2.29.91.2swapping protein fragments, 3.8.7
     torsion type, 2.29.91swiss, 2.29.86.62
strength of hydrogen bond, 2.29.23.14swissFields, 2.24.10
string, 5.8.11swissprot, 2.29.86.26
     array, 2.30.133, 5.8.1symmetrization of a matrix, 2.30.89.3

     faq, 3.10text, 2.30.88
     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, 2.30.170, 2.30.171
     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, 2.30.154.2
     column, 2.30.97timeLimit, 2.19.47
          format, 2.29.86.41tolFunc, 2.19.49
          plot, 2.29.62.32tolGrad, 2.19.48
          transformations, 2.30.102topological 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, 2.30.158.4torsions, 2.30.100.3
     grid view, 5.9.1     score, 2.31.2
     of atoms and distances, 2.30.158.10tpsa, 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, 2.30.120, 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, 2.30.190.4
tempCycle, 2.19.46translate, 2.29.100
tempLocal, 2.19.45transparency, 2.29.86.42, 5.5.3
temperature, 2.19.46     background, 2.29.107.36
     variations in optimizer, 2.19.46     grob, 2.29.23.11
template docking, 3.13.2.6     grobs, 2.23.5.57
tensor product of two vectors, 2.30.89tree, 2.29.62.37, 2.30.97.5
terminal font, 2.33.14     cluster, 2.13
     window, 2.29.44     delete, 2.29.22.36
terms, 2.17     label format, 2.30.97.5
     hydrogen bonding, 2.19.21     representatives, 2.13.1
test, 2.29.97trim string array, 2.29.99.1
     binary, 2.29.97.1trimming grid map values, 2.30.176
testing if argument exists, 2.30.59true positives, 2.30.134.4
tether, 2.23.14.11, 2.29.107.9, 5.9.4, 5.9.5truncate alignment, 2.29.62.34

     grob, 2.23.5.9, 2.23.5.10variable restraint, 2.29.86.81
tsShapeData, 2.23.14.11     selection, 2.8.9
     table format, 2.29.81.44vdW gap, 2.30.149
two alignments, 2.30.44.13vector, 2.30.100.6
     dimensional plot, 2.30.144.2     dot product, 2.30.185.1
     set comparison, 2.30.44.8, 2.30.134.2     length, 2.30.101
     sets, 2.30.70.10     product, 2.30.185.1
txdoc browser, 2.29.81.4     transformation, 2.30.102
type, 2.30.180.1vertex, 2.29.13.4.2
tzMethod, 2.22.26     connectivity, 2.30.89.13
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, 2.30.188
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, 2.30.97     arrays, 2.29.1.1.1
     new object name, 2.30.97     chemistry, 2.29.67, 2.30.100.4
     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, 2.30.169     parallelization, 3.13.3.5
url string parsing, 2.30.158     results, 3.13.3.8
user atom display, 2.23.5.3     scores storage, 3.13.3.7
     commands, 2.29.81.3     threshold, 3.13.3.2
     defaults, 2.29.107.42vls_intro, 3.13.3.1
     environment, 3.1.2.2volume, 5.10.4
     menu, 2.23.10.1vrestraint, 5.10.5
     menus, 2.28     file, 2.33.23
user-defined properties, 2.29.86.34     type, 5.10.6
     solvation parameters, 2.30.7          file, 2.33.22
user_startup, 3.1.2.4vs_, 2.8.9
     icm, 3.1.2vs_out, 2.24.15
     guide, 3vwCutoff, 2.19.52
v_, 2.8.1vwExpand, 2.19.53
van der Waals surface, 2.23.5.56vwExpandDisplay, 2.19.54
varLabelStyle, 2.22.27vwMethod, 2.22.29

wait, 2.29.104     mol2, 2.29.107.30
warning, 2.23.14.3     molcart, 2.29.107.7
     message, 2.30.189     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, 2.23.14.13, 2.29.107.35
web, 2.11, 2.29.105     png, 2.29.107.36
     table, 2.29.105.1     postscript, 2.29.107.37
webEntrezOption, 2.22.30     pov, 2.29.107.38
weighted rmsd, 2.23.14     povray, 2.29.107.38
while, 2.29.106     project, 2.29.107.2
whole string, 2.30.124.1     rarray, 2.29.107.4
window averaging, 2.30.144.1     sarray, 2.29.107.5
     layout, 2.30.154.9     sequence, 2.29.107.39
     width and height, 2.30.188     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, 2.30.88, 5.1.6
     database, 2.29.107.13     drugbank example, 2.12
     drestraint, 2.29.107.14xpdb, 2.29.81.2
          type, 2.29.107.15xplor format, 2.29.81.27
     factor, 2.29.107.16xrMethod, 2.22.32
     gamess, 2.29.107.17xrWeight, 2.19.58
     grob, 2.29.107.18xray density to rectangular energy map, 2.29.62.31
     html, 2.29.107.19xstick, 5.10.8
     iarray, 2.29.107.3     radii, 2.29.86.2
     image, 2.29.107.20xyz morphing, 3.8.8
          alignment, 2.29.107.23zega, 5.10.9
          chemical, 2.29.107.22     intro, 1.4.3.6
          parray, 2.29.107.21|, 2.14.3
     index, 2.29.81.24, 2.29.107.24 
          blast, 2.29.107.25 
          fasta, 2.29.107.24 
     library, 2.29.107.26 
     map, 2.29.107.27 
     matrix, 2.29.107.6 
     model, 2.29.107.28 
     mol, 2.29.107.29 

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