ICM Manual v.3.8
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2019, Molsoft LLC
Mar 19 2019

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, 2.30.145.2     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, 2.30.145.3Cadalign, 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, 2.30.135Chemical, 2.30.27
     pharmacophore comparison, 2.30.135.3Cluster, 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, 2.30.135     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, 2.30.163
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, 2.30.187     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, 2.30.104
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, 2.30.74Mol, 2.30.97
     model, 2.30.75MolPSA, 5.7.12
Insertion, 2.30.72Moment, 2.30.87
Integer, 2.30.76     of Inertia, 2.30.87
Integral, 2.30.77Money, 2.30.95
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, 2.30.98
     men, 2.23.10.1     chemical, 2.30.98.6
     res, 2.23.10.2          property, 2.30.98.1
Label, 2.30.79     close sequence, 2.30.98.3
Laplacian, 2.30.80     conf, 2.30.98.7
Latent, 2.30.186.3     image, 2.30.98.11
LatentVector, 2.30.186.3     molcart, 2.30.98.12
Length, 2.30.81     object parray, 2.30.98.10
LinearFit, 2.30.82     sequence, 2.30.98.8
LinearModel, 2.30.83     soap, 2.30.98.2
Log, 2.30.84     string, 2.30.98.4
LogP, 2.30.113     tree, 2.30.98.5
LogS, 2.30.113Namex, 2.30.99
M_out, 2.24.5     image, 2.30.99.2
Mac, 3.14.6.2     sequence, 2.30.99.1
Map, 2.30.85Newick tree format, 2.30.155.4
Markush structures, 2.29.52Next, 2.30.100, 2.30.100.1
Mass, 2.30.86     covalent neighbors, 2.30.100.1
Match, 2.30.88Nof, 2.30.101
Mathews, 2.30.135.4     chemical, 2.30.101.2
Matrix, 2.30.89     distance, 2.30.101.3
     alignment, 2.30.89.9     latent, 2.30.101.6
     boundary, 2.30.89.10     library, 2.30.101.4
     color, 2.30.89.4     molcart, 2.30.101.5
     grob connectivity, 2.30.89.13     soap, 2.30.101.7
     histogram, 2.30.89.12     tree, 2.30.101.1
     new, 2.30.89.1Norm, 2.30.102
     residue areas, 2.30.89.8Normalize, 2.30.103
          comparison, 2.30.89.5NotInList, 2.30.104
     stack, 2.30.89.11     R, 5.7
     sub, 2.30.89.2OBJECT, 2.23.11
     symmetric, 2.30.89.3Obj, 2.30.105
     table, 2.30.89.6Occupancy, 2.30.106
     tensor, 2.30.89.7PBS, 3.13.3.6
Max, 2.30.90PLOT, 2.23.12
     image graphic, 2.30.90.1     Yratio, 2.23.12.9
MaxHKL, 2.30.91     box, 2.23.12.1
Mean, 2.30.93     color, 2.23.12.2
Median, 2.30.92     font, 2.23.12.3
Method, 2.22.13     fontSize, 2.23.12.4
Min, 2.30.94     gridLineWidth, 2.23.12.5
Mod, 2.30.96     labelFont, 2.23.12.13

     logo, 2.23.12.10Res, 2.30.126, 2.30.127
     markSize, 2.23.12.7Resali, 2.30.127
     numberOffset, 2.23.12.8Resolution, 2.30.128
     orientation, 2.23.12.11Rfactor, 2.30.130
     rainbowStyle, 2.23.12.14Rfree, 2.30.131
     seriesLabels, 2.23.12.12Ring, 2.30.129
PLS, 2.30.101.6Rmsd, 2.30.132
     error, 2.30.135.4     of subset, 2.23.14
     models, 2.30.135.4Rot, 2.30.133
Parray, 2.30.108S, 5.8
Parray-object, 2.30.108SAR analysis, 2.29.62.27, 2.29.62.28, 2.29.89.2, 2.29.89.3
Path, 2.30.107SC, 2.29.35.2
Pattern, 2.30.109SEQUENCE.restoreOrigNames, 2.23.12.15
Pi, 2.30.110SITE, 2.23.13
Polar Surface Area, 5.7.12     defSelect, 2.23.13.2
Potential, 2.30.111     labelOffset, 2.23.13.3
Power, 2.30.112     labelStyle, 2.23.13.4
Predict, 2.30.113     labelWrap, 2.23.13.5
Probability, 2.30.114     showSeqSkip, 2.23.13.6
Profile, 2.30.115     wrapComment, 2.23.13.7
Property, 2.30.116SLN notation, 2.30.155.10
Putarg, 2.30.117SMARTS, 2.26, 2.29.10, 2.30.101.2
Putenv, 2.30.118SOAP, 2.30.98.2, 2.30.101.7, 2.30.181.1
R-groups, 2.29.52     request message, 2.30.151
REBEL, 3.7.2SSSR, 2.30.129
     faq, 3.7.2S_out, 2.24.8
     file, 2.29.52S_proteinTags, 2.24.9
RNA topology, 2.23.5.16Sarray, 2.30.134
R_2out, 2.24.7     index, 2.30.134.1
R_out, 2.24.6Score, 2.30.135
Radius, 2.30.119     alignment, 2.30.135.8
Random, 2.30.120     apf, 2.30.135.3
     string, 2.30.120.1     chemset, 2.30.135.2
Rarray, 2.30.121     conservation, 2.30.135.7
     reverse, 2.30.121.2     model, 2.30.135.4
     sequence projection, 2.30.121.1     overlap, 2.30.135.1
     alignment projection, 2.30.121.3     predictions, 2.30.135.5
          strength, 2.30.121.5     sequence, 2.30.135.6
     property assignment, 2.30.121.4Scripting Tutorials, 1.8
RarrayAlignment, 2.30.121.5Select, 2.30.136
Rarrayinverse, 2.30.121.2     break, 2.30.136.1
Real, 2.30.122          alignment, 2.30.136.14
Reference, 2.30.124          atom property, 2.30.136.7
     Guide, 2          nmembers, 2.30.136.4
Remainder, 2.30.123          string, 2.30.136.9
Replace, 2.30.125     expand, 2.30.136.6
     chemical, 2.30.125.4     fix, 2.30.136.2
     exact, 2.30.125.1     graphical, 2.30.136.5
     regexp, 2.30.125.3     neighbors, 2.30.136.3
     simple, 2.30.125.2Select_by atom numbers, 2.30.136.10

Select_by_text, 2.30.136.9     minSphereCubeSize, 2.23.14.3
Select_lists, 2.30.136.12     pdbChargeNterm, 2.23.14.4
Select_patching, 2.30.136.11     pdbReadNmrModels, 2.23.14.5
Select_projection, 2.30.136.8     rebelPatchSize, 2.18.5, 2.23.14.6
Sequence, 2.30.137     smilesXyzSeparator, 2.23.14.7
     array, 2.30.137.2     superimposeMaxDeviation, 2.23.14.10
Sequence(dna reverse), 2.30.137.1     superimposeMaxIterations, 2.23.14.8
Shannon, 2.30.47     superimposeMinAtomFraction, 2.23.14.9
Shuffle, 2.30.138     tsShape, 2.23.14.12
Sign, 2.30.139     tsWeight, 2.23.14.13
Simulations, 1.4.2     writePdbRenameRes, 2.23.14.14
Sin, 2.30.140Table, 2.30.159
Sinh, 2.30.141     alignment numbers, 2.30.159.3
Site, 2.30.142     distance, 2.30.159.10
Slide, 2.30.143     matrix, 2.30.159.4
Smiles, 2.30.144     model, 2.30.159.8
Smooth, 2.18.24, 2.30.145, 2.30.145.1, 2.30.145.3          chem, 2.30.159.9
     matrix, 2.30.145.2     pairs, 2.30.159.5
Smoothrs, 2.30.145.3     plot, 2.30.159.7
SoapMessage, 2.30.151     stack, 2.30.159.6
SolveQuadratic, 2.30.146     url_decoder, 2.30.159.1
SolveQubic, 2.30.147Table(alignment), 2.30.159.2
Sort, 2.30.152Table(stack), 2.30.159.6
Sphere, 2.23.14.3, 2.30.150Tan, 2.30.160
Split, 2.30.153Tanh, 2.30.161
     chemical, 2.30.153.4Tanimoto, 2.30.66.3
     multisep, 2.30.153.3     distance, 2.29.62.37
     regexp, 2.30.153.2          matrix, 2.30.44.7
     tree, 2.30.153.1Temperature, 2.30.163
Sql, 2.30.148Tensor, 2.30.162
Sqrt, 2.30.149Time, 2.30.164
Srmsd, 2.30.154Tointeger, 2.30.165
Sstructure, 2.30.156Tolower, 2.30.166
String, 2.30.155, 2.30.155.8Toreal, 2.30.167
     alternative, 2.30.155.7Torsion, 2.30.168
     date, 2.30.155.2Tostring, 2.30.169
     mol, 2.30.155.3Toupper, 2.30.170
     selection, 2.30.155.8ToxScore, 2.31.2
     slide gui, 2.30.155.9Tr123, 2.30.171
     substring, 2.30.155.1Tr321, 2.30.172
     chemical formula, 2.30.155.10Trace, 2.30.173
Sum, 2.30.157Trans, 2.30.174
     chemical, 2.30.157.1Transform, 2.30.175
     image, 2.30.157.2Transpose, 2.30.176
Swissprot, 2.29.107.24Trim, 2.30.177
Symgroup, 2.30.158     chemical, 2.30.178
T, 5.9     sequence, 2.30.179
TOOLS, 2.23.14Turn, 2.30.180
     edsDir, 2.23.14.1Type, 2.30.181
     membrane, 2.23.14.2     molcart, 2.30.181.2

     Z, 5.10accessible residues, 3.3.6
Unique, 2.30.182     surface, 2.29.62.14, 5.8.15
Unix, 2.30.183accessing sections, 2.29.107.24
Uppsala, 2.32.42accuracy, 2.30.135.4
     server, 2.32.43acidity constant, 2.29.86.11, 2.29.86.12
V_, 2.8.1activate fog, 2.29.23.24
Value, 2.30.184     alignment, 2.29.86.40
     soap, 2.30.185     document, 2.29.86.40
Vector, 2.30.16, 2.30.186, 2.30.186.1, 2.30.186.3     tab, 2.29.86.40
     symmetry transformation, 2.30.186.2     table, 5.9.2.4
Vectorproduct, 2.30.186.1add, 2.29.1
Vectorsymmetrytransformation, 2.30.186.2     column, 2.29.1.1
Version, 2.30.187          function, 2.29.1.1.1
View, 2.30.189     matrix, 2.29.1.2
Volume, 2.30.188     slide, 2.29.1.3
WEBAUTOLINK, 2.23.16     table, 2.29.1.4
WEBLINK, 2.23.15          row, 2.29.1.4
Warning, 2.30.190addBfactor, 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, 2.30.191     hydrogens, 2.32.13
     axes, 2.30.191.8     in place, 2.14.4
     chemical match, 2.30.191.6     to slideshow, 2.29.1.3
     fract, 2.30.191.4admet selection, 3.13.3.4
     mesh, 2.30.191.3advanced chemical search, 3.6
     points, 2.30.191.1     operations, 2.14.6
     rings, 2.30.191.2     ops, 2.14.6
     transformed xyz, 2.30.191.5ahfs, 2.30.44.6
     vector2matrix, 2.30.191.7ali_seq_project, 2.30.155.5
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, 2.30.191.4alignMinMethod, 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, 2.30.127
accessMethod, 2.22.2alignment, 2.29.22.26, 2.29.86.27, 2.29.86.35, 2.29.86.55, 5.1.1

     block length, 2.18.22     an element, 2.14.4
          secondary structure, 2.31.1     menu items, 2.23.10.1
     cleaning, 2.30.145.4     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, 2.30.136.13arithmetic 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, 2.30.155, 2.30.155.5, 2.30.155.6     derivative, 2.30.145.1
     score, 2.30.135.7     overlap, 2.30.135.1
     sequence reordering, 2.30.5     parray, 2.29.22.31
     strength, 2.30.121.5     size, 2.30.101
     structural, 2.29.3.5, 2.30.5     subset, 2.6
     to sequence transfer, 2.30.121.1arrow from selection, 2.32.36
          text conversion, 2.30.155.4     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, 2.30.136.5
alignment_as_text, 2.30.155.4as_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, 2.30.171, 2.30.172atom, 2.29.13.1, 5.1.7
          colors, 2.30.29.3     centers within, 2.30.150
          labels, 2.29.3.2     code file, 2.33.4
and, 2.14.3     coordinates, 2.30.191.1
angle rotation, 2.32.84     flickering, 2.29.86.3
angles, 2.30.101.3     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, 2.30.159.10
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, 2.30.181
     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

     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, 2.30.136.3
     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, 2.30.157.2calcSeqSimilarity, 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, 2.30.191
     to protein, 2.29.69.3cartridge, 3.5
     width, 2.23.9.14cavities, 2.29.89.1
bonded atoms, 2.30.100.1cavity, 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, 2.30.191.8
break, 2.29.6     specific icm commands, 5.9.2.4
brightness, 2.23.5.33center, 2.13.1, 2.29.9

chain breaks, 2.23.5.7, 2.23.5.8, 2.30.136.1     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, 2.30.89.4
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, 2.30.177
     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, 2.30.165
chem formula, 2.30.155.10classification, 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, 2.30.98.3
     descriptors, 2.30.41, 5.7.12     value, 2.30.56.1
     distance, 2.30.44.8, 2.30.135.2, 2.30.135.3cluster, 2.30.153.1
     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, 2.30.98.5
     formula, 2.30.155.10          size, 2.30.101.1
     fragment counting, 2.30.101.2clustering, 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, 2.30.191.6cnMethodAverage, 2.22.6
     matching, 2.29.35.4, 2.29.81.49, 2.29.81.50, 2.30.132, 2.30.154cnWeight, 2.19.6
     models, 2.30.98.1code, 2.30.44.6
     modification, 2.29.65, 2.29.67, 2.32.37coil, 5.3.4
     name, 2.30.98.6collection, 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, 2.30.101.2          alignment, 2.29.13.3
     similarity, 3.5          atom contributions, 2.29.12
     simplification, 2.30.177          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, 2.30.132, 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

     file, 2.33.15comparing two sarrays, 2.30.104
     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, 2.30.143
          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, 2.30.155.7
     volume, 2.29.13.7conf, 2.29.86.61, 2.29.107.41, 2.30.159.6, 5.3.12, 5.8.9
column, 5.3.5     data, 2.30.159.6
     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, 2.30.108     memory usage, 2.18.7
     selection, 2.30.98conformation comparison, 2.22.7
combinatorial compounds, 2.30.27conformational ensemble, 2.29.7.5.2
     libraries, 2.29.62.33, 2.30.101.4     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, 2.30.98.4, 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, 2.30.104     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, 2.30.121.5, 2.30.135.7
     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

     to real array, 2.30.167          transformations, 2.30.175
convert, 2.29.18, 2.29.18.2, 3.13.2crystallographic cell, 2.29.66
     3D to chemical, 2.30.27     occupancy, 2.30.106
     3D/0D to 2D, 2.29.62.9     symmetry intro, 1.4.2.4
     ICM object to PDB, 2.29.93crystallography, 2.30.128
     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, 2.30.107
     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, 2.30.165customization, 3.1.2
          icm-object, 2.29.18     environment, 2.28
          integer, 2.30.165     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, 2.30.159.2     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, 2.30.122     import, 2.29.62.26
cool, 2.32.40date, 2.29.21, 2.30.155.2
     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, 2.30.162     parameters, 2.22.1
covalent bound count, 2.30.136.3     value, 5.8.2
     neighbors, 2.30.100.1define axis, 3.10.3
covalently attached molecule, 2.30.100.1defining space box, 2.30.21
cpk, 2.19.35, 5.3.13dehtml, 2.30.125.3
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

     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, 2.30.104
     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, 2.30.134
     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, 2.30.136.1     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

     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, 2.30.159.5, 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, 2.30.101.3eigenvalues, 2.30.45
distribution, 1.3eigenvectors, 2.30.45
     comparison, 2.30.135electro 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, 2.30.153.4          around selection, 2.19.25
dna to protein sequence translation, 2.30.174.1          map generation, 2.19.1
     translate, 2.30.174.1          maps, 2.23.14.1
dockScan, 3.13.2.5electrostatic boundary matrix, 2.30.89.10
docking, 2.32.89     coloring, 2.23.14.6
     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, 2.30.162
donor, 3.6.1elseif, 2.29.25
     plot intro, 1.4.3.2empty model, 2.30.108
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, 2.30.135.7
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

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, 2.30.98.2
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, 2.30.125.1     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, 2.30.136.6     in sarray, 2.30.70.8
               terminal atoms, 2.30.136.6     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, 2.30.135.4     scaffold, 2.30.178
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, 2.30.136.1
          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, 2.30.136.2
fasta, 2.23.12.15, 5.5.2flattening 3D molecule, 2.32.17

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, 2.30.136.5
fogStart, 2.19.17graphics, 2.19.9, 2.29.86.4, 2.30.187, 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, 2.30.159.7
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, 2.30.191.4grob, 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, 2.30.145.4     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, 2.30.145.2          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, 2.30.132     list, 2.30.159.10

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, 2.30.107
     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, 2.30.179     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, 2.30.98.4, 5.5.8     ali, 2.33.31
     document order, 2.29.86.40     all, 2.33.32
     tag removal, 2.30.125.3     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, 2.30.101.3     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

     htm, 2.33.11          sdf-file path, 2.30.107
     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, 2.30.167
     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, 2.30.150
     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, 2.30.121.2
     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, 2.30.135.4
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, 2.30.134.1l_confirm, 2.20.9

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, 2.30.98
l_showAccessibility, 2.20.18     sequence, 2.30.98
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, 2.30.98
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, 2.30.134
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, 2.30.101.6     molcart, 2.29.60.3
learn, 2.29.51, 2.30.108     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, 2.30.162
     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, 2.30.166
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

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, 2.30.121.1
     boundary, 2.29.62.4     averaging, 2.30.145.5
     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, 2.30.93
          chem_array, 2.29.62.9     min value, 2.30.94
     grob, 2.32.36     name, 2.30.85
          from image, 2.29.62.11     operations, 5.6.6
               matrix, 2.29.62.12     transformations, 2.30.145.5
          image, 2.29.62.11     trimming, 2.30.22
          map, 2.29.62.10     value sigma, 2.30.132
          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, 2.30.121.4
     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, 2.29.62.38median value, 2.30.92
     unique, 2.29.62.39membrane, 2.23.14.2
makeAxisArrow, 2.32.36memorizing positions, 3.2.4
makeIndexChemDb, 2.32.44menu, 2.29.64
makeIndexSwiss, 2.32.45     script, 3.1.3

     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, 2.30.157          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, 2.30.157.1mol, 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, 2.30.155.3
mesh, 2.30.108, 2.30.188     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, 2.30.108
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, 2.30.113
     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, 2.30.188     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, 2.30.181monte 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

     alignment sequence, 2.29.69.7nested script, 5.8.2
     atoms, 2.29.86.3     real array, 2.30.121
     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, 2.30.120
     fragments together, 2.29.69.3normalize chemicals, 2.29.67.4
     molecule, 2.29.69.1     defined, 2.30.167
     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, 2.30.101
     images by frame, 3.9.2.2          hydrogen bonds, 2.29.87.23
     molecular simulation, 3.9.2          molecules in objects, 2.30.136.4
     rotate view, 3.9.1          occurrences, 2.30.101
     zooming, 3.9.1          residues in molecules, 2.30.136.4
moving selection to another object, 2.30.136.8          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, 2.30.108
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, 2.30.155.3     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, 2.30.113
mutating residue, 3.8.5off, 2.29.81.22
mute, 5.6.15     format, 5.5.3
mysql, 2.29.16.1oligonucleotide melting, 2.30.163
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, 2.30.187, 5.10.2
nearest sequence, 2.30.94optimal chemical superposition, 3.14.5.1
neato, 2.30.159.7optimization, 2.29.68
neighbor joining, 2.29.62.38     Hbond, 2.32.91
neighbors, 2.30.150     hydrogen bond, 2.32.91

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, 2.30.185plotRama, 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, 2.30.159.8, 2.30.159.9
pause, 2.29.70     model, 2.30.159.8, 2.30.159.9
pdb, 5.6.10, 5.7.6     weights, 2.30.159.8, 2.30.159.9
     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, 2.30.191.1
     docking, 3.12.5     size, 2.23.5.21
     folding, 1.4.2.1pointer array, 5.7.3

     surface area, 2.30.113     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, 2.30.146
          coloring, 5.7.13quantum mechanics, 2.29.81.21, 2.29.107.17
pov-ray, 2.29.107.38qubic equation, 2.30.147
pow, 2.30.37query, 3.14.6.1
precision, 2.30.135.4     molcart, 2.29.78
predict, 2.29.73question mark operator, 2.30.155.7
predictSeq, 2.32.61quit, 2.29.79
prediction model, 2.30.83     property transfer via alignment, 2.30.121.3
     quality, 2.30.135r_2out, 2.19.34
     score, 2.30.135r_out, 2.19.33
predictive models, 2.29.51.2radii.electrostatic, 2.30.119
preference, 2.22     van der Waals, 2.30.119
     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, 2.30.100.1random array, 2.30.120
principal axes, 2.30.162     order, 2.30.138
     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, 2.30.121.2, 5.7.11
printPostScript, 2.32.64     properties, 2.30.121.4
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, 2.30.98.3     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, 2.30.191.3     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
     grid docking, 3.14.2     factor, 2.29.81.20

     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, 2.30.88
     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, 2.30.125.3
          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, 2.30.148
          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, 2.30.179
          write, 2.29.81.31.1     file, 2.29.22.9
     unix, 2.29.81.10     trailing blanks, 2.30.177
          cat, 2.29.81.11removing html tags, 2.29.81.47
     variable, 2.29.81.52     outliers, 2.30.177
     view, 2.29.81.53rename, 2.29.3.1, 2.29.82
     vrestraint, 2.29.81.54     chemicals, 2.29.86.47

     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, 2.30.137.1
reorder, 2.29.69.7     lighting, 2.29.86.42
     alignment sequences, 2.29.107.1     normals, 2.29.86.42
     array, 2.30.138reversing 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, 2.30.125.1ribbon, 5.7.18
     without interpretation, 2.30.125.2     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, 2.30.129
reserved names, 2.24     center coordinates, 2.30.191.2
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, 2.30.121.5rocking, 2.29.23.5
     contact area matrix, 2.30.89.8root mean square deviation, 2.30.135.4
          areas, 2.30.7.1roots, 2.30.146, 2.30.147
     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, 2.30.121
          table, 2.30.159.3     a real, 2.30.155
     property averaging, 2.30.145.3     output, 2.29.87.45
          calculation, 2.30.63rsWeight, 2.19.36
     proximity, 2.30.89.8rs_, 2.8.7
     ranges, 2.8.11ruler, 2.19.10
     selection, 2.20.21     script, 2.29.8
          as string, 2.30.155.8running a docking job, 3.13.2.5
          function, 2.30.126     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, 2.30.159.7s_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
restraining molecules to shapes, 2.23.14.12s_icmhome, 2.21.8, 3.1.2.1

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, 2.30.162
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, 2.30.136.3
s_tempDir, 2.21.30          of the fixed torsions, 2.30.136.2
s_translateString, 2.21.31     based on alignment, 2.30.136.14
s_userDir, 2.21.32          bfactor, 2.30.136.7
s_usrlib, 2.21.33          center of mass, 2.30.136.15
s_webEntrezLink, 2.21.34          coordinates, 2.30.136.7
s_webViewer, 2.21.35          iarray, 2.30.136
s_xpdbDir, 2.21.36          length, 2.30.136.13
sa23, 3.3          occupancy, 2.30.136.7
sampling grid, 2.30.191.3          user field, 2.30.136.7
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, 2.30.136.12
     sdf file, 2.29.107.11     vw partners, 2.30.136.12
saving graphics to album, 2.29.62.20selectMinGrad, 2.19.37
     image, 2.29.107.36selectSphereRadius, 2.19.38
scaffold, 2.30.177selected stack conformations, 2.29.22.17
scaffolds, 2.29.52selecting by b-factor, 2.30.136
scoring, 3.13.1.4               y z, 2.30.136
screen X, 2.30.189     columns, 5.9.1
     coordinates, 2.30.189     from clusters, 3.14.6.4
script, 2.30.98.4, 5.8.2     neighboring elements, 2.30.100
     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, 2.30.136, 2.30.136.6
     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, 2.30.155.3, 5.7.3     gap patching, 2.30.136, 2.30.136.11
     to chem-table, 2.30.108     level, 2.8, 2.30.181
search for chemical pattern, 2.30.56.3     levels, 2.8.2

     transfer, 2.30.136, 2.30.155.8set, 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, 2.30.155.6               auto, 2.29.86.12
sequence, 2.30.171, 2.30.172, 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, 2.30.135.7          sequence, 2.29.86.19
     distance, 2.30.136     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, 2.30.179     error, 2.29.86.33
     neighbor, 2.30.98.3     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, 2.30.159.3          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, 2.30.121.3          coordinates, 2.29.86.42
     type, 5.8.3          label, 2.29.86.42
sequence-alignment mapping, 2.30.155.5, 2.30.155.6     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

     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, 2.30.135.2shadows, 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, 2.30.190
          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

     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, 2.30.143, 5.8.14
     profile, 2.29.87.39     transition time, 2.29.23.21
     residue, 2.29.87.40slides, 2.30.189
          type, 2.29.87.41slideshow, 2.29.1.3, 2.29.23.21, 2.30.143
     residuetype, 2.29.87.41sln, 5.8.8
     segment, 2.29.87.42smallest set of smallest rings, 2.30.129
     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, 2.30.108
     stack, 2.29.87.44smooth alignment, 2.30.145.4
     svariable, 2.29.87.3     interpolation, 2.29.91.3
     table, 2.29.87.45     map, 2.30.145.5
          as database, 2.29.87.17     rarray, 2.30.145.1
     term, 2.29.87.46     surface, 2.32.88
     tethers, 2.29.87.47soap, 2.27
     version, 2.29.87.48soft trim, 2.30.177
     volume, 2.29.87.51solid sphere, 2.23.5.11
          map, 2.29.87.52solubility, 2.30.113
     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, 2.30.135.2          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, 2.30.136.13     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, 2.30.125.2space group, 2.29.66
simplified representation, 2.23.5.16     transformations, 2.30.175
     compound, 2.30.178sparse atoms, 2.23.14.3

special values, 2.30.167     image, 2.29.62.20
specificity, 2.30.135.4     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, 2.30.134, 5.8.1
     group, 2.29.89.2     filtering, 2.30.177
          array, 2.29.89.3     inversion, 2.30.155.1
     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, 2.30.98.2
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, 2.30.98.12, 2.30.101.5, 2.30.181.2     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, 2.30.159.5     structure, 3.11.1
ssThreshold, 2.19.41sub-alignment to selection, 2.30.127
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, 2.30.159.6, 5.3.12, 5.8.9substring, 2.30.88, 2.30.155, 2.30.155.1
     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, 2.30.132support, 1.3
standardization, 2.29.22.11suppressing view changes, 2.29.23.21
     chemical, 2.29.67surface, 2.19.35, 2.30.108, 5.8.15
startup, 3.1.2.3     accessibility, 2.29.87.9
static RMSD, 2.30.154     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, 2.30.191.3
stereoisomer, 2.29.30     point selection, 2.30.191
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

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, 2.30.89.3testing if argument exists, 2.30.59
symmetry, 2.30.175tether, 2.23.14.12, 2.29.107.9, 5.9.4, 5.9.5
     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, 2.30.171, 2.30.172
     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, 2.30.155.2
     column, 2.30.98timeLimit, 2.19.47
          format, 2.29.86.41tolFunc, 2.19.49
          plot, 2.29.62.32tolGrad, 2.19.48
          transformations, 2.30.103topological 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, 2.30.159.4torsions, 2.30.101.3
     grid view, 5.9.1     score, 2.31.2
     of atoms and distances, 2.30.159.10tpsa, 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, 2.30.121, 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, 2.30.191.5
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, 2.30.89tree, 2.29.62.37, 2.30.98.5
terminal font, 2.33.14     cluster, 2.13
     window, 2.29.44     delete, 2.29.22.36

     representatives, 2.13.1user_startup, 3.1.2.4
trim string array, 2.29.99.1     icm, 3.1.2
trimming grid map values, 2.30.177     guide, 3
true positives, 2.30.135.4v_, 2.8.1
truncate alignment, 2.29.62.34van der Waals surface, 2.23.5.56
     values, 2.30.177varLabelStyle, 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, 2.30.150
two alignments, 2.30.44.13vector, 2.30.101.6
     dimensional plot, 2.30.145.2     dot product, 2.30.186.1
     set comparison, 2.30.44.8, 2.30.135.2     length, 2.30.102
     sets, 2.30.70.10     product, 2.30.186.1
txdoc browser, 2.29.81.4     transformation, 2.30.103
type, 2.30.181.1vertex, 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, 2.30.189
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, 2.30.98     arrays, 2.29.1.1.1
     new object name, 2.30.98     chemistry, 2.29.67, 2.30.101.4
     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, 2.30.170     parallelization, 3.13.3.5
url string parsing, 2.30.159     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

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, 2.30.190     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, 2.30.125.1     rarray, 2.29.107.4
window averaging, 2.30.145.1     sarray, 2.29.107.5
     layout, 2.30.155.9     sequence, 2.29.107.39
     width and height, 2.30.189     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 

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