ICM Manual v.3.7
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2013, Molsoft LLC
May 16 2013

Contents
 
Introduction
Reference Guide
User's Guide
References
Glossary
 
Index

Index

&, 2.12.3CCP4, 5.6.6
2D labels, 2.27.54.1CONSENSUS, 2.21.1
     to 3D, 3.16CONSENSUSCOLOR, 2.21.2
     trees, 2.27.61.36CONSENSUS_strength, 2.17.9
     smooth, 2.28.139.2Cad, 2.28.23, 2.28.23.1, 2.28.23.2
3D chemical builder, 1.4.2.8Cad1, 2.28.23.1
     font size, 2.27.23.12Cadalign, 2.28.23.2
     label, 2.27.23.12, 2.27.85.36Ceil, 2.28.24
     labels, 2.27.54.1Cell, 2.28.25
     mol file, 2.29.84Charge, 2.28.26
     plots intro, 1.4.3.7Chemical, 2.28.27
     smoothing, 2.28.139.3Cluster, 2.28.28
     superposition, 2.29.22Collada, 5.5.3
     transformations, 2.27.98.2Collection, 2.28.28.1
     tree, 2.27.61.36Color, 2.28.29
     chemical similarity, 2.28.129     from gradient, 2.28.29.1
     pharmacophore comparison, 2.28.129.2     image, 2.28.29.2
3dxml, 5.5.3Connolly surface, 5.8.7
=, 2.12.1Consensus, 2.28.30
A, 5.1Corr, 2.28.31
APF distance, 2.28.129Cos, 2.28.32
Abs, 2.28.1Cosh, 2.28.33
Acc, 2.28.2Count, 2.28.34
Acos, 2.28.3CubicRoot, 2.28.35
Acosh, 2.28.4D, 5.4
Adobe, 2.19.23DAE, 5.5.3
Align, 2.28.5DE, 2.27.34.2
     sequence, 2.28.5.1DNA Representation, 1.4.1.3
Angle, 2.28.6     alignment, 2.27.3.3
Apple, 3.14.6.2     melting temperature, 2.28.157
Area, 2.28.7     views, 1.4.1.3
     residue contacts, 2.28.7.1Date, 2.28.36
Asin, 2.28.8Deletion, 2.28.37
Asinh, 2.28.9Descriptor, 2.28.38
Ask, 2.28.10Det, 2.28.39
Askg, 2.28.11Disgeo, 2.28.40
Atan, 2.28.12Distance, 2.28.41
Atan2, 2.28.13     2 alignments, 2.28.41.11
Atanh, 2.28.14          matrices, 2.28.41.7
Atom, 2.28.15     Dayhoff, 2.28.41.9
Augment, 2.28.16     Tanimoto, 2.28.41.6
Axis, 2.28.17     alignment, 2.28.41.10
B, 5.2     as_, 2.28.41.3
BPMC, 5.2.5          rarray, 2.28.41.4
Bfactor, 2.28.19     atoms, 2.28.41.3
Blob, 2.28.18     chemical, 2.28.41.6, 2.28.41.13
Boltzmann, 2.28.20     dayhoff, 2.28.41.9
Box, 2.28.21     iarray, 2.28.41.1
Bracket, 2.28.22          alignment, 2.28.41.10
C, 5.3     matrix, 2.28.41.5, 2.28.41.7
     rarray, 2.28.41.2     dnaRibbonWorm, 2.21.5.15
     tether, 2.28.41.8     dnaStickRadius, 2.21.5.16
     tree, 2.28.41.12     formalChargeDisplay, 2.21.5.17
          cluster, 2.28.41.12     grobDotSize, 2.21.5.18
     H, 5.5     grobLineWidth, 2.21.5.19
EDS server, 2.29.42     hbondAngleSharpness, 2.21.5.23
EST-alignment, 2.27.3.3     hbondBallPeriod, 2.21.5.24
Eigen, 2.28.42     hbondBallStyle, 2.21.5.25
Energy, 2.28.43     hbondMinStrength, 2.21.5.22
Error, 2.28.44     hbondRebuild, 2.21.5.21
     soap, 2.28.45     hbondStyle, 2.21.5.20
Exist, 2.28.46     hbondWidth, 2.21.5.26
     molcart, 2.28.46.1     hetatmZoom, 2.21.5.28
Existenv, 2.28.47     hydrogenDisplay, 2.21.5.29
Exp, 2.28.49     light, 2.21.5.30
Extension, 2.28.48     lightPosition, 2.21.5.31
FILTER, 2.21.3     mapLineWidth, 2.21.5.32
     Z, 2.21.3.1     occupancyDisplay, 2.21.5.33
     gz, 2.21.3.2     occupancyRadiusRatio, 2.21.5.34
     uue, 2.21.3.3     quality, 2.21.5.35, 2.28.85.1
FTP, 2.21.4     rainbowBarStyle, 2.21.5.36
     createFile, 2.21.4.1     resLabelDrag, 2.21.5.37
     keepFile, 2.21.4.2     resLabelShift, 2.21.5.38
     proxy, 2.21.4.3     ribbonCylinderRadius, 2.21.5.39
Field, 2.28.50, 2.28.50.1     ribbonGapDistance, 2.21.5.40
     user, 2.28.50.1     ribbonRatio, 2.21.5.41
File, 2.28.51     ribbonWidth, 2.21.5.42
Find, 2.28.52     ribbonWorm, 2.21.5.43
     chemical, 2.28.52.3     rocking, 2.21.5.44
          pattern, 2.28.52.3     rockingRange, 2.21.5.45
     in array, 2.28.52.1     rockingSpeed, 2.21.5.46
          table, 2.28.52.2     selectionLevel, 2.21.5.47
FlexLM license info, 2.28.180     selectionStyle, 2.21.5.48
Floor, 2.28.53     sketchAccents, 2.21.5.27
Formula, 2.28.54     stereoMode, 2.21.5.49
GRAPHICS, 2.21.5     stickRadius, 2.21.5.28, 2.21.5.50
     atomLabelShift, 2.21.5.1     surfaceDotDensity, 2.21.5.52
     atomValueCircles, 2.21.5.2     surfaceDotSize, 2.21.5.51
     ballRadius, 2.21.5.3, 2.21.5.28     surfaceProbeRadius, 2.21.5.53
     ballStickRatio, 2.21.5.4     transparency, 2.21.5.54
     chainBreakLabelDisplay, 2.21.5.7     wormRadius, 2.21.5.55
     chainBreakStyle, 2.21.5.6GRID, 2.21.6
     clashWidth, 2.21.5.5     gcghExteriorPenalty, 2.21.6.1
     cpkClipCaps, 2.21.5.8     gpGaussianRadius, 2.21.6.6
     displayLineLabels, 2.21.5.9     margin, 2.21.6.2
     displayMapBox, 2.21.5.10     maxEl, 2.21.6.3
     dnaBallRadius, 2.21.5.11     maxVw, 2.21.6.5
     dnaRibbonRatio, 2.21.5.12     minEl, 2.21.6.4
     dnaRibbonStyle, 2.21.5.13GROB, 2.21.7
     dnaRibbonWidth, 2.21.5.14     arrowRadius, 2.21.7.3
     contourSigmaIncrement, 2.21.7.5     scale, 2.21.9.4
     relArrowHead, 2.21.7.4     stereoAngle, 2.21.9.6
     relArrowSize, 2.21.7.2     stereoBase, 2.21.9.5
GUI, 2.21.8     stereoText, 2.21.9.11
     defaults, 3.14.6.2     writeScale, 2.21.9.19
     dialog customize programming, 2.26I_out, 2.22.4
     plot, 2.27.61.31Iarray, 2.28.62, 2.28.62.4, 2.28.62.5
     preferences, 2.27.81.4     atom numbers, 2.28.62.4
     tableRowMarkColors, 2.21.8.4     bits to integers, 2.28.62.3
     windowLayout, 2.21.8.5     inverse, 2.28.62.2
     workspaceFolderStyle, 2.21.8.8     residue numbers, 2.28.62.5
     workspaceStyle, 2.21.8.6     reverse, 2.28.62.2
     workspaceTabStyle, 2.21.8.7     stack, 2.28.62.6
Getarg, 2.28.55Icm Options, 2.1
Getenv, 2.28.56IcmSequence, 2.28.63
Gradient, 2.28.57Image, 2.28.64
Graphics, 1.4.1     collection, 3.9.2.1
Grob, 2.28.58     frame by frame, 3.9.2.2
Group, 2.28.59Index, 2.28.65
HTTP.proxy, 2.21.4.4     chemical, 2.28.65.2
Hartree-Fock, 2.27.80.20, 2.27.106.17     compare, 2.28.65.10
Header, 2.28.60     element in array, 2.28.65.8
Histogram, 2.28.61     fork, 2.28.65.1
     N, 5.6     regexp, 2.28.65.4
ICM desktop, 2.21.8.5     string, 2.28.65.3
     documents, 2.27.80.3     table label, 2.28.65.6
     modules, 1.4.4          selection, 2.28.65.5
     object, 2.29.13     tree, 2.28.65.9
     residue library, 2.19.24     unique elements, 2.28.65.7
ICM-shell, 3.1, 5.8.5Indexx, 2.28.66
     intro, 1.7.1Info, 2.28.68
     script, 2.27.8     image, 2.28.69
ICMFF force field, 2.29.78     model, 2.28.70
ICMHOME, 3.1.2.1Insertion, 2.28.67
     shell variable, 3.1.2.1Integer, 2.28.71
IMAGE, 2.21.9Integral, 2.28.72
     bondLength2D, 2.21.9.15Interrupt, 2.28.73
     color, 2.21.9.8Introduction, 1
     compress, 2.21.9.9JSON, 2.27.80.55
     gammaCorrection, 2.21.9.7LIBRARY, 2.21.10
     generateAlpha, 2.21.9.10     men, 2.21.10.1
     lineWidth, 2.21.9.3     res, 2.21.10.2
     lineWidth2D, 2.21.9.14Label, 2.28.74
     orientation, 2.21.9.16Laplacian, 2.28.75
     paperSize, 2.21.9.17Latent, 2.28.179.3
     previewResolution, 2.21.9.13LatentVector, 2.28.179.3
     previewer, 2.21.9.12Length, 2.28.76
     printerDPI, 2.21.9.2LinearFit, 2.28.77
     quality, 2.21.9.1LinearModel, 2.28.78
     rgb2bw, 2.21.9.18Log, 2.28.79
LogS, 2.28.107Next, 2.28.94, 2.28.94.1
M_out, 2.22.5     covalent neighbors, 2.28.94.1
Mac, 3.14.6.2Nof, 2.28.95
Map, 2.28.80     chemical, 2.28.95.2
Markush structures, 2.27.51     distance, 2.28.95.3
Mass, 2.28.81     latent, 2.28.95.6
Match, 2.28.83     library, 2.28.95.4
Mathews, 2.28.129.3     molcart, 2.28.95.5
Matrix, 2.28.84     soap, 2.28.95.7
     alignment, 2.28.84.8     tree, 2.28.95.1
     boundary, 2.28.84.9Norm, 2.28.96
     grob connectivity, 2.28.84.12Normalize, 2.28.97
     histogram, 2.28.84.11NotInList, 2.28.98
     new, 2.28.84.1     R, 5.7
     residue areas, 2.28.84.7OBJECT, 2.21.11
          comparison, 2.28.84.4Obj, 2.28.99
     stack, 2.28.84.10Occupancy, 2.28.100
     sub, 2.28.84.2PBS, 3.13.3.6
     symmetrical, 2.28.84.3PLOT, 2.21.12
     table, 2.28.84.5     Yratio, 2.21.12.9
     tensor, 2.28.84.6     box, 2.21.12.1
Max, 2.28.85     color, 2.21.12.2
     image graphic, 2.28.85.1     font, 2.21.12.3
MaxHKL, 2.28.86     fontSize, 2.21.12.4
Mean, 2.28.87     gridLineWidth, 2.21.12.5
Method, 2.20.12     labelFont, 2.21.12.13
Min, 2.28.88     lineWidth, 2.21.12.6
Mod, 2.28.90     logo, 2.21.12.10
Mol, 2.28.91     markSize, 2.21.12.7
MolPSA, 5.7.12     numberOffset, 2.21.12.8
Moment, 2.28.82     orientation, 2.21.12.11
     of Inertia, 2.28.82     rainbowStyle, 2.21.12.14
Money, 2.28.89     seriesLabels, 2.21.12.12
NOE averaging, 2.20.5PLS, 2.28.95.6
Name, 2.28.92     error, 2.28.129.3
     chemical, 2.28.92.6     models, 2.28.129.3
          property, 2.28.92.1Parray, 2.28.102
     close sequence, 2.28.92.3Parray-object, 2.28.102
     conf, 2.28.92.7Path, 2.28.101
     image, 2.28.92.11Pattern, 2.28.103
     molcart, 2.28.92.12Pi, 2.28.104
     object parray, 2.28.92.10Polar Surface Area, 5.7.12
     sequence, 2.28.92.8Potential, 2.28.105
     soap, 2.28.92.2Power, 2.28.106
     string, 2.28.92.4Predict, 2.28.107
     tree, 2.28.92.5Probability, 2.28.108
Namex, 2.28.93Profile, 2.28.109
     image, 2.28.93.2Property, 2.28.110
     sequence, 2.28.93.1Putarg, 2.28.111
Newick tree format, 2.28.149.4Putenv, 2.28.112
REBEL, 3.7.2SSSR, 2.28.123
     faq, 3.7.2S_out, 2.22.8
     file, 2.27.51Sarray, 2.28.128
RNA topology, 2.21.5.13     index, 2.28.128.1
R_2out, 2.22.7Score, 2.28.129
R_out, 2.22.6     alignment, 2.28.129.7
Radius, 2.28.113     apf, 2.28.129.2
Random, 2.28.114     conservation, 2.28.129.6
     string, 2.28.114.1     model, 2.28.129.3
Rarray, 2.28.115     overlap, 2.28.129.1
     reverse, 2.28.115.2     predictions, 2.28.129.4
     sequence projection, 2.28.115.1     sequence, 2.28.129.5
     alignment projection, 2.28.115.3Select, 2.28.130
          strength, 2.28.115.5     break, 2.28.130.1
     property assignment, 2.28.115.4          alignment, 2.28.130.14
RarrayAlignment, 2.28.115.5          atom property, 2.28.130.7
Rarrayinverse, 2.28.115.2          nmembers, 2.28.130.4
Real, 2.28.116          string, 2.28.130.9
Reference, 2.28.118     expand, 2.28.130.6
     Guide, 2     fix, 2.28.130.2
Remainder, 2.28.117     graphical, 2.28.130.5
Replace, 2.28.119     neighbors, 2.28.130.3
     chemical, 2.28.119.4Select_by atom numbers, 2.28.130.10
     exact, 2.28.119.1Select_by_sequence, 2.28.130.13
     regexp, 2.28.119.3Select_by_text, 2.28.130.9
     simple, 2.28.119.2Select_lists, 2.28.130.12
Res, 2.28.120, 2.28.121Select_patching, 2.28.130.11
Resali, 2.28.121Select_projection, 2.28.130.8
Resolution, 2.28.122Sequence, 2.28.131
Rfactor, 2.28.124     array, 2.28.131.2
Rfree, 2.28.125Sequence(dna reverse), 2.28.131.1
Ring, 2.28.123Shuffle, 2.28.132
Rmsd, 2.28.126Sign, 2.28.133
     of subset, 2.21.14Simulations, 1.4.2
Rot, 2.28.127Sin, 2.28.134
S, 5.8Sinh, 2.28.135
SAR analysis, 2.27.61.27, 2.27.88.2Site, 2.28.136
SC, 2.27.34.2Slide, 2.28.137
SEQUENCE.restoreOrigNames, 2.21.12.15Smiles, 2.28.138
SITE, 2.21.13Smooth, 2.16.23, 2.28.139, 2.28.139.1, 2.28.139.3
     defSelect, 2.21.13.2     matrix, 2.28.139.2
     labelOffset, 2.21.13.3Smoothrs, 2.28.139.3
     labelStyle, 2.21.13.4SoapMessage, 2.28.145
     labelWrap, 2.21.13.5SolveQuadratic, 2.28.140
     showSeqSkip, 2.21.13.6SolveQubic, 2.28.141
     wrapComment, 2.21.13.7Sort, 2.28.146
SLN notation, 2.28.149.10Sphere, 2.21.14.3, 2.28.144
SMARTS, 2.24, 2.27.10, 2.28.95.2Split, 2.28.147
SOAP, 2.28.92.2, 2.28.95.7, 2.28.174.1     chemical, 2.28.147.4
     request message, 2.28.145     multisep, 2.28.147.3
     tree, 2.28.147.1Tointeger, 2.28.159
Sql, 2.28.142Tolower, 2.28.160
Sqrt, 2.28.143Toreal, 2.28.161
Srmsd, 2.28.148Torsion, 2.28.162
Sstructure, 2.28.150Tostring, 2.28.163
String, 2.28.149, 2.28.149.8Toupper, 2.28.164
     alternative, 2.28.149.7Tr123, 2.28.165
     date, 2.28.149.2Tr321, 2.28.166
     mol, 2.28.149.3Trace, 2.28.167
     selection, 2.28.149.8Trans, 2.28.168
     slide gui, 2.28.149.9Transform, 2.28.169
     substring, 2.28.149.1Transpose, 2.28.170
     chemical formula, 2.28.149.10Trim, 2.28.171
Sum, 2.28.151     sequence, 2.28.172
     chemical, 2.28.151.1Turn, 2.28.173
     image, 2.28.151.2Type, 2.28.174
Swissprot, 2.27.106.23     molcart, 2.28.174.2
Symgroup, 2.28.152     soap, 2.28.174.1
T, 5.9     Z, 5.10
TOOLS, 2.21.14Unique, 2.28.175
     edsDir, 2.21.14.1Unix, 2.28.176
     membrane, 2.21.14.2Uppsala, 2.29.42
     minSphereCubeSize, 2.21.14.3     server, 2.29.43
     pdbReadNmrModels, 2.21.14.4V_, 2.8.1
     smilesXyzSeparator, 2.21.14.5Value, 2.28.177
     superimposeMaxDeviation, 2.21.14.8     soap, 2.28.178
     superimposeMaxIterations, 2.21.14.6Vector, 2.28.16, 2.28.179, 2.28.179.1, 2.28.179.3
     superimposeMinAtomFraction, 2.21.14.7     symmetry transformation, 2.28.179.2
     tsShape, 2.21.14.10Vectorproduct, 2.28.179.1
     tsWeight, 2.21.14.11Vectorsymmetrytransformation, 2.28.179.2
     writePdbRenameRes, 2.21.14.12Version, 2.28.180
Table, 2.28.153View, 2.28.182
     alignment numbers, 2.28.153.3Volume, 2.28.181
     distance, 2.28.153.9WEBAUTOLINK, 2.21.16
     matrix, 2.28.153.4WEBLINK, 2.21.15
     model, 2.28.153.7Warning, 2.28.183
          chem, 2.28.153.8Wavefront format, 2.27.80.21
     pairs, 2.28.153.5XML, 2.10
     stack, 2.28.153.6Xyz, 2.28.184
     url_decoder, 2.28.153.1     axes, 2.28.184.7
Table(alignment), 2.28.153.2     chemical match, 2.28.184.5
Table(stack), 2.28.153.6     fract, 2.28.184.3
Tan, 2.28.154     mesh, 2.28.184.2
Tanh, 2.28.155     points, 2.28.184.1
Tanimoto, 2.28.62.3     transformed xyz, 2.28.184.4
     distance, 2.27.61.35     vector2matrix, 2.28.184.6
          matrix, 2.28.41.6ZEGA, 5.10.9
Temperature, 2.28.157     intro, 1.4.3.6
Tensor, 2.28.156_NAME, 2.27.85.44
Time, 2.28.158_chemBatch, 3.1.2.5
_confGen, 3.16     intro, 1.4.3.3
_dockScan, 3.13.2.5     number, 2.27.3.1
_macro, 2.30.1     res numbers, 2.27.3.1
     file, 2.30.1     sequence, 2.27.3.2
_startup, 3.1.2.3     sequences, 2.27.3.2
     file, 2.30.2alignMethod, 2.20.2
     icm, 2.30.2alignMinCoverage, 2.17.2
a_, 2.8.1alignMinMethod, 2.17.2
abbr, 1.6alignOldStatWeight, 2.17.3
abbreviations, 1.6alignSS, 2.29.1
absolute to cell x y z, 2.28.184.3alignTwoSequences, 2.29.2
accFunction, 2.22.2aligned residues, 2.28.121
acceptor, 3.6.1alignment, 5.1.1
access large sdf file, 2.27.80.23     as table, 2.28.153.2
accessMethod, 2.20.1     block length, 2.16.21
accessible residues, 3.3.6          secondary structure, 2.29.1
     surface, 2.27.61.14, 5.8.16     cleaning, 2.28.139.4
accessing sections, 2.27.106.23     color by property, 2.27.85.32
accuracy, 2.28.129.3     coloring, 2.19.1
activate fog, 2.27.23.24     distance, 2.28.130.13
     alignment, 2.27.85.37     editor, 2.4
     document, 2.27.85.37     extraction, 2.28.5
     tab, 2.27.85.37     gap format, 5.1.1.1
     table, 5.9.2.4     intro, 1.4.3.4
add, 2.27.1     projection, 2.28.149, 2.28.149.5, 2.28.149.6
     column, 2.27.1.1     score, 2.28.129.6
          function, 2.27.1.1.1     sequence reordering, 2.28.5
     matrix, 2.27.1.2     strength, 2.28.115.5
     slide, 2.27.1.3     structural, 2.27.3.4, 2.28.5
     table, 2.27.1.4     to sequence transfer, 2.28.115.1
          row, 2.27.1.4          text conversion, 2.28.149.4
addBfactor, 2.17.1     weighted, 2.28.5
adding atoms to non-ICM objects, 2.27.7.1     gapExtension, 2.17.15
     columns to table, 2.27.1.1     gapOpen, 2.17.16
     hydrogens, 2.29.13alignment_as_text, 2.28.149.4
     in place, 2.12.4aliphatic amines, 2.27.66.2
     to slideshow, 2.27.1.3all, 5.1.2
admet selection, 3.13.3.4     torsions table, 3.3.11
advanced chemical search, 3.6alpha, 2.21.5.54, 2.27.85.39, 5.1.3
     operations, 2.12.6     channel, 2.21.9.10
     ops, 2.12.6alternative flag, 2.27.85.17
ali_seq_project, 2.28.149.5amber, 5.1.4
alias, 2.27.2amino acid, 2.19.24, 2.28.165, 2.28.166
align, 2.27.3          labels, 2.27.3.1
     3D, 2.27.3.4and, 2.12.3
          faq, 3.3.2angles, 2.28.95.3
          heavy, 2.27.3.5angular hbond dependence, 2.21.5.23
          how to, 3.3.2animated story, 5.8.15
     chemical, 2.27.84.1animation, 2.27.23.5, 2.27.23.6, 3.9
     fragments, 2.27.3.3annotation, 2.27.85.25
append, 5.1.5atomSingleStyle, 2.20.4
     a tables, 2.27.1.4atomic contributions, 2.27.86.20, 2.27.86.21
     column, 2.27.4.3     coordinate transfer, 2.27.85.3
     command, 2.27.4     property fields, 3.15
     sequence, 2.27.4.1     solvation contributions, 2.28.7
          to group, 2.27.4.1     in residue, 2.28.59
     stack, 2.27.4.2     alternative position, 2.27.85.17
     tables, 2.27.49     selecting, 2.8.8
          by shared column, 2.27.4.3     translate, 2.27.85.3
appending, 2.27.1.1attenuation by occupancy, 2.27.61.25
     an element, 2.12.4auc enrichment, 2.29.21
     menu items, 2.21.10.1auto saving log, 2.20.10
     representations to a slide, 2.27.23.21autoSavePeriod, 2.16.1
     rows to matrix, 2.27.1.2avi, 2.27.106.30
area under curve, 2.29.21axis, 5.1.8
arguments, 2.27.60axisLength, 2.17.4
arithmetic operations, 2.12.2background, 2.28.29.2
arithmetics, 2.12ball, 2.27.85.2, 5.2.2
array, 2.27.68.4, 5.1.6, 5.7.3.1base, 5.2.1
     assignment, 2.12.1     pair diagram, 2.21.5.13
     derivative, 2.28.139.1basis set, 2.27.80.20, 2.27.106.17
     overlap, 2.28.129.1batch chemical processing, 3.1.2.5
     parray, 2.27.22.29     docking, 3.13.2.5
     size, 2.28.95beta, 5.2.3
     subset, 2.6bfactor circles, 2.21.5.2
arrow from selection, 2.29.36biased probability monte carlo, 2.27.67
     length, 2.27.85.25binary file table of contents, 2.27.80.2
as2_out, 2.22.13     files, 2.27.106.2
as_, 2.8.8     string, 5.8.11
as_graph, 2.21.5.47, 2.21.5.48, 2.28.130.5     key, 2.27.85.40
as_out, 2.22.12binding energy, 3.7.4
assign, 2.27.5     pocket finding, 3.4.2
     residue, 2.27.6.1     pockets, 2.27.88.1
     ring conformation to template, 2.27.62.4     site analysis, 3.4.2
     sstructure, 2.27.5.1biological symmetry, 2.27.85.9
          segment, 2.16.19, 2.27.5.2     vector, 2.28.62.3
assignment, 2.12.1     to integers compression, 2.28.62.3
atom, 2.27.13.1, 5.1.7blast files, 2.27.106.24
     code file, 2.30.4blast-formatted database, 2.27.34.3, 2.27.106.24
     coordinates, 2.28.184.1blending, 2.27.106.30
     flickering, 2.27.85.3     images, 2.28.151.2
     label font, 2.30.15blob, 5.8.11
     labels, 2.27.85.2bold, 2.27.85.35.1
     name, 2.28.74bond angle bending, 2.30.5
     pairs, 2.27.85.64, 2.27.85.65, 2.28.153.9     errors, 2.27.86.12
     proximity to surface, 2.27.86.9     stretching, 2.30.6
     selection by number, 2.28.62.4     to protein, 2.27.68.3
     type, 2.28.174bonded atoms, 2.28.94.1
     user field, 2.28.50.1born radii, 2.27.86.9
atomLabelStyle, 2.20.3boundary element, 5.2.4
box, 2.28.21chain breaks, 2.21.5.6, 2.21.5.7, 2.28.130.1
break, 2.27.6     symbol, 2.27.85.9
brightness, 2.21.5.30change atom position, 2.27.85.3
build, 2.27.7     sequence position in multiple alignment, 2.27.68.6
     atom, 2.27.7.1     unix directory, 2.27.85.20
     column, 2.27.7.2changing local stick radii, 2.27.85.82
     faq, 3.8.1     surface dot size, 2.21.5.51
     from string, 2.27.7.8channel, 2.21.14.2
     helix, 3.10.5charge, 5.3.2
     how to, 3.8.1     compounds, 2.27.66.2
     hydrogen, 2.27.7.9     change, 2.27.85.10
     loop, 2.27.7.6chem formula, 2.28.149.10
     model, 2.27.7.5, 2.27.106.9chemSuper3D, 2.29.22
     molcart, 2.27.7.10chemical, 2.21.14.5, 2.23, 2.27.34.9
     sequence, 2.27.7.3     2D drawings, 2.27.61.9
     smiles, 2.27.7.7     SMARTS search, 2.27.34.5
     string, 2.27.7.8     database, 3.5
     tautomer, 2.27.7.4     decomposition, 2.27.61.27, 2.27.88.2
built-in functions, 5.5.5     descriptors, 2.28.38, 5.7.12
     plot, 2.27.85.50     distance, 2.28.129.2
     atoms, 2.27.14     diversity, 3.14.6.4
     contact surface, 2.27.14     drawing, 2.21.9.14
     molecule, 2.27.13.1          quality, 2.21.9.15
     number of bonds, 2.28.130.3     formula, 2.28.149.10
     variables, 2.27.14     fragment counting, 2.28.95.2
calcArea, 2.29.3     keys, 2.27.61.21
calcBindingEnergy, 2.29.4     match coordinates, 2.28.184.5
calcDihedralAngle, 2.29.5     matching, 2.27.34.4, 2.27.80.47, 2.27.80.48, 2.28.126, 2.28.148
calcEnergyStrain, 2.29.20     models, 2.28.92.1
calcEnsembleAver, 2.29.6     modification, 2.27.64, 2.27.66, 2.29.37
calcMaps, 2.29.7     name, 2.28.92.6
calcPairSeqIdsFromAli, 2.29.8     normalization, 2.27.66
calcPepHelicity, 2.29.9          rules, 2.27.66.4
calcProtUnfoldingEnergy, 2.29.10     pattern, 2.24, 2.27.84.1
calcRmsd, 2.29.11          search, 2.28.52.3
calcSeqContent, 2.29.12     reaction product generation, 2.27.61.32
calc_nosauc, 2.29.21     search, 2.27.34.10, 2.27.84.1, 2.28.95.2
calculate phases, 3.11.2     similarity, 3.5
call, 2.27.8     spreadsheet, 2.27.12, 2.27.80.46, 2.27.80.47, 2.27.80.48, 2.27.85.44, 2.27.106.11
carboxylic acid, 2.27.66.2     structure from smiles, 2.27.85.7
cartesian cooridnates, 2.28.184     substructure, 2.27.34.4
cartridge, 3.5          mask, 2.27.61.21
cavities, 2.27.88.1     superposition, 2.20.6, 2.28.126, 3.15
cavity, 5.3.1     table, 2.23
     analysis, 3.3.13     text format, 5.6.11
ccp4 maps, 2.27.80.26     view, 2.27.85.51
cd, 2.27.85.20chemistry, 2.23, 2.28.27
cell axis vectors, 2.28.184.7chiral isomer generation, 2.27.29
     specific icm commands, 5.9.2.4chirality, 2.18.16, 2.27.29
center, 2.11.1, 2.27.9choosing ligands, 3.13.1.2
circular permutation of coordinates, 2.27.65     molecule, 2.27.13.1
clamp values to range, 2.28.171     names, 2.28.29
clashThreshold, 2.17.5     object, 2.27.11.2
     labels, 2.28.159     specification, 2.27.11.1
clear, 2.27.10     surface by conservation, 2.27.13.3
     graphical selection, 2.27.10     volume, 2.27.13.7
     screen, 2.27.10column, 5.3.5
click and lock, 5.9.2.4     function, 2.27.7.2
clipping plane, 2.21.5.8, 5.3.3     selection, 2.28.92
closer than threshold, 2.28.41.7combinatorial compounds, 2.28.27
closest sequence, 2.28.92.3     libraries, 2.27.61.32, 2.28.95.4
     value, 2.28.52.1     PDB, 2.29.90
cluster, 2.28.147.1     transformations, 3.10.4
     center, 2.28.65.9combining plots, 2.27.61.31
     centers, 2.11.1     receptor and ligand stacks, 2.27.4.2
     selection, 2.28.65.9command, 2.28.92.4, 5.3.10
     tree, 2.28.92.5     line editing, 2.2
          size, 2.28.95.1          help, 2.27.44
clustering, 2.11, 2.27.61.35, 2.27.61.36, 2.27.88.7          options, 2.1
clusters, 2.11, 2.11.1     word list, 3.1.5
cnMethodAverage, 2.20.5commands, 2.20.10, 5.1.1
cnWeight, 2.17.6communication protocols, 2.25
coil, 5.3.4comp, 2.28.98
collection, 2.10, 5.3.6comp_matrix, 2.27.85.19, 2.27.86.16, 5.3.11
color, 2.21.5.30, 2.27.11compare, 2.16.11, 2.16.14, 2.27.14
     accessibility, 2.27.13     angles, 2.27.14.2
     background, 2.27.13.2     atom, 2.27.14.1
          example, 3.2.7     by rmsd without superposition, 2.27.14.1
          accessibility, 3.2.11     chemical tables, 2.27.34.10
          alignment, 2.27.13.3     patch only, 2.27.14.3
          atom contributions, 2.27.12     rmsd, 2.27.14.1
          bfactor, 3.2.9     surface, 2.27.14.3
          charge, 3.2.12     variables, 2.27.14.2
          electrostatic potential, 2.16.5compareMethod, 2.20.6
          hydrophobicity, 3.2.10comparing two sarrays, 2.28.98
          pharmacophore, 2.27.12comparison operations, 2.12.5
          potential, 2.29.25complete view, 2.28.137
          shape depth, 2.27.13compound accessibilities, 3.14.4.1
     chemical, 2.27.12, 2.27.84.1     array, 2.23
     file, 2.30.15compress, 2.27.15
     grob, 2.27.13.4     binary, 2.27.15.3
          by atom selection, 2.27.13.4.3     conf, 2.27.15.2
               atoms, 2.21.7.1     grob, 2.27.15.1
          map, 2.27.13.4.4     in place, 2.27.15.3
          matrix, 2.27.13.4.2     objects, 2.27.15
          potential, 2.27.13.4.5     stack, 2.27.15.2
          unique, 2.27.13.4.1compressed table view, 2.27.85.23
     label, 2.27.13.5conditional buttons, 5.5.5
     map, 2.27.13.6     string, 2.28.149.7
          by value, 2.27.23.16conf, 2.27.85.57, 2.27.106.40, 2.28.153.6, 5.3.12, 5.8.9
confgen, 3.16convertObject, 2.29.13
configuration, 2.30.14converting a chemical, 2.27.18.3
     memory usage, 2.16.6          pdb-chemical, 3.13.2
conformation comparison, 2.20.6     alignment to table, 2.28.153.2
conformational generator, 2.27.62.1, 3.16     chemicals, 3.13.2.3
     interpolation, 2.27.23.6     table columns into matrix, 2.28.84.5
     stack, 2.27.106.40, 5.3.12, 5.8.9     to, 2.28.116
          compression, 2.27.15.2cool, 2.29.40
          file, 2.30.7     pictures, 2.21.5.27
     transition, 2.29.38cooling schedule, 2.17.43
conformer storage, 2.27.59.5, 2.27.90.2coordinate frame, 2.17.4, 2.27.23.4
conformers, 3.16coordinates, 2.21.14.5
connect, 2.27.16copy, 2.27.19
     chains with alignments, 2.27.53     chemical image, 2.21.9.15
     molcart, 2.27.16.1     file, 2.19.26
consensus, 2.17.7     site, 2.27.85.26
     coloring, 2.17.9, 2.21.2correlation matrix, 2.28.156
     definitions, 2.21.1covalent bound count, 2.28.130.3
consensusStrength, 2.17.7     neighbors, 2.28.94.1
conservation, 2.28.115.5, 2.28.129.6covalently attached molecule, 2.28.94.1
constant, 2.5cpk, 5.3.13
constants, 2.5create a covalent bond, 2.27.61.2
contact areas, 2.28.84     pharmacophore, 2.29.85
continue, 2.27.17creating a local patch object, 2.27.18.2
contour surfaces, 2.21.7.5credits, 4.5
contouring density, 2.27.61.14crypt, 2.27.20
contrast, 2.21.5.30crystal axis vectors, 2.28.16
conversion, 5.1.6     symmetry transformation, 3.10.2
     to real array, 2.28.161          transformations, 2.28.169
convert, 2.27.18, 2.27.18.2, 3.13.2crystallographic cell, 2.27.65
     3D to chemical, 2.28.27     occupancy, 2.28.100
     3D/0D to 2D, 2.27.61.9     symmetry intro, 1.4.2.4
     ICM object to PDB, 2.27.92crystallography, 2.28.122
     and reroot, 2.27.18.4csv format, 2.27.80.43
     chemical 3D, 2.29.81csym, 1.4.2.4
               and optmimize geometry, 2.29.82cube, 2.21.14.2
     comp, 2.27.18.1current, 5.3.9
     comparison, 2.27.18.1     map, 5.3.7
     fragments, 2.27.18.2     object, 5.3.8
     mol, 2.27.18.3     working directory, 2.28.101
     object 3D and optmimize geometry, 2.29.83cursor action, 5.9.2.4
          macro, 2.29.13custom field, 2.27.85.48
     pdb, 3.8.2     interaction, 2.27.86.37
     to 3D, 2.27.85.8customization, 3.1.2
          ICM object, 2.29.84     and paste chemicals, 2.21.9.14, 2.21.9.15
          iarray, 2.28.159cyclic temperature protocol, 2.17.43
          icm-object, 2.27.18cylinder, 2.21.14.2
          integer, 2.28.159cz32, 4.5
convert2Dto3D, 2.29.83data visualization, 2.27.61.36
convert3Dto3D, 2.29.84database, 5.4.1
     connection, 2.27.16.1     sequence, 2.27.22.22
     file, 3.5.1     session, 2.27.22.10
     import, 2.27.61.26     shell object, 2.27.22.1
date, 2.27.21, 2.28.149.2     site, 2.27.22.23
     array, 2.27.21     sstructure, 2.27.22.24
dcMethod, 2.20.7     stack, 2.27.22.27
dcWeight, 2.17.8          object, 2.27.22.28
decomposition, 2.27.61.27, 2.27.88.2     system, 2.27.22.9
defCell, 2.22.1     table, 2.27.22.30
defSymGroup, 2.16.2          rows, 2.27.22.30
default atom colors, 2.27.85.15     term, 2.27.22.31
     value, 5.8.2     tether, 2.27.22.33
define axis, 3.10.3     tree, 2.27.22.34
defining space box, 2.28.21     variable, 2.27.22.6
dehtml, 2.28.119.3     views, 2.27.22
delete, 2.27.22     backbone, 2.28.130.1
     3D graphics panel, 2.27.101     restraint, 2.27.22.17
     alias, 2.27.22.2deleting sites by number, 2.27.22.23
     array element, 2.27.22.6delphi, 2.29.25
          index, 2.27.22.6density correlation, 2.17.8, 3.11.3
          selection, 2.27.22.1     fitting, 2.20.7
     atom, 2.27.22.7     in unit cell, 2.27.61.23
     bond, 2.27.22.14densityCutoff, 2.17.10
     boundary, 2.27.22.15dependent columns, 2.27.1.1.1
     chemical, 2.27.22.35depth cueing, 2.27.13.7, 5.4.2
          fragment, 2.27.22.35depth-cueing, 2.17.14
          selection, 2.27.22.35desolvation, 2.20.24
     class, 2.27.22detecting bad covalent geometry, 2.27.86.12
     conf, 2.27.22.16     proximity, 2.28.41.7
     directory, 2.27.22.8dialog generation, 2.28.11
     disulfide bond, 2.27.22.25     in html documents, 2.27.43
     drestraint, 2.27.22.17          tables, 2.27.43
     element, 2.27.22.29     scripting, 2.28.11
     file, 2.27.22.9dielConst, 2.17.11
     from array, 2.27.22.6dielConstExtern, 2.17.12
     hydrogen, 2.27.22.11dielectric constant, 2.17.11
     label, 2.27.22.18, 2.27.22.19diff, 2.28.98
          chemical, 2.27.22.19dihedral angle, 2.27.61.19
     link, 2.27.22.20          calculation, 3.3.10
     map, 2.27.22.21directory, 2.27.22.8, 2.27.61.5, 2.28.128
     molcart, 2.27.22.3display, 2.27.23
     molecule, 2.27.22.13     GUI window, 2.27.23.26
     object, 2.27.22.12     box, 2.27.23.7
     parray, 2.27.22.34     clash, 2.17.5, 2.27.23.8
          element, 2.27.22.34     drestraint, 2.27.23.9
     peptide bond, 2.27.22.26     field, 2.21.5.2
     plot, 2.27.22.4     from script, 2.27.23.3
     salts, 2.27.66.3     gradient, 2.27.23.10
     selection, 2.27.22.5     grob, 2.27.23.11
     selftether, 2.27.22.32          label, 2.27.23.12
     hbond, 2.27.23.13dots, 2.27.74
     label, 2.27.23.15dotted surface, 2.21.5.53
     map, 2.21.5.10, 2.27.23.16double click action, 5.9.2.4
     model, 2.27.23.1drestraint, 2.27.86.18, 5.4.6
     new, 2.27.23.2     generate from structure, 2.27.61.7
     off-screen, 2.27.23.3     global weight, 2.17.6
     offscreen, 2.27.23.3     set, 2.27.85.21
     origin, 2.27.23.4     type, 5.4.7
     ribbon, 2.27.23.18drop, 2.17.13
     rotate, 2.27.23.5drug, 2.10
     site, 2.27.23.19ds3D, 2.29.31
     skin, 2.27.23.20dsCellBox, 2.29.15
     slide, 2.27.23.21dsChem, 2.29.17
     stack, 2.27.23.6dsCustom, 2.29.18
     string, 2.27.23.22dsPocket, 2.29.28
     surface, 2.27.23.20dsPropertySkin, 2.29.19
          area, 2.21.5.2dsPrositePdb, 2.29.24
     tethers, 2.27.23.23dsRebel, 2.16.5, 2.29.25
     trajectory, 2.27.23.17dsSeqPdbOutput, 2.29.26
     volume, 2.27.23.24dsSkinLabel, 2.29.27
     window, 2.3, 2.27.23.25dsStackConf, 2.29.29
distance, 2.21.5.21, 5.4.3dsVarLabels, 2.29.30
     averaging, 2.20.5dsXyz, 2.29.32
     contact-based, 2.28.23, 2.28.23.1dump database, 2.27.106.7
     geometry, 5.4.4dynamic gui, 5.5.5
     matrix, 2.28.153.5, 2.29.8ecepp, 5.5.1
          between stack conformations, 2.28.84.10edit, 2.27.24
     restraint, 5.4.6     files, 2.21.14.1
          file, 2.30.9electro intro, 1.4.2.9
          type file, 2.30.8electroMethod, 2.20.8
     restraints, 2.27.85.21     density, 2.21.7.5, 2.27.85.33, 2.27.86.21, 2.29.42, 2.29.43
distances, 2.28.95.3          around selection, 2.17.22
distribution, 1.3          map generation, 2.17.1
     comparison, 2.28.129          maps, 2.21.14.1
disulfide bond, 5.4.5electrostatic boundary matrix, 2.28.84.9
diverse subset, 3.14.6.4     isopotential surfaces, 2.27.61.13
dividing chemical into individual molecules, 2.28.147.4     potential, 2.27.13.4.5
dna to protein sequence translation, 2.28.168.1     solvation, 3.7.2
     translate, 2.28.168.1     surface, 2.29.25
dockScan, 3.13.2.5     troubleshooting, 5.7.13
docking, 2.29.87     intro, 1.4.2.9
     intro, 3.13.2.1ellipsoid, 2.28.156
     result viewing, 2.29.28elseif, 2.27.25
     simple models, 3.14.3endfor, 2.27.26
     timing, 3.13.1.3endif, 2.27.27
     with template, 3.13.2.6endmacro, 2.27.28
documents, 5.5.8endwhile, 2.27.32
dominant color, 2.28.29.2energetics, 3.7
donor, 3.6.1     function, 2.21.14.3
     plot intro, 1.4.3.2     terms, 2.15
entropy of alignment, 2.28.129.6fast Fourier transform, 2.27.61.24
     atom, 2.27.18.4     sequence search, 2.27.34.3
enumerate, 2.27.29, 2.27.30, 2.27.31fasta, 2.21.12.15, 5.5.2
     chiral, 2.27.29     format, 2.27.106.1
     library, 2.27.31feature table, 5.8.6.1
     tautomer, 2.27.30     in sequences, 2.27.85.25
enumeration, 2.28.27ffMethod, 2.20.11
eps files, 2.19.23field name, 2.28.92.2
error SOAP services, 2.28.45file, 2.27.106.23
     ignoring, 2.19.25     exists, 2.28.46
error/warning bits cleanup, 2.27.10     list, 2.28.55
errorAction, 2.20.9     length, 2.28.51
     vrestraint vs_var, 2.27.85.78     object origin, 2.28.51
evalSidechainFlex, 2.29.88     permissions, 2.28.51
evol tree intro, 1.4.3.5     time modified, 2.28.51
evolutionary tree intro, 1.4.3.5     type, 2.28.51
exact, 2.27.34.9, 2.27.34.10files, 2.30
     match, 2.28.119.1filling volume, 2.21.5.8
example scripts, 3.14filter, 2.27.34.10, 2.27.59.3
exit, 2.27.33     functions, 5.5.4
exitSeslogStyle, 2.20.10filtering table rows, 5.5.4
expanding substructure match, 2.27.85.66find, 2.27.34
export, 2.27.106.7     alignment, 2.27.34.1
     animation, 2.27.106.30     and replace a chemical pattern, 2.27.66.1
     pdb, 2.21.14.12               chemical fragment, 2.27.66
exporting sdf, 2.27.106.11     chemical, 2.27.34.5
expression shortcuts, 2.9.1.2          pattern, 2.27.66
     comparison, 2.12.5          substructure, 2.28.65.2
     arithmetics, 2.12.2     database, 2.17.2, 2.27.34.2
     assignment, 2.12.1          fast, 2.27.34.3
     comparison, 2.12.5     family of commands, 2.27.34
     logical, 2.12.3     in sarray, 2.28.65.8
extending to bonded hydrogens, 2.28.130.6     molcart, 2.27.34.9, 3.5
               terminal atoms, 2.28.130.6     molecule, 2.27.34.4
external process, 2.27.61.1     pattern, 2.27.34.8
extracting from Markush, 2.27.51     pdb, 2.27.34.6
     icm script arguments, 2.28.55     pharmacophore, 2.27.34.11
     stack from object, 2.27.59.5     prosite, 2.27.34.7
ez25, 3.7     table, 2.27.34.10
factor, 5.8.14findFuncMin, 2.29.33, 2.29.34
false negatives, 2.28.129.3findFuncZero, 2.29.35
family, 2.27.85.35.1findSymNeighbors, 2.29.16
faq, 1.3find_related_sequences, 2.29.33
     cheminformatics, 3.14.6finding long covalent bonds, 2.28.130.1
     chemsuper, 3.14.5     to density, 2.20.7
     mac gui preferences, 3.14.6.2fix, 2.27.35
     molcart dump, 3.14.6.3fixed branches, 2.28.130.2
          query, 3.14.6.1flattening 3D molecule, 2.29.17
     multiple chem overlay, 3.14.5.1flow control, 2.13
     residue table, 3.14.4.1fog, 2.17.14, 2.27.13.7, 2.27.23.24, 5.4.2
fogStart, 2.17.14     card, 2.21.5.49
fold search, 5.8.4     controls, 2.3, 2.30.15, 5.4.2
foldbank.db, 2.30.3     exists, 2.28.46
folding procedure, 3.14.1     intro, 1.4.1, 1.4.1.4
font, 2.27.54.1     learning, 3.2.1
     size, 2.27.85.35.1, 2.30.14     attributes, 2.17.4
     sizes, 3.14.6.2     fogStart, 2.17.14
     specification, 2.27.85.35.1     view vector, 2.27.85.76
for, 2.27.36greedy matching, 2.9.1.4
fork, 2.27.37, 2.28.65.1grid energy, 2.27.86.21
formal charge, 2.21.5.17, 5.3.2     potentials, 2.27.61.25
formatdb, 2.27.106.24grob, 5.5.3
fprintf, 2.27.38     coloring, 2.27.13
fractional coordinates, 2.28.184.3     files, 2.30.10
     to abs coordinates, 2.28.16     inside-out flip, 2.27.85.39
fragmented molecule, 2.27.18.2     normal directions, 2.27.85.39
frame, 2.27.90, 2.27.106.30     vertex, 2.21.5.18
fullscreen, 2.27.85.81     translate, 2.27.99
function, 2.27.39, 2.27.60group, 2.27.42
     columns, 2.27.1.1.1     by column, 2.27.42.4
functions, 5.1.1     column, 2.27.42.4
     selecting in objects, 2.8.10     replacement, 2.27.64
gamess, 5.5.6     sequence, 2.27.42.1
     expansion, 2.28.139.4          unique, 2.27.42.2
gapExtension, 2.17.15     table, 2.27.42.3
gapFunction, 2.22.3grouping table by a column, 2.27.85.23
gapOpen, 2.17.16gui, 2.27.43, 5.9.2.4
gaussian averaging, 2.28.139.2     exists, 2.28.46
gcMethod, 2.20.12     functions, 5.5.5
genbank, 2.21.12.15     panels, 2.27.101
generalized arrays, 5.1.6     programming, 2.26, 2.27.43, 2.27.85.23
generate intermediate conformers, 2.29.38gvim text editor, 5.8.2
generating movie images, 3.9.2.1gzip files, 2.27.15.3
genomics, 1.4.3.1hash, 2.10, 5.3.6
     clustering, 2.27.42.2     table, 5.3.6
     intro, 1.4.3.1haze, 2.17.14
geometry optimization, 2.27.62.1hb, 2.17.18
     started, 1.7hbCutoff, 2.17.18
getting data from outside, 2.25hbond, 2.21.5.22, 2.21.5.23, 2.27.22.6, 5.5.7
     started, 1.7     color, 2.27.23.14
global, 2.27.40     display, 2.21.5.24, 2.21.5.25
glossary, 5     energy, 2.27.23.14
goto, 2.27.41     list, 2.28.153.9
     term, 2.17.17, 2.27.85.69     show, 2.27.86.23
gpWeights, 2.17.17hbondMinStrength, 2.21.5.22
graph matching, 2.28.126     faq, 3.3.4
graphical box, 2.27.23.7     how to, 3.3.4
     row selection, 2.28.65.5header, 2.27.1.1
     selection, 2.28.130.5helical axis, 2.29.36
graphics, 2.27.85.4, 2.28.180, 3.2, 5.3.3     cylinders, 2.21.5.39
     content calculation, 3.7.6          literature, 4.3
help, 2.27.44, 2.27.44.1, 2.27.44.2     archive, 2.27.80.2
     browser, 2.27.44.1     arguments, 2.28.55
     commands, 2.27.44.3     binary, 2.28.101
     functions, 2.27.44.4     branching, 2.13.2
     getting, 3.1.1     commands, 2.27
     word, 2.27.44.2     controls, 2.13
     getting, 3.1.1     flags, 2.1
heterogenous environment, 2.21.14.2     functions, 2.28
hidden blocks, 5.1.1.1     graphics, 3.2
     display, 2.27.23.3     history, 1.2
     hydrogens, 2.21.5.29     jumps, 2.13.3
     stack in object, 2.27.90.2     learning, 3.1.4
hierarchical, 2.11     loops, 2.13.1
highEnergyAction, 2.20.13     macros, 2.29
his-tags, 2.28.172     main refs, 4.2
histogram, 2.27.61.31     menus, 2.21.10.1
     2D, 2.28.84     method literature, 4.4
history, 2.27.45, 2.27.106.39     molecules, 2.14
     delete, 2.27.22.10     object file, 2.30.18
     of ICM, 1.2     session, 2.20.10
homodel, 2.29.41     shell, 3.1
homology modeling, 1.4.2.2, 2.27.7.5, 2.27.85.64, 2.27.85.65, 2.29.1, 3.14.4     support, 1.3
          faq, 3.14.4     table, 2.21
          intro, 1.4.2.2     ali, 2.30.31
     output, 2.27.7.5.3     all, 2.30.32
     steps, 2.27.7.5.1     bbt, 2.30.5
     to export a molcart table, 3.14.6.3     bst, 2.30.6
html, 2.27.43, 2.28.92.4, 5.5.8     cfg, 2.30.14
     document order, 2.27.85.37     clr, 2.30.15
     tag removal, 2.28.119.3     cmp, 2.30.33
html-formatted text, 5.5.8     cn, 2.30.9
hydration, 2.21.14.2, 2.28.7     cnf, 2.30.7
     parameters, 2.30.13     cnt, 2.30.8
hydrogen bond, 2.21.5.22, 2.21.5.23, 2.27.61.17, 5.5.7     cod, 2.30.4
     bonding parameters, 2.30.12     col, 2.30.24
          cutoff, 2.17.18     gro, 2.30.10
     bonds, 2.28.95.3     hbt, 2.30.12
     display, 2.21.5.29     hdt, 2.30.13
     placement, 2.27.85.24     htm, 2.30.11
hydrophobicity profile, 3.3.12     iar, 2.30.35
iSee, 5.8.15     map, 2.30.16
i_2out, 2.16.4     mat, 2.30.37
i_out, 2.16.3     ob, 2.30.18
iarray, 2.27.22.6, 2.28.52.1, 2.28.62.2, 2.28.65.8, 5.6.1     pdb, 2.30.28
     making, 2.28.62.1     prf, 2.30.34
icb files, 5.8.15     rar, 2.30.38
     GUI, 2.27.85.37     res, 2.30.20
     algorithms, 4.3     rs, 2.30.23
     application refs, 4.4     rst, 2.30.22
     se, 2.30.30     lists, 2.18.27, 2.21.14.3
     seq, 2.30.29interactive docking, 1.4.2.8
     tab, 2.30.25interatomic potential, 2.27.85.48, 2.27.86.37
     tot, 2.30.26interface comparison, 2.27.14.3
     trj, 2.30.17     residues, 3.3.5
     var, 2.30.21     torsions, 3.3.7
     vwt, 2.30.27     view, 2.29.28
icmCavityFinder, 2.29.14intermolecular bond, 2.27.68.3
icmMacroShape, 2.29.86internal coordinate file, 2.30.21
icmPmfProfile, 2.29.23     coordinates, 2.8.9
icmPocketFinder, 2.29.87     positional restraints, 5.9.4
icmscript, 2.27.80.3interpolate, 2.28.29.1
     arguments, 2.28.55interpolation, 2.28.29.1
if, 2.27.46interruptAction, 2.20.14
ignoring swiss secondary structure, 2.22.9inverting array order, 2.28.62.2, 2.28.115.2
illegal smiles, 2.28.65.2italic, 2.27.85.35.1
image, 3.2.6iterative overlay, 2.27.93
     annotation, 3.2.5     superposition, 2.21.14, 2.27.94
     center, 3.2.8join, 2.27.49
     format, 5.9.3     tables, 2.27.49
     high quality, 3.2.2keep, 2.27.48
     parray, 5.7.3.3kernel models quality, 2.28.129.3
     resolution, 3.2.2     mapping, 2.30.15
     rotation, 3.2.3kmz, 5.5.3
implicit continuous solvation, 2.30.13l_antiAlias, 2.18.1
     solvation, 2.27.85.68l_autoLink, 2.18.2
imposing tether, 2.27.85.64, 2.27.85.65l_bpmc, 2.18.3
     place, 2.12.4l_breakRibbon, 2.18.4
          ops, 2.12.4l_bufferedOutput, 2.18.5
incidence, 2.28.84.12l_bug, 2.18.6
increasing the number of shell variables, 2.30.14l_caseSensitivity, 2.18.7
increment charge, 2.27.85.10l_commands, 2.18.8
index expressions, 2.6l_confirm, 2.18.9
     in array, 2.28.65.4l_easyRotate, 2.18.10
     substring, 2.28.65.3l_info, 2.18.11
     table, 2.27.106.23l_minRedraw, 2.18.12
          entry, 2.28.128.1l_neutralAcids, 2.18.13
          sdf-file path, 2.28.101l_out, 2.18.14
indices of labeled table rows, 2.28.65.6l_print, 2.18.15
          selected table rows, 2.28.65.5l_racemicMC, 2.18.16
infinity, 2.28.161l_readMolArom, 2.18.17
info, 2.27.47l_showAccessibility, 2.18.18
     molcart, 2.27.47.1l_showMC, 2.18.19
inner join, 2.27.49l_showMinSteps, 2.18.20
insert rows, 2.27.1.4l_showResCodeInSelection, 2.18.21
integer, 5.6.2l_showSites, 2.18.23
     array, 2.28.62, 5.6.1l_showSpecialChar, 2.18.22
     output, 2.16.4l_showSstructure, 2.18.24
     shell variables, 2.16l_showTerms, 2.18.26
interaction cutoff, 2.18.27l_showWater, 2.18.25
l_warn, 2.18.28listUpdateThreshold, 2.17.20
l_wrapLine, 2.18.29literature, 4.1
l_writeStartObjMC, 2.18.30load, 2.27.59
l_xrUseHydrogen, 2.18.31     conf, 2.27.59.1
label, 2.27.23.22, 5.6.3     frame, 2.27.59.2
     fonts, 2.30.15     molcart, 2.27.59.3
large text, 2.27.80.39     object, 2.27.59.6
latent, 2.28.95.6     solution, 2.27.59.4
learn, 2.27.50     stack object, 2.27.59.5
     atom, 2.27.50.1loadEDS, 2.29.42
left join, 2.27.49loadEDSweb, 2.29.43
     triangle of a matrix, 2.28.84.3local, 3.5.1
library to replacement groups, 2.27.61.27, 2.27.88.2logarithm, 2.28.79
ligand based screening, 3.15logical, 5.6.4
     binding, 2.29.28     operations, 2.12.3
     dock faq, 3.13.2     variables, 2.18
     docking, 3.13, 3.13.1, 3.13.2logical_ops, 2.12.3
          intro, 1.4.2.6logicals, 2.18
     editing, 1.4.2.8long axes, 2.28.156
     editor, 2.29.37loop database rebuilding, 2.27.106.27
     fit, 3.13     interrupt, 2.17.44
     setting, 3.13.2     modeling, 1.4.2.3
     view, 2.21.5.28          intro, 1.4.2.3
light, 2.21.5.31     search, 2.27.7.5.2
limits, 2.30.14     resolution shape, 2.29.86
line thickness, 2.21.12.5lower case, 2.28.160
          in 2D chemicals, 2.21.9.14ma29, 3.11
lineWidth, 2.17.19macro, 2.27.60, 5.6.5
linear chemical notation, 2.24macro_def, 5.6.5
     regression, 2.28.78main ICM references, 4.2
     group, 2.27.51     concepts, 3.10.1
     internal variables of molecular object, 2.27.52make, 2.27.61
     ms2ali, 2.27.53     3d label, 2.27.61.15
     sequences to 3D objects, 2.27.53     angle, 2.27.61.18
     to alignment, 2.27.53     background, 2.27.61.1
     variable, 2.27.52     bond, 2.27.61.2
     variables, 2.27.52          chain, 2.27.61.3
linked alignment, 2.28.92          multi, 2.27.61.3
     sequence, 2.28.92     boundary, 2.27.61.4
linux shell, 2.27.95, 5.10.2     directory, 2.27.61.5
list, 2.27.54     distance, 2.27.61.16
     binary, 2.27.55     disulfide bond, 2.27.61.6
     database, 2.27.56     drestraint, 2.27.61.7
     directory, 2.27.57     factor, 2.27.61.8
     font, 2.27.54.1     flat, 2.27.61.9
     html documents, 2.28.92          chem_array, 2.27.61.9
     molcart, 2.27.58     grob, 2.29.36
          database, 2.27.58          from image, 2.27.61.11
     of files, 2.28.128               matrix, 2.27.61.12
     updates, 2.27.62          image, 2.27.61.11
          matrix, 2.27.61.12mapAtomMargin, 2.17.22
          potential, 2.27.61.13mapSigmaLevel, 2.17.21
          skin, 2.27.61.14mapping chemical equivalences, 2.28.65
     hbond, 2.27.61.17     properties to sequence, 2.28.115.4
     image, 2.27.61.20     and factors, 3.11
     key, 2.27.61.21mass-spectrometry functions, 2.27.29, 2.27.30, 2.27.31
     map, 2.27.61.22matching chemicals, 2.28.65.2
          cell, 2.27.61.23     hydrogens, 2.27.85.66
          factor, 2.27.61.24matrix, 5.6.7
          potential, 2.27.61.25     derivatives, 2.28.75
          xray, 2.27.61.30     new, 2.28.84.1
     molcart, 2.27.61.26     map value, 2.28.85
     molsar, 2.27.61.27maxColorPotential, 2.16.5
     pca, 2.27.61.28maxMemory, 2.16.6
     peptide bond, 2.27.61.29     movie, 3.9.2
     plot, 2.27.61.31mcBell, 2.17.23
     reaction, 2.27.61.32mcJump, 2.17.24
     sequence, 2.27.61.34mcShake, 2.17.25
          alignment, 2.27.61.33mcStep, 2.17.26
          from alignment, 2.27.61.33mean force, 2.27.85.48, 2.27.86.37
     torsion, 2.27.61.19membrane, 2.21.14.2
     tree, 2.27.61.35memorizing positions, 3.2.4
          object, 2.27.61.36menu, 2.27.63
     unique, 2.27.61.37     script, 3.1.3
makeAxisArrow, 2.29.36merge PDB, 2.29.90
makeIndexChemDb, 2.29.44     arrays to table, 2.27.42.3
makeIndexSwiss, 2.29.45     continuation lines, 2.27.80.38
makePdbFromStereo, 2.29.46     objects, 2.27.68.2
makePharma, 2.29.85     parts of molecule, 2.27.68.3
makeSimpleDockObj, 2.29.47     pdb, 3.4.4
makeSimpleModel, 2.29.48     sarray into string, 2.28.151
making predictive models, 2.27.50     stacks, 3.7.7
manual style, 1.5     tables, 2.27.4.3, 2.27.49
map, 2.17.22, 2.21.5.10, 5.6.6merge2, 3.8.7
     aa property to sequence, 2.28.115.1mergePdb, 2.29.90
     averaging, 2.28.139.5     several chemical, 2.28.151.1
     calculation, 2.27.61.24merging into one molecule, 2.27.68.3
     conversion, 2.27.61.30mesh, 2.28.181
     file, 2.30.16     point radius, 2.21.5.18
     fitting, 2.20.7     score, 3.13.3.3
     format, 5.6.6mfMethod, 2.20.15
     mean value, 2.28.87mfWeight, 2.17.27
     min value, 2.28.88mimel, 5.6.8
     name, 2.28.80mimelDepth, 2.17.28
     operations, 5.6.6mimelMolDensity, 2.17.29
     transformations, 2.28.139.5minNumGrad, 2.27.62
     trimming, 2.28.22minTetherWindow, 2.16.7
     value sigma, 2.28.126minimization exit criteria, 2.27.62
          on atoms, 2.27.85.33minimize, 2.16.9, 2.27.62
     contouring, 2.27.61.14     cartesian, 2.27.62.1
     stack, 2.27.62.3     volume, 2.28.107
     tether, 2.16.7, 2.27.62.4molecule, 2.7
     drop, 2.17.13     create, 3.8.4
minimizeMethod, 2.20.16     properties, 2.27.85.32
missing bonds, 2.27.68.3     rotation, 3.2.3
     loop, 2.21.5.6, 2.21.5.7     translation, 3.2.3, 3.2.4
     residues, 2.28.50.1     create, 1.7.2
     triangles, 2.28.181     intro, 1.7.2, 2.7
mkUniqPdbSequences, 2.29.49     sort/reorder, 2.27.87.4
mm26, 3.8     selecting, 2.8.6
mmcif, 5.6.10monte carlo, 2.27.67
mmff, 5.6.9montecarlo, 2.16.10, 2.16.12, 2.16.13, 2.16.14, 2.16.18, 2.20.6, 2.27.67
     type, 2.28.174     local, 2.16.15
     show atom types, 2.27.86.11     trajectory, 2.27.23.17
mnSolutions, 2.16.8moprphing, 2.29.38
mncalls, 2.16.9more, 5.6.13
mncallsMC, 2.16.10morph, 2.27.23.6
mnconf, 2.16.11     to tether target, 2.29.38
mnhighEnergy, 2.16.12morph2tz, 2.29.38
mnreject, 2.16.13morphing, 2.27.23.6, 2.27.85.64, 2.27.85.65, 2.27.90.3
mnvisits, 2.16.14mouse controls, 2.3
model reliability, 2.29.23     file, 2.27.106.30
modify, 2.27.64move, 2.27.68
     and reroot, 2.27.18.4     alignment sequence, 2.27.68.6
     chem, 2.27.66     atoms, 2.27.85.3
          charge, 2.27.66.2     bonding, 2.27.68.3
          delete salt, 2.27.66.3     column, 2.27.68.5
          normalize, 2.27.66.4     element, 2.27.68.4
     chemical find replace, 2.27.66.1     file, 2.19.28, 2.27.81.3
     molcart, 2.27.66.5     fragments together, 2.27.68.3
     rotate, 2.27.65     molecule, 2.27.68.1
modifyGroupSmiles, 2.29.37     ms_molecule, 2.27.68.1
modules, 1.4.4     multiple molecules, 2.27.68.2
mol, 2.27.80.47, 2.27.80.48, 2.27.106.11, 2.27.106.23, 5.6.11     object, 2.27.68.2
     file, 2.28.149.3     sequence, 2.27.68.6
     to icm, 2.27.18.3     table column, 2.27.68.5
     translation, 3.2.4movie, 2.27.90.3
mol-file to chem-table element, 2.28.102     images by frame, 3.9.2.2
mol-format, 2.21.14.5     molecular simulation, 3.9.2
mol2, 5.6.12     rotate view, 3.9.1
molcart, 2.27.16.1, 3.5     zooming, 3.9.1
     connection options, 3.5.2moving selection to another object, 2.28.130.8
molecular, 2.28.54, 5.7.3.1mpeg, 2.27.106.30
     arrays, 5.7.3ms_, 2.8.6
     manipulations, 3.8multi center drestraint, 2.20.5
     modifications, 3.8.5multi-part molecule, 2.27.18.2
     object, 5.7.1multicore, 2.28.65.1
     objects, 2.14multiline input, 2.27.80.4
     surface, 2.27.86.9, 5.8.7multiple NMR models, 2.21.14.4
     views, 1.4.1.1     alignment, 2.27.3.2
     conformation storage, 5.8.9     selecting, 2.8.5
     mol as text, 2.28.149.3obsolete, 2.17.51
     object file, 2.27.80.2occlusion shading, 2.27.13
     sequence alignment intro, 1.4.3.4octanol transfer, 2.28.107
     smiles file format, 2.27.80.44off, 2.27.80.21
multiprocessor, 2.27.37     format, 5.5.3
mutate residue, 2.27.64oligonucleotide melting, 2.28.157
mutating residue, 3.8.5on-line help, 2.27.44.1, 2.27.44.2
mute, 5.6.15     third, 2.28.35
mysql, 2.27.16.1only, 5.7.2
nLocalDeformVar, 2.16.15openGL window, 2.27.101
nProc, 2.16.17operating system, 2.27.95, 2.28.180, 5.10.2
nSsearchStep, 2.16.16optimal chemical superposition, 3.14.5.1
name, 2.28.74optimization, 2.27.67
     atom fields, 2.27.85.32     Hbond, 2.29.89
naming compounds, 2.27.85.44     hydrogen bond, 2.29.89
nearest sequence, 2.28.88optimizeHbonds, 2.29.89
neighbor joining, 2.27.61.36or, 2.12.3
nested script, 5.8.2order, 2.27.68.6
     real array, 2.28.115original sequence names, 2.21.12.15
nice, 2.29.39os_, 2.8.5
     image, 3.2.2other variables, 2.22
non-redundant, 3.4.3out-of density atoms, 2.27.86.21
normal distribution, 2.28.114output, 2.16.3
normalize chemicals, 2.27.66.4overlay by atom pairs, 2.27.93
     defined, 2.28.161          chemical substructure, 2.29.22
nota, 1.5overview, 1.4
notational conventions, 1.5pK shift, 3.7.3
nproc, 2.27.37packing density, 3.3.8
nucleotides, 2.19.24pair-distances, 2.27.22.6
number, 2.16.17pairdistance parray, 2.21.5.21
     of dots, 2.21.5.52pairwise interactions, 2.27.85.48
          elements, 2.28.95panel layout, 2.21.8.5
          hydrogen bonds, 2.27.86.23paragraphs, 2.27.106.23
          molecules in objects, 2.28.130.4parallel, 2.16.17
          occurrences, 2.28.95     computing, 2.28.65.1
          residues in molecules, 2.28.130.4     processing, 2.27.37
          van der Waals contacts, 2.27.86.13parallelization, 2.28.65.1
     transfer from sequence, 2.27.3.1parameter list file, 3.14.6.2
nvis, 2.28.62.6parray, 2.27.22.6, 5.7.3
object, 2.27.13.1, 5.7.1parrayTo3D, 2.29.82
     parray, 5.7.3.1parrayToMol, 2.29.81
     properties, 2.27.85.32parse SOAP message, 2.28.178
     stack, 5.8.9parsing, 2.28.83
     to chemarray, 2.28.27     web pages, 2.27.80.45
     user fields, 2.28.50.1partial least squares, 2.27.50
     assign comment, 2.27.85.16     slide display, 2.27.23.21
     source file, 2.28.51     sum, 2.28.72
     translate, 2.27.99passing arguments, 5.8.2
     merge, 3.8.6     by reference, 2.27.60
     search, 2.27.34.2     model, 2.28.153.7, 2.28.153.8
pause, 2.27.69     weights, 2.28.153.7, 2.28.153.8
pdb, 5.6.10, 5.7.6pmf, 2.20.15
     file creation time, 2.28.36     residue profile, 2.29.23
     files, 2.30.28pmf-file, 2.30.19
     format, 2.27.80.46pmffile, 2.30.19
     merge, 3.4.4png, 2.27.106.35, 5.7.5
     sequence generation, 3.4.3pocket, 2.29.28, 2.29.87, 3.13.1.1
pdbDirStyle, 2.20.17point coordinates, 2.28.184.1
peptide, 5.7.7     size, 2.21.5.18
     docking, 3.12.5pointer array, 5.7.3
     folding, 1.4.2.1polar hydrogens, 2.21.5.29
          intro, 1.4.2.1     surface area, 2.28.107
personal gui controls, 3.1.2polarization charge, 3.7.2, 5.7.13
     setup, 3.1.2positional constraint, 2.21.14.10
ph30, 3.12postscript, 2.19.23
ph4, 5.7.8potential surface coloring, 5.7.13
     object faq, 3.6.1pov-ray, 2.27.106.37
pharmacophore, 2.27.12, 3.5, 5.7.8pow, 2.28.35
     faq, 3.6precision, 2.28.129.3
     grid type definitions, 2.27.85.69predict, 2.27.72
     object, 3.6.1predictSeq, 2.29.60
     objects, 3.6prediction model, 2.28.78
pharmacophores, 3.6     quality, 2.28.129
     psi plot, 2.29.57     score, 2.28.129
pipe, 2.27.80.42preference, 2.20
planar angle, 2.27.61.18preferences, 3.1.2.3
plot, 2.27.70prepSwiss, 2.29.61
     3D 2Dfunction, 3.12.3previous atom, 2.28.94.1
          shape, 3.12.4principal axes, 2.28.156
     area, 2.27.71     component analysis, 3.3.9
     grid line width, 2.21.12.5     inertia moments, 2.28.82
     histogram, 3.12.2print, 2.27.73
     how to, 3.12     bar, 2.27.74
     simple, 3.12.1     image, 2.27.76
plot2DSeq, 2.29.50     to string, 2.27.89
plotBestEnergies, 2.29.53printMatrix, 2.29.62
plotCluster, 2.29.55printPostScript, 2.29.63
plotFlexibility, 2.29.54printTorsions, 2.29.64
plotMatrix, 2.29.56printf, 2.27.75
plotRama, 2.29.57problem, 3.14.6.2
plotRose, 2.29.58processors, 2.16.17
plotSeqDotMatrix, 2.29.51profile, 5.7.9
plotSeqDotMatrix2, 2.29.52program overview, 1.4
plotSeqProperty, 2.29.59progress bar, 2.27.74
     3d, 1.4.3.7progression, 2.27.74
plotting van der Waals, 3.7.1project setup, 3.13.2.2
          faq, 3.7.1projected alignment, 2.28.92.3
pls, 2.27.50projecting surface charge, 3.7.2
     column contributions, 2.28.153.7, 2.28.153.8property, 2.27.85.49, 2.27.85.50, 2.27.85.51
     map, 2.27.85.69     csv, 2.27.80.43
     superposition, 2.27.85.69     database, 2.27.80.16
prosite, 5.7.10     drestraint, 2.27.80.17
     pattern, 5.7.4          type, 2.27.80.18
protein docking, 2.28.184.2     entries from database, 2.27.80.7
          intro, 1.4.2.5     factor, 2.27.80.19
     grid docking, 3.14.2     file by chunk, 2.27.80.39
     health, 2.29.57     from file, 2.27.80.1
     topology, 2.21.5.39          string, 2.27.80.4
psa, 5.7.12     fromstring, 2.27.80.4
purple box, 2.28.21     ftp http, 2.27.80.8
quadratic equation, 2.28.140     gamess, 2.27.80.20
quantum mechanics, 2.27.80.20, 2.27.106.17     grob, 2.27.80.21
qubic equation, 2.28.141     html, 2.27.80.3
query, 3.14.6.1          file, 2.27.80.3
     molcart, 2.27.77     iarray, 2.27.80.22
question mark operator, 2.28.149.7     index, 2.27.80.23
quit, 2.27.78          table, 2.27.80.7
     property transfer via alignment, 2.28.115.3     json, 2.27.80.55
r_2out, 2.17.31     library, 2.27.80.24
r_out, 2.17.30          mmff, 2.27.80.25
radii.electrostatic, 2.28.113     librarymmff, 2.27.80.25
     van der Waals, 2.28.113     map, 2.27.80.26
rainbow, 2.28.29.1     matrix, 2.27.80.27
ramachandran faq, 3.3.3     mol, 2.18.13, 2.27.80.7, 2.27.80.28
     how to, 3.3.3     mol2, 2.27.80.7, 2.27.80.29
random array, 2.28.114     object, 2.27.80.31
     order, 2.28.132          parray, 2.27.80.31.1
randomSeed, 2.16.18     pdb, 2.21.14.4, 2.27.80.2, 2.27.80.32
randomize, 2.16.18, 2.27.79          sequence, 2.27.80.33
     angles, 2.27.79.1     profile, 2.27.80.34
     coordinates, 2.27.79     prosite, 2.27.80.35
     torsions, 2.27.79     rarray, 2.27.80.36
rarray, 2.27.22.6, 2.28.52.1, 2.28.115.2, 5.7.11     sarray, 2.27.80.38, 2.27.80.39
     properties, 2.28.115.4     sequence, 2.27.80.7, 2.27.80.40
rdBlastOutput, 2.29.67          database, 2.27.80.40.1
rdSeqTab, 2.29.68     smiles, 2.27.80.44
reaction, 2.27.61.32     stack, 2.27.80.41
     group file, 2.27.51     string, 2.27.80.42
read, 2.27.80, 2.27.80.54, 2.27.80.55     table, 2.27.80.43
     FILTER, 2.27.80.5          csv, 2.27.80.43
     alignment, 2.27.80.11          html, 2.27.80.45
     all, 2.27.80.6          mmcif, 2.27.80.46
     binary, 2.27.80.2          mol, 2.27.80.48
     blob, 2.27.80.37          mol2, 2.27.80.47
     color, 2.27.80.12     text, 2.27.80.39
     column, 2.27.80.49     trajectory, 2.27.80.30
     comp_matrix, 2.27.80.13          and save a fragment, 2.27.80.30.1
     conf, 2.27.80.14          write, 2.27.80.30.1
     csd, 2.27.80.15     unix, 2.27.80.9
     variable, 2.27.80.50rename, 2.27.81
     view, 2.27.80.51     chemicals, 2.27.85.44
     vrestraint, 2.27.80.52     file, 2.27.81.3
          type, 2.27.80.53     molcart, 2.27.81.2
     with filter, 2.27.80.5     object, 2.27.81.1
     xml, 2.27.80.54     system, 2.27.81.3
readMolNames, 2.22.10     atom, 2.27.81.1
readcomp_matrix, 2.27.80.13     molecule, 2.27.81.1
reading external tool output, 2.27.61.1     residue, 2.27.81.1
     from standard input, 2.27.80.42renaming, 2.21.12.15
     pdb from ftp, 2.19.18reorder, 2.27.68.6
               web, 2.19.19     alignment sequences, 2.27.106.1
     restraint, 2.27.80.52     array, 2.28.132
real, 5.7.14     objects, 2.27.87.3
     array, 5.7.11replace matching array element, 2.28.119.1
     shell variables, 2.17     without interpretation, 2.28.119.2
     space refinement, 2.27.61.30replacing scaffold in a library, 2.27.66.1
reals, 2.17reproducible randomness, 2.16.18
rebel, 2.16.5, 5.7.13reroot, 2.27.18.4
rebuild molcart index, 2.27.7.10     selections, 3.3.6
recalculate dependent values, 2.27.7.2resLabelShift, 2.17.32
     values, 2.27.1.1.1resLabelStyle, 2.20.19
receptor, 3.13.1.1reserved names, 2.22
     preparation, 3.13.1.1residue, 2.27.13.1, 5.7.16
redefine hydrogen coordinates, 2.27.85.24     accumulators, 2.28.59
references, 4     alignment, 2.27.85.64, 2.27.85.65
refineModel, 2.29.65     conservation, 2.28.115.5
reflections, 2.21.5.30     contact area matrix, 2.28.84.7
refresh view, 2.27.23.2          areas, 2.28.7.1
refs, 4.1     field, 2.27.85.32
regexp, 2.9, 2.28.83     gap, 2.21.5.6, 2.21.5.7
     back references, 2.9.1.3     label, 2.27.3.1
     syntax, 2.9.1     library file, 2.30.20
regression, 2.27.50     name, 2.28.74
regul, 2.29.66          translation, 2.21.14.12
regular expression, 2.9, 2.28.65.4, 2.28.83     number, 2.28.62.5
          filter, 2.27.80.1          table, 2.28.153.3
     expression, 2.28.119.3     property averaging, 2.28.139.3
regularization, 2.16.7, 2.27.62.4, 5.7.15          calculation, 2.28.59
     procedure, 3.8.3     proximity, 2.28.84.7
rejectAction, 2.20.18     ranges, 2.8.11
relational database, 2.28.142     selection, 2.18.21
relative accessible area of atoms, 2.20.1          as string, 2.28.149.8
release notes, 1.1          function, 2.28.120
remarkObj, 2.29.69     table, 3.14.4.1
remove expression tags, 2.28.172     tethering, 2.27.85.64, 2.27.85.65
     file, 2.27.22.9     user field, 2.28.50.1
     trailing blanks, 2.28.171residue_selections, 2.8.11
removing html tags, 2.27.80.45     selecting, 2.8.7
     outliers, 2.28.171resizing, 2.28.64
     preference, 2.27.81.4s_inxDir, 2.19.9
restraining molecules to shapes, 2.21.14.10s_javaCodeBase, 2.19.12
restraints, 2.15, 2.27.85.64, 2.27.85.65s_labelHeader, 2.19.13
     torsion, 2.27.85.77s_lib, 2.19.14
return, 2.27.82s_logDir, 2.19.15
reverse complement, 2.28.131.1s_out, 2.19.16
     lighting, 2.27.85.39s_pdbDir, 2.19.17
     normals, 2.27.85.39s_pdbDirFtp, 2.19.18
reversing order, 2.28.62.2s_pdbDirWeb, 2.19.19
rgb, 5.7.17s_printCommand, 2.19.21
     matrix, 2.28.29s_projectDir, 2.19.20
ribbon, 5.7.18s_prositeDat, 2.19.22
     bullets, 2.21.5.6s_psViewer, 2.19.23
     diagram, 2.21.5.39, 2.21.5.40s_reslib, 2.19.24
ribbonColorStyle, 2.20.20s_skipMessages, 2.19.25
ribbonStyle, 2.20.21s_sysCp, 2.19.26
right join, 2.27.49s_sysLs, 2.19.27
rigid chemical superposition, 2.27.93s_sysMv, 2.19.28
ring, 2.28.123s_sysRm, 2.19.29
     sampling, 3.16s_tempDir, 2.19.30
     templates, 2.27.85.8s_translateString, 2.19.31
rocking, 2.27.23.5s_userDir, 2.19.32
root mean square deviation, 2.28.129.3s_usrlib, 2.19.33
roots, 2.28.140, 2.28.141s_webEntrezLink, 2.19.34
rotate, 2.27.83s_webViewer, 2.19.35
     grob, 2.27.83.2s_xpdbDir, 2.19.36
     object, 2.27.83.1sa23, 3.3
     view, 2.27.83.3sampling grid, 2.28.184.2
rotation, 2.27.23.5sarray, 2.27.22.6, 5.8.1
     angle, 2.28.17     transformation in place, 2.27.98.1
rounding, 2.28.115save print, 3.2.6
     a real, 2.28.149     sdf file, 2.27.106.11
     output, 2.27.86.45saving graphics to album, 2.27.61.20
rsWeight, 2.17.33     image, 2.27.106.35
rs_, 2.8.7scaffolds, 2.27.51
run script, 2.27.8scoring, 3.13.1.4
running a docking job, 3.13.2.5screen X, 2.28.182
     dock job, 3.13.2.4     coordinates, 2.28.182
     script from html, 5.8.2script, 2.28.92.4, 5.8.2
s-s bond, 5.4.5     file name, 2.28.51
s_alignment_rainbow, 2.19.1     inside ICM, 5.8.2
s_blastdbDir, 2.19.2     name, 5.8.2
s_editor, 2.19.3     image generation, 2.27.23.3
s_entryDelimiter, 2.19.4scripting molecular movements, 3.2.4
s_errorFormat, 2.19.5sdf, 2.21.14.5, 2.27.106.23, 5.6.11
s_fieldDelimiter, 2.19.6     file, 2.27.80.47, 2.27.80.48, 2.27.85.44, 2.27.106.11, 2.28.149.3, 5.7.3
s_helpEngine, 2.19.7     to chem-table, 2.28.102
s_icmPrompt, 2.19.10search for chemical pattern, 2.28.52.3
s_icmhome, 2.19.8, 3.1.2.1     pdb headers, 3.4.5
s_imageViewer, 2.19.11     prosite, 3.4.1
searchObjSegment, 2.29.72     variable, 2.22.11
searchPatternDb, 2.29.70     atoms, 2.8.8
searchPatternPdb, 2.29.71     functions, 2.8.10
searchSeqDb, 2.29.73     molecules, 2.8.6
searchSeqFullPdb, 2.29.75     objects, 2.8.5
searchSeqPdb, 2.29.74     output, 2.22.14
searchSeqProsite, 2.29.76     residues, 2.8.7
searchSeqSwiss, 2.29.77     torsions, 2.8.9
searches and alignments, 3.4     variables, 2.8.9
second moments, 2.28.156selections, 2.27.85.32
secondary structure derivation from 3D, 2.27.5.1     in molecular objects, 2.8
          schematic, 2.21.5.39selftether, 2.21.14.10, 5.9.4
segMinLength, 2.16.19seq_ali_project, 2.28.149.6
segment, 5.8.4sequence, 2.28.165, 2.28.166, 5.8.3
select, 2.27.84     alignment, 2.28.5.1, 2.29.2
     atoms by number of bonded atoms, 2.28.130.3          intro, 1.4.3.3
          of the fixed torsions, 2.28.130.2     analysis intro, 1.4.3
     based on alignment, 2.28.130.14     assembly, 2.27.42.2
          bfactor, 2.28.130.7     belongs to alignment, 2.28.65
          center of mass, 2.28.130.15     conservation, 2.28.129.6
          coordinates, 2.28.130.7     distance, 2.28.130
          iarray, 2.28.130          matrix from alignment, 2.28.84.8
          length, 2.28.130.13     dotplot, 1.4.3.2
          occupancy, 2.28.130.7     from pdb, 2.27.61.34
          user field, 2.28.130.7     identity, 2.29.8
     chemical, 2.27.84.1     intro, 1.4.3
     lines, 2.27.80.1     modification, 2.28.172
     tether partners, 2.28.130.12     neighbor, 2.28.92.3
     vw partners, 2.28.130.12     parray, 5.7.3.2
selectMinGrad, 2.17.34     pattern, 5.7.4
selectSphereRadius, 2.17.35     position correspondence, 2.28.153.3
selected stack conformations, 2.27.22.16     positional weights, 2.27.85.1
selecting by b-factor, 2.28.130     redundancy removal, 2.27.42.2
               y z, 2.28.130     search, 2.27.34.2
     columns, 5.9.1     selection, 2.27.22.22
     from clusters, 3.14.6.4     structure alignment, 2.29.1
     neighboring elements, 2.28.94     to alignment transfer, 2.28.115.3
     residues, 3.3.6     type, 5.8.3
     saving, 2.28.62.4sequence-alignment mapping, 2.28.149.5, 2.28.149.6
selection, 2.8, 2.28.130, 2.28.130.6sequence-structure alignment, 2.28.5.1
     elements, 2.8.4     output format, 2.16.20, 2.16.21
     examples, 2.8.3sequenceBlock, 2.16.20
     functions, 2.8.10sequenceColorScheme, 2.20.22
     gap patching, 2.28.130, 2.28.130.11sequenceLine, 2.16.21
     level, 2.8, 2.28.174sequences, 3.4
     levels, 2.8.2     not in alignments, 2.27.22.22
     simplification, 2.28.130.11set, 2.27.85
     transfer, 2.28.130, 2.28.149.8     alternative atom, 2.27.85.17
     type, 2.8     area, 2.27.85.1
     types, 2.8.1     atom, 2.27.85.3
     background image, 2.27.85.4     object, 2.27.85.45
     bfactor, 2.27.85.5     occupancy, 2.27.85.46
     biological symmetry, 2.27.85.60     plane, 2.27.85.47
     bond topology, 2.27.85.7     pmf, 2.27.85.48
          type, 2.27.85.6     property, 2.27.85.49, 2.27.85.51
          and formal charges, 2.27.85.7          chemical view, 2.27.85.51
     cartesian, 2.27.85.8          column, 2.27.85.50
     chain, 2.27.85.9     radii graphical, 2.27.85.82
     charge, 2.27.85.10     randomSeed, 2.27.85.52
          formal, 2.27.85.11     randomize, 2.27.85.52
               auto, 2.27.85.12     resolution, 2.27.85.53
               pKa model, 2.27.85.12     selftether, 2.27.85.64
          mmff, 2.27.85.13     site, 2.27.85.25
     chargemmff, 2.27.85.13          residue, 2.27.85.27
     chiral, 2.27.85.14     slide, 2.27.85.28
     color, 2.27.85.15     sstructure backbone, 2.27.85.55
     comment, 2.27.85.16, 2.27.85.17          sequence, 2.27.85.56
          sequence, 2.27.85.18          to sequence, 2.27.85.56
     comp_matrix, 2.27.85.19     stack, 2.27.85.57
     current map, 2.27.85.42          energy, 2.27.85.57, 2.27.90.1
          object, 2.27.85.45     stereo, 2.27.85.54
     directory, 2.27.85.20     swiss, 2.27.85.58
     drestraint, 2.27.85.21          name, 2.27.85.58
          type, 2.27.85.22     symmetry, 2.27.85.61
     electrostatic radii, 2.27.85.75          bio, 2.27.85.60
     error, 2.27.85.31          crystal, 2.27.85.59
     field, 2.27.85.32          group, 2.27.85.59
          map, 2.27.85.33          to a torsion, 2.27.85.61
          name, 2.27.85.34     table, 2.27.85.62
     font, 2.27.85.35     tautomer, 2.27.85.29
          grob, 2.27.85.36     terms, 2.27.85.63
     foreground, 2.27.85.37     tether, 2.27.85.65
     format, 2.27.85.38          append, 2.27.85.66
     grob, 2.27.85.39     texture, 2.27.85.30
          coordinates, 2.27.85.39     type, 2.27.85.67
          label, 2.27.85.39          mmff, 2.27.85.73
     group, 2.27.85.59          molecule, 2.27.85.71
          column, 2.27.85.23          object, 2.27.85.70
     hydrogen, 2.27.85.24          property, 2.27.85.69
     key, 2.27.85.40          sequence, 2.27.85.72
     label, 2.27.85.41          surface, 2.27.85.68
          3d label, 2.27.85.41.4     variable grid, 2.27.85.80
          chemical, 2.27.85.41.3     variablegrid, 2.27.85.80
          distance, 2.27.85.41.1     view, 2.27.85.76
          table, 2.27.85.41.2     vrestraint, 2.27.85.77
     map, 2.27.85.42     vrestraintvs_var, 2.27.85.78
     molcart, 2.27.85.43          radii, 2.27.85.74
     molecular variables, 2.27.85.79     vwelradii, 2.27.85.75
     name, 2.27.85.44     vwradii, 2.27.85.74
          sequence, 2.27.85.44.1     window, 2.27.85.81
          radii, 2.27.85.82     molecule, 2.27.86.34
setResLabel, 2.29.79     molecules, 2.27.86.6
setcomp_matrix, 2.27.85.19     object, 2.27.86.35
seticmff, 2.29.78     pdb, 2.27.86.36
setting conf properties, 2.27.85.57     pharmacophore type, 2.27.86.53
setvs_var, 2.27.85.79     pmf, 2.27.86.37
sf-term, 2.27.85.68     preferences, 2.27.86.38
sfWeight, 2.17.36     profile, 2.27.86.39
sh24, 3.4     residue, 2.27.86.40
shadows, 2.21.5.31          type, 2.27.86.41
shell, 3.1, 5.8.5     residuetype, 2.27.86.41
     functions, 2.27.39     segment, 2.27.86.42
     intro, 1.7.1     selftether, 2.27.86.1
     progression, 2.27.74     sequence, 2.27.86.43
     warning message, 2.28.183     shell variable, 2.27.86.3
shineStyle, 2.20.23     site, 2.27.86.2
shininess, 2.17.37     stack, 2.27.86.44
show, 2.27.86, 2.27.86.39     svariable, 2.27.86.3
     alias, 2.27.86.7     table, 2.27.86.45
     aliases, 2.27.86.7          as database, 2.27.86.17
     alignment, 2.27.86.8     term, 2.27.86.46
     area, 2.27.86.9     tethers, 2.27.86.47
     atom, 2.27.86.10     version, 2.27.86.48
          type, 2.27.86.11     volume, 2.27.86.51
     atoms, 2.27.86.10          map, 2.27.86.52
     bond, 2.27.86.12     volumemap, 2.27.86.52
     clash, 2.27.86.13     vrestraint, 2.27.86.49
     color, 2.27.86.14          type, 2.27.86.50
     column, 2.27.86.15     vrestraints, 2.27.86.49
     comp_matrix, 2.27.86.16showcomp_matrix, 2.27.86.16
     database, 2.27.86.17showing weak hydrogen bonds, 2.21.5.22
     drestraint, 2.27.86.18side chain, 2.29.88
          type, 2.27.86.19          flexibility, 2.29.88
     energy, 2.27.86.20sigma level, 2.21.7.5
          atom, 2.27.86.21signal recognition measure, 2.29.21
     gradient, 2.27.86.22similar chains, 2.28.130.13
     hbond, 2.27.86.23similarity, 2.27.34.9, 2.27.34.10
          exact, 2.27.86.24simple expressions, 2.9.1.1
     hbondexact, 2.27.86.24     string substitution, 2.28.119.2
     html, 2.27.86.25simplified representation, 2.21.5.13
     iarray, 2.27.86.26     mesh structure, 2.27.15.1
     integer, 2.27.86.27simulation duration, 2.17.44
     key, 2.27.86.4     temperature, 2.17.43
     label, 2.27.86.28     intro, 1.4.2
     library, 2.27.86.29site, 2.27.11.2, 5.8.6
     link, 2.27.86.30     arrows, 2.27.85.25
     logical, 2.27.86.31     table, 5.8.6.1
     map, 2.27.86.5     by residue selection, 2.27.22.23
     mol, 2.27.86.32     sequences, 5.8.6.1
     mol2, 2.27.86.33sixthe power, 2.20.5
     intro, 1.4.1.2sprintf, 2.27.89
slide, 2.27.1.3, 2.28.137, 5.8.15sql, 2.27.77, 2.27.85.43, 2.28.46.1, 2.28.92.12, 2.28.95.5, 2.28.174.2
     transition time, 2.27.23.21sqlite, 3.5.1
slides, 2.28.182sqrt, 2.28.35
slideshow, 2.27.1.3, 2.27.23.21, 2.28.137square matrix to element pairs, 2.28.153.5
sln, 5.8.8ssThreshold, 2.17.38
smallest set of smallest rings, 2.28.123ssWeight, 2.17.39
smart, 2.21.14.5ssbond, 5.4.5
smarts, 2.28.65.2ssearch, 2.16.16, 2.27.91
smiles, 2.21.14.5, 2.24ssearchStep, 2.17.40
     to chem-table element, 2.28.102ssign sstructure segment, 2.27.5.2
smooth alignment, 2.28.139.4stack, 2.16.11, 2.16.12, 2.16.14, 2.20.6, 2.27.85.57, 2.27.90, 2.27.90.1, 2.28.62.6, 2.28.153.6, 5.3.12, 5.8.9
     interpolation, 2.27.90.3     bin size, 2.27.14
     map, 2.28.139.5     cleaning, 2.27.22.16
     rarray, 2.28.139.1     extension, 2.27.4.2
     surface, 2.29.86     multiplication, 2.27.4.2
soap, 2.25     merge, 3.7.7
soft trim, 2.28.171standard chemical form, 2.27.66.4
solid sphere, 2.21.5.8     deviation, 2.28.126
solubility, 2.28.107standardization, 2.27.22.11
solvation, 2.20.24, 2.21.14.2     chemical, 2.27.66
     energy, 2.17.36, 2.20.24startup, 3.1.2.3
solvent accessible area, 2.16.22static RMSD, 2.28.148
          surface, 2.21.5.52, 2.21.5.53, 2.27.86.9     and dynamic hbonds, 2.21.5.21
sort, 2.27.87, 2.27.87.3stereo, 2.21.5.49, 2.27.29, 2.27.85.54
     array, 2.27.87.1     reconstruction, 3.8.9
     arrays, 2.27.87.1stereo-specific hydrogens, 2.27.22.11
     molecules, 2.27.87.4stereoisomer, 2.27.29
     object, 2.27.87.3stereoisomers, 2.18.16
     stack, 2.27.87.5stick, 5.8.10
     table, 2.27.87.2store, 2.27.90
sortSeqByLength, 2.29.80     conf, 2.27.90, 2.27.90.1
space group, 2.27.65     frame, 2.27.90.3
     transformations, 2.28.169     image, 2.27.61.20
sparse atoms, 2.21.14.3     stack object, 2.27.90.2
spawn background job, 2.27.61.1     torsion type, 2.27.90
special values, 2.28.161strength of hydrogen bond, 2.27.23.14
specificity, 2.28.129.3string, 5.8.12
split, 2.27.88     array, 2.28.128, 5.8.1
     column values, 2.27.88.5     filtering, 2.28.171
     grob, 2.27.88.1     inversion, 2.28.149.1
     group, 2.27.88.2     label, 2.27.23.12
     object, 2.27.88.6     matching, 2.9, 2.28.83
          to molecules, 2.27.88.6     variables, 2.19
     sequence, 2.27.88.4strings, 2.19
     table, 2.27.88.3strip, 2.27.92
          cell, 2.27.88.5struct, 2.28.92.2
          to columns, 2.27.88.3structural alignment, 2.27.3.4, 2.28.5.2
     tree, 2.27.88.7          optimization, 2.27.34.1
splitting selection, 2.8.11     superposition, 2.27.3.4
     comparison, 2.28.23.2     actions, 5.9.2.4
     factors, 3.11.1     column, 2.28.92
     structure, 3.11.1          format, 2.27.85.38
sub-alignment to selection, 2.28.121          plot, 2.27.61.31
sub-matrix, 2.28.84.2          transformations, 2.28.97
subalignment, 2.28.5.3, 5.1.1     creation, 2.27.42.3
submap, 2.28.80     display style, 5.9.1
subroutine, 2.27.60     expression, 5.9.2
subset, 2.6     from matrix, 2.28.153.4
substring, 2.28.83, 2.28.149, 2.28.149.1     grid view, 5.9.1
substructure, 2.27.34.9, 2.27.34.10     of atoms and distances, 2.28.153.9
     search, 2.27.34.4     operations, 5.9.2.1
superimpose, 2.21.14, 2.27.93     plot, 5.9.2.3
     faq, 3.3.1     principal component analysis, 2.27.61.28
     how to, 3.3.1     print, 2.27.86.45
     minimize, 2.27.94     row, 2.27.68.4
support, 1.3          label mark, 2.27.85.41.2
suppressing view changes, 2.27.23.21          mark, 2.28.74
surface, 5.8.16     selected row numbers, 2.28.65
     accessibility, 2.27.86.9     subset, 5.9.2.2
     area, 2.29.3, 5.8.16     show html, 2.27.104.1
     charge, 5.7.13targa, 5.9.3
     color, 2.27.85.15target coordinates, 5.9.4
     dot density, 2.21.5.52tautomer, 2.27.30
     energy, 2.20.24, 2.27.85.68tempCycle, 2.17.43
     mesh, 2.28.184.2tempLocal, 2.17.42
     point selection, 2.28.184temperature, 2.17.43
     term, 2.17.36     variations in optimizer, 2.17.43
surfaceAccuracy, 2.16.22template docking, 3.13.2.6
surfaceMethod, 2.20.24tensor product of two vectors, 2.28.84
surfaceTension, 2.17.41terminal font, 2.30.14
svariable, 5.8.13     window, 2.27.43
swapping protein fragments, 3.8.7terms, 2.15
swiss, 2.27.85.58     hydrogen bonding, 2.17.18
swissFields, 2.22.9test, 2.27.96
swissprot, 2.27.85.25     binary, 2.27.96.1
symmetrization of a matrix, 2.28.84.3testing if argument exists, 2.28.55
symmetry, 2.28.169tether, 2.21.14.10, 2.27.106.9, 5.9.4, 5.9.5
     faq, 3.10text, 2.28.83
     group, 2.16.2     search in tables, 2.28.52.2
     problem, 2.27.65     to script, 5.8.2
syntax highlighting, 5.8.2texture, 5.5.3
sys, 2.27.95tga, 5.9.3
system, 5.10.2then, 2.27.97
     command, 2.27.95thread to template, 2.27.62.4
     copy, 2.19.26threading, 2.28.5.1
     file move, 2.19.28     letter code, 2.28.165, 2.28.166
     list file, 2.19.27thumbnails, 2.28.64
     remove, 2.19.29tif, 5.9.6
table, 2.27.22.4, 2.27.85.49, 2.27.85.50, 2.27.85.51, 5.9.1time, 2.28.36, 2.28.149.2
tolFunc, 2.17.46     atomic order, 2.27.61.37
tolGrad, 2.17.45     column values, 2.27.42.4
topological psa, 5.7.12     names, 2.28.92
torsion rmsd comparison, 2.27.14.2     new object name, 2.28.92
torsions, 2.28.95.3     smiles, 2.27.61.37
tpsa, 5.7.12unix, 2.27.95, 5.10.2
trajectory, 2.27.59.2, 2.27.90, 2.27.90.3, 5.6.14     grep, 2.27.80.1
     file, 2.30.17unlink alignments, 2.27.22.20
     frame writing, 2.27.23.17     sequences, 2.27.22.20
     smoothing, 2.27.23.17     variables, 2.27.22.20
transform, 2.27.98, 2.27.98.2update database, 2.27.66.5
     general, 2.27.98     speadsheet, 2.27.1.1.1
     grob coordinates, 2.27.98.2updates, 1.1
     molecules, 2.27.98.2updating atom pairs, 2.18.27
     sarray, 2.27.98.1upper case, 2.28.164
transformation, 2.28.115, 5.9.7url string parsing, 2.28.153
     vector, 5.9.7user atom display, 2.21.5.2
     and symmetry, 3.10     environment, 3.1.2.2
transforming points, 2.28.184.4     menu, 2.21.10.1
translate, 2.27.99user-defined properties, 2.27.85.32
transparency, 2.27.85.39, 5.5.3     solvation parameters, 2.28.7
     background, 2.27.106.35user_startup, 3.1.2.4
     grob, 2.27.23.11     icm, 3.1.2
     grobs, 2.21.5.54     guide, 3
tree, 2.27.61.35, 2.28.92.5v_, 2.8.1
     cluster, 2.11van der Waals surface, 2.21.5.53
     delete, 2.27.22.34varLabelStyle, 2.20.26
     label format, 2.28.92.5variable restraint, 2.27.85.77
     representatives, 2.11.1     selection, 2.8.9
trim string array, 2.27.98.1vector, 2.28.95.6
trimming grid map values, 2.28.171     dot product, 2.28.179.1
true positives, 2.28.129.3     length, 2.28.96
truncate alignment, 2.27.61.33     product, 2.28.179.1
     values, 2.28.171     transformation, 2.28.97
tsShapeData, 2.21.14.10vertex, 2.27.13.4.2
     table format, 2.27.80.43     connectivity, 2.28.84.12
two alignments, 2.28.41.11vertexes, 2.27.13.4.2
     dimensional plot, 2.28.139.2vertical alignment block, 2.27.61.33
txdoc browser, 2.27.80.3     workspace, 2.21.8.5
type, 2.28.174.1vertices, 2.27.13.4.2
tzMethod, 2.20.25vicinity, 2.17.48
tzWeight, 2.17.47video, 2.27.106.30
uncharge functional groups, 2.27.66.2view point, 2.28.182
unclip, 2.27.23.2     restoration, 2.28.68
underline, 2.27.85.35.1     transition, 2.27.85.76
undisplay, 2.27.100views, 5.8.15
     graphics, 2.27.101virtual, 5.10.3
     window, 2.27.101     arrays, 2.27.1.1.1
unfix, 2.27.102     chemistry, 2.27.66, 2.28.95.4
unique, 2.27.13.1, 5.10.1     field, 2.27.7.2
               intro, 1.4.2.7     array, 2.27.106.8
visitsAction, 2.20.27          table, 2.27.106.8
vls, 3.13, 3.13.1, 3.13.2, 3.13.3     binary, 2.27.106.2
     cluster, 3.13.3.6     blast, 2.27.106.24
     faq, 3.13.3     column, 2.27.106.12
     intro, 1.4.2.7     database, 2.27.106.13
     job queueing, 3.13.3.6     drestraint, 2.27.106.14
     overview, 3.13.1          type, 2.27.106.15
     parallelization, 3.13.3.5     factor, 2.27.106.16
     results, 3.13.3.8     gamess, 2.27.106.17
     scores storage, 3.13.3.7     grob, 2.27.106.18
     threshold, 3.13.3.2     html, 2.27.106.19
vls_intro, 3.13.3.1     iarray, 2.27.106.3
volume, 5.10.4     image, 2.27.106.20
vrestraint, 5.10.5          chemical, 2.27.106.22
     file, 2.30.23          parray, 2.27.106.21
     type, 5.10.6     index, 2.27.106.23
          file, 2.30.22          blast, 2.27.106.24
vs_, 2.8.9     library, 2.27.106.25
vs_out, 2.22.14     map, 2.27.106.26
vwCutoff, 2.17.49     matrix, 2.27.106.6
vwExpand, 2.17.50     model, 2.27.106.27
vwExpandDisplay, 2.17.51     mol, 2.27.106.28
vwMethod, 2.20.28     mol2, 2.27.106.29
vwSoftMaxEnergy, 2.17.52     molcart, 2.27.106.7
wait, 2.27.103     movie, 2.27.106.30
warning, 2.21.14.3     object, 2.27.106.31
     message, 2.28.183          parray, 2.27.106.33
     suppression, 2.18.28          simple, 2.27.106.32
water.dielectric constant, 2.17.12     pdb, 2.21.14.12, 2.27.106.34
waterRadius, 2.17.53     png, 2.27.106.35
wavefront format, 2.27.61.11     postscript, 2.27.106.36
web, 2.27.104     pov, 2.27.106.37
     table, 2.27.104.1     povray, 2.27.106.37
webEntrezOption, 2.20.29     project, 2.27.106.2
weighted rmsd, 2.21.14     rarray, 2.27.106.4
while, 2.27.105     sarray, 2.27.106.5
whole string, 2.28.119.1     sequence, 2.27.106.38
window averaging, 2.28.139.1     session, 2.27.106.39
     layout, 2.28.149.9     several array, 2.27.106.8
     width and height, 2.28.182     simple object, 2.27.106.32
windowSize, 2.16.23     stack, 2.27.106.40
     movie, 2.27.106.30     table, 2.27.106.10
wire, 5.10.7          mol, 2.27.106.11
wireBondSeparation, 2.17.54          with links, 2.27.106.19
wireStyle, 2.20.30     tether, 2.27.106.9
workspace, 2.27.101     tethers, 2.27.106.9
write, 2.27.106     trajectory, 2.27.23.17
     album, 2.27.106.21     vs_var, 2.27.106.41
     alignment, 2.27.106.1writevs_var, 2.27.106.41
xml, 2.27.80.54, 2.28.83, 5.1.6 
     drugbank example, 2.10 
xpdb, 2.27.80.2 
xplor format, 2.27.80.26 
xrMethod, 2.20.31 
xrWeight, 2.17.55 
xray density to rectangular energy map, 2.27.61.30 
xstick, 5.10.8 
     radii, 2.27.85.2 
xyz morphing, 3.8.8 
zega, 5.10.9 
     intro, 1.4.3.6 
|, 2.12.3 

Copyright© 1989-2012, Molsoft,LLC - All Rights Reserved. Copyright© 1989-2013, Molsoft,LLC - All Rights Reserved. This document contains proprietary and confidential information of Molsoft, LLC. The content of this document may not be disclosed to third parties, copied or duplicated in any form, in whole or in part, without the prior written permission from Molsoft, LLC.