ICM Manual v.3.6
by Ruben Abagyan Copyright © 2008, Molsoft LLC Sep 1 2010
|
Index
| &, 2.11.3 | Cell, 2.28.24 |
| 2D labels, 2.27.53.1 | Charge, 2.28.25 |
| to 3D, 3.13.2.3 | Chemical, 2.28.26 |
| chemical builder, 1.4.2.8 | Cluster, 2.28.27 |
| font size, 2.27.23.12 | Collada, 5.5.3 |
| label, 2.27.23.12, 2.27.81.32 | Collection, 2.28.27.1 |
| labels, 2.27.53.1 | Color, 2.28.28 |
| mol file, 2.29.83 | from gradient, 2.28.28.1 |
| plots intro, 1.4.3.7 | image, 2.28.28.2 |
| smoothing, 2.28.134.2 | Connolly surface, 5.9.7 |
| superposition, 2.29.22 | Consensus, 2.28.29 |
| transformations, 2.27.94.2 | Corr, 2.28.30 |
| 3dxml, 5.5.3 | Cos, 2.28.31 |
| =, 2.11.1 | Cosh, 2.28.32 |
| A, 5.1 | Count, 2.28.33 |
| Abs, 2.28.1 | CubicRoot, 2.28.34 |
| Acc, 2.28.2 | D, 5.4 |
| Acos, 2.28.3 | DAE, 5.5.3 |
| Acosh, 2.28.4 | DE, 2.27.34.2 |
| Adobe, 2.18.23 | DNA Representation, 1.4.1.3 |
| Align, 2.28.5 | alignment, 2.27.3.3 |
| sequence, 2.28.5.1 | melting temperature, 2.28.150 |
| Angle, 2.28.6 | views, 1.4.1.3 |
| Area, 2.28.7 | Date, 2.28.35 |
| residue contacts, 2.28.7.1 | Deletion, 2.28.36 |
| Asin, 2.28.8 | Disgeo, 2.28.37 |
| Asinh, 2.28.9 | Distance, 2.28.38 |
| Ask, 2.28.10 | 2 alignments, 2.28.38.11 |
| Askg, 2.28.11 | matrices, 2.28.38.7 |
| Atan, 2.28.12 | Dayhoff, 2.28.38.9 |
| Atan2, 2.28.13 | Tanimoto, 2.28.38.6 |
| Atanh, 2.28.14 | alignment, 2.28.38.10 |
| Atom, 2.28.15 | as_, 2.28.38.3 |
| Augment, 2.28.16 | rarray, 2.28.38.4 |
| Axis, 2.28.17 | atoms, 2.28.38.3 |
| B, 5.2 | chemical, 2.28.38.6, 2.28.38.13 |
| BPMC, 5.2.5 | dayhoff, 2.28.38.9 |
| Bfactor, 2.28.18 | iarray, 2.28.38.1 |
| Boltzmann, 2.28.19 | alignment, 2.28.38.10 |
| Box, 2.28.20 | matrix, 2.28.38.5, 2.28.38.7 |
| Bracket, 2.28.21 | multiple atomic, 2.28.38.4 |
| C, 5.3 | rarray, 2.28.38.2 |
| CCP4, 5.7.6 | tether, 2.28.38.8 |
| CONSENSUS, 2.21.1 | tree, 2.28.38.12 |
| CONSENSUSCOLOR, 2.21.2 | cluster, 2.28.38.12 |
| CONSENSUS_strength, 2.16.9 | H, 5.5 |
| Cad, 2.28.22, 2.28.22.1, 2.28.22.2 | EDS server, 2.29.42 |
| Cad1, 2.28.22.1 | EST-alignment, 2.27.3.3 |
| Cadalign, 2.28.22.2 | Eigen, 2.28.39 |
| Ceil, 2.28.23 | Energy, 2.28.40 |
| soap, 2.28.42 | hydrogenDisplay, 2.21.5.26 |
| Exist, 2.28.43 | light, 2.21.5.27 |
| molcart, 2.28.43.1 | lightPosition, 2.21.5.28 |
| Existenv, 2.28.44 | mapLineWidth, 2.21.5.29 |
| Exp, 2.28.46 | occupancyDisplay, 2.21.5.30 |
| Extension, 2.28.45 | occupancyRadiusRatio, 2.21.5.31 |
| FILTER, 2.21.3 | quality, 2.21.5.32, 2.28.80.1 |
| Z, 2.21.3.1 | rainbowBarStyle, 2.21.5.33 |
| gz, 2.21.3.2 | resLabelDrag, 2.21.5.34 |
| uue, 2.21.3.3 | resLabelShift, 2.21.5.35 |
| FTP, 2.21.4 | ribbonRatio, 2.21.5.36 |
| createFile, 2.21.4.1 | ribbonWidth, 2.21.5.37 |
| keepFile, 2.21.4.2 | ribbonWorm, 2.21.5.38 |
| proxy, 2.21.4.3 | rocking, 2.21.5.39 |
| Field, 2.28.47, 2.28.47.1 | rockingRange, 2.21.5.40 |
| user, 2.28.47.1 | rockingSpeed, 2.21.5.41 |
| File, 2.28.48 | selectionLevel, 2.21.5.42 |
| Find, 2.28.49 | selectionStyle, 2.21.5.43 |
| chemical, 2.28.49.3 | sketchAccents, 2.21.5.24 |
| pattern, 2.28.49.3 | stereoMode, 2.21.5.44 |
| in array, 2.28.49.1 | stickRadius, 2.21.5.25, 2.21.5.45 |
| table, 2.28.49.2 | surfaceDotDensity, 2.21.5.47 |
| FlexLM license info, 2.28.173 | surfaceDotSize, 2.21.5.46 |
| Floor, 2.28.50 | surfaceProbeRadius, 2.21.5.48 |
| Formula, 2.28.51 | transparency, 2.21.5.49 |
| GRAPHICS, 2.21.5 | wormRadius, 2.21.5.50 |
| atomLabelShift, 2.21.5.1 | GRID, 2.21.6 |
| atomValueCircles, 2.21.5.2 | gcghExteriorPenalty, 2.21.6.1 |
| ballRadius, 2.21.5.3, 2.21.5.25 | gpGaussianRadius, 2.21.6.6 |
| ballStickRatio, 2.21.5.4 | margin, 2.21.6.2 |
| chainBreakLabelDisplay, 2.21.5.7 | maxEl, 2.21.6.3 |
| chainBreakStyle, 2.21.5.6 | maxVw, 2.21.6.5 |
| clashWidth, 2.21.5.5 | minEl, 2.21.6.4 |
| displayLineLabels, 2.21.5.8 | GROB, 2.21.7 |
| displayMapBox, 2.21.5.9 | arrowRadius, 2.21.7.3 |
| dnaBallRadius, 2.21.5.10 | atomSphereRadius, 2.21.7.1 |
| dnaRibbonRatio, 2.21.5.11 | contourSigmaIncrement, 2.21.7.5 |
| dnaRibbonWidth, 2.21.5.12 | relArrowHead, 2.21.7.4 |
| dnaRibbonWorm, 2.21.5.13 | relArrowSize, 2.21.7.2 |
| dnaStickRadius, 2.21.5.14 | GUI, 2.21.8 |
| formalChargeDisplay, 2.21.5.15 | dialog customize programming, 2.26 |
| grobLineWidth, 2.21.5.16 | plot, 2.27.59.31 |
| hbondAngleSharpness, 2.21.5.20 | tableRowMarkColors, 2.21.8.4 |
| hbondBallPeriod, 2.21.5.21 | windowLayout, 2.21.8.5 |
| hbondBallStyle, 2.21.5.22 | workspaceFolderStyle, 2.21.8.8 |
| hbondMinStrength, 2.21.5.19 | workspaceStyle, 2.21.8.6 |
| hbondRebuild, 2.21.5.18 | workspaceTabStyle, 2.21.8.7 |
| hbondStyle, 2.21.5.17 | Getarg, 2.28.52 |
| hbondWidth, 2.21.5.23 | Getenv, 2.28.53 |
| hetatmZoom, 2.21.5.25 | Gradient, 2.28.54 |
| Grob, 2.28.55 | Index, 2.28.62 |
| Group, 2.28.56 | chemical, 2.28.62.1 |
| HTTP.proxy, 2.21.4.4 | element in array, 2.28.62.7 |
| Hartree-Fock, 2.27.76.20, 2.27.102.17 | regexp, 2.28.62.3 |
| Header, 2.28.57 | string, 2.28.62.2 |
| Histogram, 2.28.58 | table label, 2.28.62.5 |
| N, 5.7 | selection, 2.28.62.4 |
| ICM desktop, 2.21.8.5 | tree, 2.28.62.8 |
| documents, 2.27.76.3 | unique elements, 2.28.62.6 |
| modules, 1.4.4 | Indexx, 2.28.63 |
| object, 2.29.13 | Info, 2.28.65 |
| residue library, 2.18.24 | image, 2.28.66 |
| ICM-shell, 3.1, 5.9.5 | Insertion, 2.28.64 |
| intro, 1.7.1 | Integer, 2.28.67 |
| script, 2.27.8 | Integral, 2.28.68 |
| ICMHOME, 3.1.2.1 | Interrupt, 2.28.69 |
| shell variable, 3.1.2.1 | Introduction, 1 |
| IMAGE, 2.21.9 | LIBRARY, 2.21.10 |
| bondLength2D, 2.21.9.15 | men, 2.21.10.1 |
| color, 2.21.9.8 | res, 2.21.10.2 |
| compress, 2.21.9.9 | Label, 2.28.70 |
| gammaCorrection, 2.21.9.7 | Latent, 2.28.172.3 |
| generateAlpha, 2.21.9.10 | LatentVector, 2.28.172.3 |
| lineWidth, 2.21.9.3 | Length, 2.28.71 |
| lineWidth2D, 2.21.9.14 | LinearFit, 2.28.72 |
| orientation, 2.21.9.16 | LinearModel, 2.28.73 |
| paperSize, 2.21.9.17 | Log, 2.28.74 |
| previewResolution, 2.21.9.13 | LogP, 2.28.102 |
| previewer, 2.21.9.12 | LogS, 2.28.102 |
| printerDPI, 2.21.9.2 | M_out, 2.22.5 |
| quality, 2.21.9.1 | Map, 2.28.75 |
| rgb2bw, 2.21.9.18 | Markush structures, 2.27.50 |
| scale, 2.21.9.4 | Mass, 2.28.76 |
| stereoAngle, 2.21.9.6 | Match, 2.28.78 |
| stereoBase, 2.21.9.5 | Mathews, 2.28.124.2 |
| stereoText, 2.21.9.11 | Matrix, 2.28.79 |
| writeScale, 2.21.9.19 | alignment, 2.28.79.8 |
| I_out, 2.22.4 | boundary, 2.28.79.9 |
| Iarray, 2.28.59, 2.28.59.4, 2.28.59.5 | grob connectivity, 2.28.79.12 |
| atom numbers, 2.28.59.4 | histogram, 2.28.79.11 |
| bits to integers, 2.28.59.3 | new, 2.28.79.1 |
| inverse, 2.28.59.2 | residue areas, 2.28.79.7 |
| residue numbers, 2.28.59.5 | comparison, 2.28.79.4 |
| reverse, 2.28.59.2 | stack, 2.28.79.10 |
| stack, 2.28.59.6 | sub, 2.28.79.2 |
| Icm Options, 2.1 | symmetrical, 2.28.79.3 |
| IcmSequence, 2.28.60 | table, 2.28.79.5 |
| Image, 2.28.61 | tensor, 2.28.79.6 |
| collection, 3.9.2.1 | Max, 2.28.80 |
| frame by frame, 3.9.2.2 | image graphic, 2.28.80.1 |
| Mean, 2.28.82 | lineWidth, 2.21.12.3 |
| Method, 2.19.12 | logo, 2.21.12.6 |
| Min, 2.28.83 | markSize, 2.21.12.4 |
| Mod, 2.28.85 | numberOffset, 2.21.12.1 |
| Mol, 2.28.86 | orientation, 2.21.12.8 |
| MolPSA, 5.8.12 | rainbowStyle, 2.21.12.12 |
| Moment, 2.28.77 | seriesLabels, 2.21.12.9 |
| of Inertia, 2.28.77 | PLS, 2.28.90.6 |
| Money, 2.28.84 | error, 2.28.124.2 |
| NOE averaging, 2.19.5 | models, 2.28.124.2 |
| Name, 2.28.87 | Parray, 2.28.97 |
| chemical, 2.28.87.6 | Parray-object, 2.28.97 |
| property, 2.28.87.1 | Path, 2.28.96 |
| close sequence, 2.28.87.3 | Pattern, 2.28.98 |
| image, 2.28.87.9 | Pi, 2.28.99 |
| molcart, 2.28.87.10 | Polar Surface Area, 5.8.12 |
| object parray, 2.28.87.8 | Potential, 2.28.100 |
| sequence, 2.28.87.7 | Power, 2.28.101 |
| soap, 2.28.87.2 | Predict, 2.28.102 |
| string, 2.28.87.4 | Probability, 2.28.103 |
| tree, 2.28.87.5 | Profile, 2.28.104 |
| Namex, 2.28.88 | Property, 2.28.105 |
| image, 2.28.88.2 | Putarg, 2.28.106 |
| sequence, 2.28.88.1 | Putenv, 2.28.107 |
| Newick tree format, 2.28.142.3 | R-groups, 2.27.50 |
| Next, 2.28.89, 2.28.89.1 | REBEL, 3.7.2 |
| covalent neighbors, 2.28.89.1 | faq, 3.7.2 |
| Nof, 2.28.90 | file, 2.27.50 |
| chemical, 2.28.90.2 | R_2out, 2.22.7 |
| distance, 2.28.90.3 | R_out, 2.22.6 |
| latent, 2.28.90.6 | Radius, 2.28.108 |
| library, 2.28.90.4 | Random, 2.28.109 |
| molcart, 2.28.90.5 | string, 2.28.109.1 |
| soap, 2.28.90.7 | Rarray, 2.28.110 |
| tree, 2.28.90.1 | reverse, 2.28.110.2 |
| Norm, 2.28.91 | sequence projection, 2.28.110.1 |
| Normalize, 2.28.92 | alignment projection, 2.28.110.3 |
| NotInList, 2.28.93 | strength, 2.28.110.5 |
| R, 5.8 | property assignment, 2.28.110.4 |
| OBJECT, 2.21.11 | RarrayAlignment, 2.28.110.5 |
| Obj, 2.28.94 | Rarrayinverse, 2.28.110.2 |
| Occupancy, 2.28.95 | Real, 2.28.111 |
| PBS, 3.13.3.6 | array, 2.28.110 |
| PLOT, 2.21.12 | Reference, 2.28.113 |
| Yratio, 2.21.12.5 | Guide, 2 |
| box, 2.21.12.13 | Remainder, 2.28.112 |
| color, 2.21.12.7 | Replace, 2.28.114 |
| font, 2.21.12.10 | chemical, 2.28.114.4 |
| fontSize, 2.21.12.2 | exact, 2.28.114.1 |
| labelFont, 2.21.12.11 | regexp, 2.28.114.3 |
| Res, 2.28.115, 2.28.116 | array, 2.28.126.2 |
| Resali, 2.28.116 | Sequence(dna reverse), 2.28.126.1 |
| Resolution, 2.28.117 | Shuffle, 2.28.127 |
| Rfactor, 2.28.119 | Sign, 2.28.128 |
| Rfree, 2.28.120 | Simulations, 1.4.2 |
| Ring, 2.28.118 | Sin, 2.28.129 |
| Rmsd, 2.28.121 | Sinh, 2.28.130 |
| of subset, 2.21.14 | Site, 2.28.131 |
| Rot, 2.28.122 | Slide, 2.28.132 |
| S, 5.9 | Smiles, 2.28.133 |
| SAR analysis, 2.27.59.27, 2.27.84.2 | Smooth, 2.15.23, 2.28.134, 2.28.134.1, 2.28.134.2 |
| SC, 2.27.34.2 | Smoothrs, 2.28.134.2 |
| SITE, 2.21.13 | SoapMessage, 2.28.138 |
| defSelect, 2.21.13.2 | Sort, 2.28.139 |
| labelOffset, 2.21.13.3 | Sphere, 2.21.14.2, 2.28.137 |
| labelStyle, 2.21.13.4 | Split, 2.28.140 |
| labelWrap, 2.21.13.5 | chemical, 2.28.140.4 |
| showSeqSkip, 2.21.13.6 | multisep, 2.28.140.3 |
| wrapComment, 2.21.13.7 | regexp, 2.28.140.2 |
| SLN notation, 2.28.142.9 | tree, 2.28.140.1 |
| SMARTS, 2.24, 2.27.10, 2.28.90.2 | Sql, 2.28.135 |
| SOAP, 2.28.87.2, 2.28.90.7, 2.28.167.1 | Sqrt, 2.28.136 |
| request message, 2.28.138 | Srmsd, 2.28.141 |
| SSSR, 2.28.118 | Sstructure, 2.28.143 |
| S_out, 2.22.8 | String, 2.28.142, 2.28.142.7 |
| Sarray, 2.28.123 | alternative, 2.28.142.6 |
| index, 2.28.123.1 | mol, 2.28.142.2 |
| Score, 2.28.124 | selection, 2.28.142.7 |
| alignment, 2.28.124.6 | slide gui, 2.28.142.8 |
| conservation, 2.28.124.5 | substring, 2.28.142.1 |
| model, 2.28.124.2 | chemical formula, 2.28.142.9 |
| overlap, 2.28.124.1 | Sum, 2.28.144 |
| predictions, 2.28.124.3 | chemical, 2.28.144.1 |
| sequence, 2.28.124.4 | image, 2.28.144.2 |
| Select, 2.28.125 | Swissprot, 2.27.102.23 |
| break, 2.28.125.1 | Symgroup, 2.28.145 |
| atom property, 2.28.125.7 | T, 5.10 |
| nmembers, 2.28.125.4 | TOOLS, 2.21.14 |
| string, 2.28.125.9 | edsDir, 2.21.14.1 |
| expand, 2.28.125.6 | minSphereCubeSize, 2.21.14.2 |
| fix, 2.28.125.2 | pdbReadNmrModels, 2.21.14.3 |
| graphical, 2.28.125.5 | superimposeMaxDeviation, 2.21.14.6 |
| neighbors, 2.28.125.3 | superimposeMaxIterations, 2.21.14.4 |
| Select_by atom numbers, 2.28.125.10 | superimposeMinAtomFraction, 2.21.14.5 |
| Select_by_sequence, 2.28.125.13 | tsWeight, 2.21.14.7 |
| Select_by_text, 2.28.125.9 | Table, 2.28.146 |
| Select_lists, 2.28.125.12 | alignment numbers, 2.28.146.3 |
| Select_patching, 2.28.125.11 | distance, 2.28.146.9 |
| Select_projection, 2.28.125.8 | matrix, 2.28.146.4 |
| Sequence, 2.28.126 | model, 2.28.146.7 |
| stack, 2.28.146.6 | axes, 2.28.177.7 |
| url_decoder, 2.28.146.1 | chemical match, 2.28.177.5 |
| Table(alignment), 2.28.146.2 | fract, 2.28.177.3 |
| Table(stack), 2.28.146.6 | mesh, 2.28.177.2 |
| Tan, 2.28.147 | points, 2.28.177.1 |
| Tanh, 2.28.148 | transformed xyz, 2.28.177.4 |
| Tanimoto, 2.28.59.3 | vector2matrix, 2.28.177.6 |
| distance, 2.27.59.35 | ZEGA, 5.11.9 |
| matrix, 2.28.38.6 | intro, 1.4.3.6 |
| Temperature, 2.28.150 | _NAME, 2.27.81.40 |
| Tensor, 2.28.149 | _chemBatch, 3.1.2.5 |
| Time, 2.28.151 | _confGen, 3.13.2.3 |
| Tointeger, 2.28.152 | _dockScan, 3.13.2.7 |
| Tolower, 2.28.153 | _macro, 2.30.1 |
| Toreal, 2.28.154 | file, 2.30.1 |
| Torsion, 2.28.155 | _startup, 3.1.2.3 |
| Tostring, 2.28.156 | file, 2.30.2 |
| Toupper, 2.28.157 | icm, 2.30.2 |
| Tr123, 2.28.158 | a_, 2.8.1 |
| Tr321, 2.28.159 | abbr, 1.6 |
| Trace, 2.28.160 | abbreviations, 1.6 |
| Trans, 2.28.161 | absolute to cell x y z, 2.28.177.3 |
| Transform, 2.28.162 | accFunction, 2.22.2 |
| Transpose, 2.28.163 | acceptor, 3.6.1 |
| Trim, 2.28.164 | access large sdf file, 2.27.76.23 |
| sequence, 2.28.165 | accessMethod, 2.19.1 |
| Turn, 2.28.166 | accessible residues, 3.3.6 |
| Type, 2.28.167 | surface, 2.27.59.14, 5.9.15 |
| molcart, 2.28.167.2 | accessing sections, 2.27.102.23 |
| soap, 2.28.167.1 | accuracy, 2.28.124.2 |
| Z, 5.11 | activate fog, 2.27.23.24 |
| Unique, 2.28.168 | alignment, 2.27.81.33 |
| Unix, 2.28.169 | document, 2.27.81.33 |
| Uppsala, 2.29.42 | tab, 2.27.81.33 |
| server, 2.29.43 | table, 5.10.2.4 |
| V_, 2.8.1 | add, 2.27.1 |
| Value, 2.28.170 | column, 2.27.1.1 |
| soap, 2.28.171 | function, 2.27.1.1.1 |
| Vector, 2.28.16, 2.28.172, 2.28.172.1, 2.28.172.3 | matrix, 2.27.1.2 |
| symmetry transformation, 2.28.172.2 | slide, 2.27.1.3 |
| Vectorproduct, 2.28.172.1 | table, 2.27.1.4 |
| Vectorsymmetrytransformation, 2.28.172.2 | row, 2.27.1.4 |
| Version, 2.28.173 | addBfactor, 2.16.1 |
| View, 2.28.175 | adding atoms to non-ICM objects, 2.27.7.1 |
| Volume, 2.28.174 | columns to table, 2.27.1.1 |
| WEBAUTOLINK, 2.21.16 | hydrogens, 2.29.13 |
| WEBLINK, 2.21.15 | in place, 2.11.4 |
| Warning, 2.28.176 | to slideshow, 2.27.1.3 |
| Wavefront format, 2.27.76.21 | admet selection, 3.13.3.4 |
| Xyz, 2.28.177 | advanced chemical search, 3.6 |
| ops, 2.11.6 | alternative flag, 2.27.81.15 |
| ali_seq_project, 2.28.142.4 | amber, 5.1.4 |
| alias, 2.27.2 | amino acid, 2.18.24, 2.28.158, 2.28.159 |
| align, 2.27.3 | labels, 2.27.3.1 |
| 3D, 2.27.3.4 | and, 2.11.3 |
| faq, 3.3.2 | angles, 2.28.90.3 |
| heavy, 2.27.3.5 | angular hbond dependence, 2.21.5.20 |
| how to, 3.3.2 | animated story, 5.9.14 |
| chemical, 2.27.80.1 | animation, 2.27.23.5, 2.27.23.6, 3.9 |
| fragments, 2.27.3.3 | annotation, 2.27.81.23 |
| intro, 1.4.3.3 | append, 5.1.5 |
| number, 2.27.3.1 | a tables, 2.27.1.4 |
| res numbers, 2.27.3.1 | column, 2.27.4.3 |
| sequence, 2.27.3.2 | command, 2.27.4 |
| sequences, 2.27.3.2 | sequence, 2.27.4.1 |
| alignMethod, 2.19.2 | to group, 2.27.4.1 |
| alignMinCoverage, 2.16.2 | stack, 2.27.4.2 |
| alignMinMethod, 2.16.2 | tables, 2.27.48 |
| alignOldStatWeight, 2.16.3 | by shared column, 2.27.4.3 |
| alignSS, 2.29.1 | appending, 2.27.1.1 |
| alignTwoSequences, 2.29.2 | an element, 2.11.4 |
| aligned residues, 2.28.116 | menu items, 2.21.10.1 |
| alignment, 5.1.1 | representations to a slide, 2.27.23.21 |
| as table, 2.28.146.2 | rows to matrix, 2.27.1.2 |
| block length, 2.15.21 | area under curve, 2.29.21 |
| secondary structure, 2.29.1 | arguments, 2.27.58 |
| cleaning, 2.28.134.3 | arithmetic operations, 2.11.2 |
| color by property, 2.27.81.29 | arithmetics, 2.11 |
| coloring, 2.18.1 | array, 2.27.65.4, 5.8.3.1 |
| distance, 2.28.125.13 | assignment, 2.11.1 |
| editor, 2.4 | derivative, 2.28.134.1 |
| extraction, 2.28.5 | overlap, 2.28.124.1 |
| gap format, 5.1.1.1 | parray, 2.27.22.29 |
| intro, 1.4.3.4 | size, 2.28.90 |
| projection, 2.28.142, 2.28.142.4, 2.28.142.5 | subset, 2.6 |
| score, 2.28.124.5 | arrow from selection, 2.29.36 |
| sequence reordering, 2.28.5 | length, 2.27.81.23 |
| strength, 2.28.110.5 | as2_out, 2.22.13 |
| structural, 2.27.3.4, 2.28.5 | as_, 2.8.8 |
| to sequence transfer, 2.28.110.1 | as_graph, 2.21.5.42, 2.21.5.43, 2.28.125.5 |
| text conversion, 2.28.142.3 | as_out, 2.22.12 |
| weighted, 2.28.5 | assign, 2.27.5 |
| gapExtension, 2.16.15 | ring conformation to template, 2.27.60.4 |
| gapOpen, 2.16.16 | sstructure, 2.27.5.1 |
| alignment_as_text, 2.28.142.3 | segment, 2.15.19, 2.27.5.2 |
| aliphatic amines, 2.27.63.2 | assignment, 2.11.1 |
| all, 5.1.2 | structure, 2.27.5.1 |
| torsions table, 3.3.11 | atom, 2.27.13.1, 5.1.6 |
| alpha, 2.21.5.49, 2.27.81.35, 5.1.3 | code file, 2.30.4 |
| channel, 2.21.9.10 | coordinates, 2.28.177.1 |
| name, 2.28.70 | box, 2.28.20 |
| pairs, 2.27.81.58, 2.28.146.9 | break, 2.27.6 |
| proximity to surface, 2.27.82.8 | brightness, 2.21.5.27 |
| selection by number, 2.28.59.4 | build, 2.27.7 |
| type, 2.28.167 | atom, 2.27.7.1 |
| user field, 2.28.47.1 | column, 2.27.7.2 |
| atomLabelStyle, 2.19.3 | faq, 3.8.1 |
| atomSingleStyle, 2.19.4 | from string, 2.27.7.7 |
| atomic coordinate transfer, 2.27.81.2 | helix, 3.10.5 |
| solvation contributions, 2.28.7 | how to, 3.8.1 |
| alternative position, 2.27.81.15 | hydrogen, 2.27.7.8 |
| selecting, 2.8.8 | loop, 2.27.7.5 |
| translate, 2.27.81.2 | model, 2.27.7.4, 2.27.102.9 |
| attenuation by occupancy, 2.27.59.25 | molcart, 2.27.7.9 |
| auc enrichment, 2.29.21 | sequence, 2.27.7.3 |
| auto saving log, 2.19.10 | smiles, 2.27.7.6 |
| autoSavePeriod, 2.15.1 | string, 2.27.7.7 |
| avi, 2.27.102.30 | built-in functions, 5.5.5 |
| axis, 5.1.7 | atoms, 2.27.14 |
| axisLength, 2.16.4 | contact surface, 2.27.14 |
| background, 2.28.28.2 | molecule, 2.27.13.1 |
| ball, 5.2.2 | number of bonds, 2.28.125.3 |
| base, 5.2.1 | variables, 2.27.14 |
| basis set, 2.27.76.20, 2.27.102.17 | calcArea, 2.29.3 |
| batch chemical processing, 3.1.2.5 | calcBindingEnergy, 2.29.4 |
| docking, 3.13.2.7 | calcDihedralAngle, 2.29.5 |
| beta, 5.2.3 | calcEnergyStrain, 2.29.20 |
| bfactor circles, 2.21.5.2 | calcEnsembleAver, 2.29.6 |
| binary file table of contents, 2.27.76.2 | calcMaps, 2.29.7 |
| files, 2.27.102.2 | calcPairSeqIdsFromAli, 2.29.8 |
| key, 2.27.81.36 | calcPepHelicity, 2.29.9 |
| binding energy, 3.7.4 | calcProtUnfoldingEnergy, 2.29.10 |
| pocket finding, 3.4.2 | calcRmsd, 2.29.11 |
| pockets, 2.27.84.1 | calcSeqContent, 2.29.12 |
| site analysis, 3.4.2 | calc_nosauc, 2.29.21 |
| biological symmetry, 2.27.81.8 | calculate phases, 3.11.2 |
| vector, 2.28.59.3 | call, 2.27.8 |
| to integers compression, 2.28.59.3 | carboxylic acid, 2.27.63.2 |
| blast files, 2.27.102.24 | cartesian cooridnates, 2.28.177 |
| blast-formatted database, 2.27.34.3, 2.27.102.24 | cartridge, 3.5 |
| blending, 2.27.102.30 | cavities, 2.27.84.1 |
| images, 2.28.144.2 | cavity, 5.3.1 |
| bold, 2.27.81.31.1 | analysis, 3.3.13 |
| bond angle bending, 2.30.5 | ccp4 maps, 2.27.76.26 |
| stretching, 2.30.6 | cd, 2.27.81.18 |
| to protein, 2.27.65.3 | cell axis vectors, 2.28.177.7 |
| bonded atoms, 2.28.89.1 | specific icm commands, 5.10.2.4 |
| born radii, 2.27.82.8 | center, 2.10.1, 2.27.9 |
| boundary element, 5.2.4 | chain breaks, 2.21.5.6, 2.21.5.7, 2.28.125.1 |
| matrix, 2.28.79.9 | symbol, 2.27.81.8 |
| sequence position in multiple alignment, 2.27.65.6 | screen, 2.27.10 |
| unix directory, 2.27.81.18 | click and lock, 5.10.2.4 |
| changing local stick radii, 2.27.81.74 | clipping plane, 5.3.3 |
| surface dot size, 2.21.5.46 | closer than threshold, 2.28.38.7 |
| charge, 5.3.2 | closest sequence, 2.28.87.3 |
| compounds, 2.27.63.2 | value, 2.28.49.1 |
| change, 2.27.81.9 | cluster, 2.28.140.1 |
| chem formula, 2.28.142.9 | center, 2.28.62.8 |
| chemSuper3D, 2.29.22 | centers, 2.10.1 |
| chemical, 2.23, 2.27.34.9 | selection, 2.28.62.8 |
| 2D drawings, 2.27.59.9 | tree, 2.28.87.5 |
| SMARTS search, 2.27.34.5 | size, 2.28.90.1 |
| database, 3.5 | clustering, 2.10, 2.27.59.35, 2.27.84.6 |
| decomposition, 2.27.59.27, 2.27.84.2 | clusters, 2.10, 2.10.1 |
| descriptors, 5.8.12 | cnMethodAverage, 2.19.5 |
| diversity, 3.14.6.3 | cnWeight, 2.16.6 |
| drawing, 2.21.9.14 | coil, 5.3.4 |
| quality, 2.21.9.15 | collection, 2.21 |
| formula, 2.28.142.9 | color, 2.21.5.27, 2.27.11 |
| fragment counting, 2.28.90.2 | accessibility, 2.27.13 |
| keys, 2.27.59.21 | background, 2.27.13.2 |
| match coordinates, 2.28.177.5 | example, 3.2.7 |
| matching, 2.27.34.4, 2.27.76.45, 2.27.76.46, 2.28.121, 2.28.141 | accessibility, 3.2.11 |
| models, 2.28.87.1 | alignment, 2.27.13.3 |
| modification, 2.27.62, 2.27.63, 2.29.37 | atom contributions, 2.27.12 |
| name, 2.28.87.6 | bfactor, 3.2.9 |
| normalization, 2.27.63 | charge, 3.2.12 |
| rules, 2.27.63.4 | electrostatic potential, 2.15.5 |
| pattern, 2.24, 2.27.80.1 | hydrophobicity, 3.2.10 |
| search, 2.28.49.3 | pharmacophore, 2.27.12 |
| reaction product generation, 2.27.59.32 | potential, 2.29.25 |
| search, 2.27.34.10, 2.27.80.1, 2.28.90.2 | shape depth, 2.27.13 |
| similarity, 3.5 | chemical, 2.27.12, 2.27.80.1 |
| spreadsheet, 2.27.12, 2.27.76.44, 2.27.76.45, 2.27.76.46, 2.27.81.40, 2.27.102.11 | file, 2.30.15 |
| structure from smiles, 2.27.81.6 | grob, 2.27.13.4 |
| substructure, 2.27.34.4 | by atom selection, 2.27.13.4.3 |
| mask, 2.27.59.21 | atoms, 2.21.7.1 |
| superposition, 2.19.6, 2.28.121 | map, 2.27.13.4.4 |
| table, 2.23 | matrix, 2.27.13.4.2 |
| view, 2.27.81.45 | potential, 2.27.13.4.5 |
| chemistry, 2.23, 2.28.26 | unique, 2.27.13.4.1 |
| chiral isomer generation, 2.27.29 | label, 2.27.13.5 |
| chirality, 2.17.16, 2.27.29 | map, 2.27.13.6 |
| choosing ligands, 3.13.1.2 | by value, 2.27.23.16 |
| cif, 2.27.76.44 | molecule, 2.27.13.1 |
| clamp values to range, 2.28.164 | names, 2.28.28 |
| clashThreshold, 2.16.5 | object, 2.27.11.2 |
| labels, 2.28.152 | 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 |
| function, 2.27.7.2 | stack, 2.27.102.40, 5.3.11, 5.9.9 |
| selection, 2.28.87 | compression, 2.27.15.2 |
| combinatorial compounds, 2.28.26 | file, 2.30.7 |
| libraries, 2.27.59.32, 2.28.90.4 | transition, 2.29.38 |
| PDB, 2.29.89 | conformer storage, 2.27.57.5, 2.27.86.2 |
| transformations, 3.10.4 | conformers, 3.13.2.3 |
| combining plots, 2.27.59.31 | connect, 2.27.16 |
| receptor and ligand stacks, 2.27.4.2 | chains with alignments, 2.27.52 |
| command, 2.28.87.4, 5.3.9 | molcart, 2.27.16.1 |
| line editing, 2.2 | consensus, 2.16.7 |
| help, 2.27.43 | coloring, 2.16.9, 2.21.2 |
| options, 2.1 | definitions, 2.21.1 |
| word list, 3.1.5 | consensusStrength, 2.16.7 |
| commands, 2.19.10 | conservation, 2.28.110.5, 2.28.124.5 |
| communication protocols, 2.25 | constant, 2.5 |
| comp, 2.28.93 | constants, 2.5 |
| comp_matrix, 2.27.81.17, 2.27.82.14, 5.3.10 | contact areas, 2.28.79 |
| compare, 2.15.11, 2.15.14, 2.27.14 | continue, 2.27.17 |
| angles, 2.27.14.2 | contour surfaces, 2.21.7.5 |
| atom, 2.27.14.1 | contouring density, 2.27.59.14 |
| by rmsd without superposition, 2.27.14.1 | contrast, 2.21.5.27 |
| chemical tables, 2.27.34.10 | conversion to real array, 2.28.154 |
| patch only, 2.27.14.3 | convert, 2.27.18, 2.27.18.2, 3.13.2 |
| rmsd, 2.27.14.1 | 3D to chemical, 2.28.26 |
| surface, 2.27.14.3 | 3D/0D to 2D, 2.27.59.9 |
| variables, 2.27.14.2 | ICM object to PDB, 2.27.88 |
| compareMethod, 2.19.6 | and reroot, 2.27.18.4 |
| comparing two sarrays, 2.28.93 | chemical 3D, 2.29.80 |
| comparison operations, 2.11.5 | and optmimize geometry, 2.29.81 |
| complete view, 2.28.132 | comp, 2.27.18.1 |
| compound accessibilities, 3.14.4.1 | comparison, 2.27.18.1 |
| array, 2.23 | fragments, 2.27.18.2 |
| compress, 2.27.15 | mol, 2.27.18.3 |
| binary, 2.27.15.3 | object 3D and optmimize geometry, 2.29.82 |
| conf, 2.27.15.2 | macro, 2.29.13 |
| grob, 2.27.15.1 | pdb, 3.8.2 |
| in place, 2.27.15.3 | to 3D, 2.27.81.7 |
| objects, 2.27.15 | ICM object, 2.29.83 |
| stack, 2.27.15.2 | iarray, 2.28.152 |
| compressed table view, 2.27.81.21 | icm-object, 2.27.18 |
| conditional buttons, 5.5.5 | integer, 2.28.152 |
| string, 2.28.142.6 | convert2Dto3D, 2.29.82 |
| conf, 2.27.81.51, 2.27.102.40, 2.28.146.6, 5.3.11, 5.9.9 | convert3Dto3D, 2.29.83 |
| data, 2.28.146.6 | convertObject, 2.29.13 |
| confgen, 3.13.2.3 | converting a chemical, 2.27.18.3 |
| configuration, 2.30.14 | pdb-chemical, 3.13.2 |
| memory usage, 2.15.6 | alignment to table, 2.28.146.2 |
| conformation comparison, 2.19.6 | chemicals, 3.13.2.4 |
| conformational generator, 2.27.60.1, 3.13.2.3 | table columns into matrix, 2.28.79.5 |
| interpolation, 2.27.23.6 | to, 2.28.111 |
| pictures, 2.21.5.24 | defining space box, 2.28.20 |
| cooling schedule, 2.16.43 | dehtml, 2.28.114.3 |
| coordinate frame, 2.16.4, 2.27.23.4 | delete, 2.27.22 |
| copy, 2.27.19 | 3D graphics panel, 2.27.97 |
| chemical image, 2.21.9.15 | alias, 2.27.22.2 |
| file, 2.18.26 | array element, 2.27.22.6 |
| site, 2.27.81.24 | index, 2.27.22.6 |
| correlation matrix, 2.28.149 | selection, 2.27.22.1 |
| covalent bound count, 2.28.125.3 | atom, 2.27.22.7 |
| neighbors, 2.28.89.1 | bond, 2.27.22.14 |
| covalently attached molecule, 2.28.89.1 | boundary, 2.27.22.15 |
| cpk, 5.3.12 | chemical, 2.27.22.34 |
| create a covalent bond, 2.27.59.2 | fragment, 2.27.22.34 |
| pharmacophore, 2.29.84 | selection, 2.27.22.34 |
| creating a local patch object, 2.27.18.2 | class, 2.27.22 |
| credits, 4.5 | conf, 2.27.22.16 |
| crypt, 2.27.20 | directory, 2.27.22.8 |
| crystal axis vectors, 2.28.16 | disulfide bond, 2.27.22.25 |
| symmetry transformation, 3.10.2 | drestraint, 2.27.22.17 |
| transformations, 2.28.162 | element, 2.27.22.29 |
| crystallographic occupancy, 2.28.95 | file, 2.27.22.9 |
| symmetry intro, 1.4.2.4 | from array, 2.27.22.6 |
| crystallography, 2.28.117 | hydrogen, 2.27.22.11 |
| csv format, 2.27.76.41 | label, 2.27.22.18, 2.27.22.19 |
| csym, 1.4.2.4 | chemical, 2.27.22.19 |
| current, 5.3.8 | link, 2.27.22.20 |
| icm-process number, 2.15.4 | map, 2.27.22.21 |
| map, 5.3.6 | molcart, 2.27.22.3 |
| object, 5.3.7 | molecule, 2.27.22.13 |
| working directory, 2.28.96 | object, 2.27.22.12 |
| cursor action, 5.10.2.4 | parray, 2.27.22.33 |
| customization, 3.1.2 | element, 2.27.22.33 |
| and paste chemicals, 2.21.9.14, 2.21.9.15 | peptide bond, 2.27.22.26 |
| cyclic temperature protocol, 2.16.43 | plot, 2.27.22.4 |
| cz32, 4.5 | salts, 2.27.63.3 |
| database, 5.4.1 | selection, 2.27.22.5 |
| browser, 2.27.57.3 | sequence, 2.27.22.22 |
| connection, 2.27.16.1 | session, 2.27.22.10 |
| file, 3.5.1 | shell object, 2.27.22.1 |
| import, 2.27.59.26 | site, 2.27.22.23 |
| date, 2.27.21 | sstructure, 2.27.22.24 |
| array, 2.27.21 | stack, 2.27.22.27 |
| dcMethod, 2.19.7 | object, 2.27.22.28 |
| dcWeight, 2.16.8 | system, 2.27.22.9 |
| decomposition, 2.27.59.27, 2.27.84.2 | table, 2.27.22.30 |
| defCell, 2.22.1 | rows, 2.27.22.30 |
| defSymGroup, 2.15.2 | term, 2.27.22.31 |
| default atom colors, 2.27.81.13 | tether, 2.27.22.32 |
| value, 5.9.2 | tree, 2.27.22.33 |
| define axis, 3.10.3 | variable, 2.27.22.6 |
| backbone, 2.28.125.1 | surface, 2.27.23.20 |
| restraint, 2.27.22.17 | area, 2.21.5.2 |
| deleting sites by number, 2.27.22.23 | tethers, 2.27.23.23 |
| delphi, 2.29.25 | trajectory, 2.27.23.17 |
| density correlation, 2.16.8, 3.11.3 | volume, 2.27.23.24 |
| fitting, 2.19.7 | window, 2.3, 2.27.23.25 |
| in unit cell, 2.27.59.23 | distance, 2.21.5.18, 5.4.3 |
| densityCutoff, 2.16.10 | averaging, 2.19.5 |
| dependent columns, 2.27.1.1.1 | contact-based, 2.28.22, 2.28.22.1 |
| depth cueing, 2.27.13.7, 5.4.2 | geometry, 5.4.4 |
| depth-cueing, 2.16.14 | matrix, 2.28.146.5, 2.29.8 |
| desolvation, 2.19.24 | between stack conformations, 2.28.79.10 |
| detecting proximity, 2.28.38.7 | restraint, 5.4.6 |
| dialog generation, 2.28.11 | file, 2.30.9 |
| in html documents, 2.27.42 | type file, 2.30.8 |
| tables, 2.27.42 | restraints, 2.27.81.19 |
| scripting, 2.28.11 | distances, 2.28.90.3 |
| dielConst, 2.16.11 | distribution, 1.3 |
| dielConstExtern, 2.16.12 | comparison, 2.28.124 |
| dielectric constant, 2.16.11 | disulfide bond, 5.4.5 |
| diff, 2.28.93 | diverse subset, 3.14.6.3 |
| dihedral angle, 2.27.59.19 | dividing chemical into individual molecules, 2.28.140.4 |
| calculation, 3.3.10 | dna to protein sequence translation, 2.28.161.1 |
| directory, 2.27.22.8, 2.27.59.5, 2.28.123 | translate, 2.28.161.1 |
| display, 2.27.23 | dockScan, 3.13.2.7 |
| GUI window, 2.27.23.26 | docking, 2.29.86 |
| box, 2.27.23.7 | intro, 3.13.2.1 |
| clash, 2.16.5, 2.27.23.8 | result viewing, 2.29.28 |
| drestraint, 2.27.23.9 | simple models, 3.14.3 |
| field, 2.21.5.2 | timing, 3.13.1.3 |
| from script, 2.27.23.3 | with template, 3.13.2.8 |
| gradient, 2.27.23.10 | documents, 5.6.2 |
| grob, 2.27.23.11 | dominant color, 2.28.28.2 |
| label, 2.27.23.12 | donor, 3.6.1 |
| gui, 2.27.23.26 | plot intro, 1.4.3.2 |
| hbond, 2.27.23.13 | dots, 2.27.70 |
| label, 2.27.23.15 | dotted surface, 2.21.5.48 |
| map, 2.21.5.9, 2.27.23.16 | double click action, 5.10.2.4 |
| model, 2.27.23.1 | drestraint, 2.27.82.16, 5.4.6 |
| new, 2.27.23.2 | generate from structure, 2.27.59.7 |
| off-screen, 2.27.23.3 | global weight, 2.16.6 |
| offscreen, 2.27.23.3 | set, 2.27.81.19 |
| origin, 2.27.23.4 | type, 5.4.7 |
| ribbon, 2.27.23.18 | drop, 2.16.13 |
| rotate, 2.27.23.5 | ds3D, 2.29.31 |
| site, 2.27.23.19 | dsCellBox, 2.29.15 |
| skin, 2.27.23.20 | dsChem, 2.29.17 |
| slide, 2.27.23.21 | dsCustom, 2.29.18 |
| stack, 2.27.23.6 | dsPocket, 2.29.28 |
| string, 2.27.23.22 | dsPropertySkin, 2.29.19 |
| dsRebel, 2.15.5, 2.29.25 | exact, 2.27.34.9, 2.27.34.10 |
| dsSeqPdbOutput, 2.29.26 | match, 2.28.114.1 |
| dsSkinLabel, 2.29.27 | example scripts, 3.14 |
| dsStackConf, 2.29.29 | exit, 2.27.33 |
| dsVarLabels, 2.29.30 | exitSeslogStyle, 2.19.10 |
| dsXyz, 2.29.32 | expanding substructure match, 2.27.81.59 |
| dump database, 2.27.102.7 | export, 2.27.102.7 |
| dynamic gui, 5.5.5 | animation, 2.27.102.30 |
| ecepp, 5.5.1 | exporting sdf, 2.27.102.11 |
| edit, 2.27.24 | expression shortcuts, 2.9.1.2 |
| files, 2.21.14.1 | comparison, 2.11.5 |
| electro intro, 1.4.2.9 | arithmetics, 2.11.2 |
| electroMethod, 2.19.8 | assignment, 2.11.1 |
| density, 2.21.7.5, 2.29.42, 2.29.43 | comparison, 2.11.5 |
| around selection, 2.16.22 | logical, 2.11.3 |
| map generation, 2.16.1 | extending to bonded hydrogens, 2.28.125.6 |
| maps, 2.21.14.1 | terminal atoms, 2.28.125.6 |
| electrostatic boundary matrix, 2.28.79.9 | external process, 2.27.59.1 |
| isopotential surfaces, 2.27.59.13 | extracting from Markush, 2.27.50 |
| potential, 2.27.13.4.5 | icm script arguments, 2.28.52 |
| solvation, 3.7.2 | stack from object, 2.27.57.5 |
| surface, 2.29.25 | ez25, 3.7 |
| troubleshooting, 5.8.13 | factor, 5.9.13 |
| intro, 1.4.2.9 | false negatives, 2.28.124.2 |
| ellipsoid, 2.28.149 | family, 2.27.81.31.1 |
| elseif, 2.27.25 | faq, 1.3 |
| endfor, 2.27.26 | cheminformatics, 3.14.6 |
| endif, 2.27.27 | chemsuper, 3.14.5 |
| endmacro, 2.27.28 | molcart dump, 3.14.6.2 |
| endwhile, 2.27.32 | query, 3.14.6.1 |
| energetics, 3.7 | multiple chem overlay, 3.14.5.1 |
| function, 2.21.14.2 | residue table, 3.14.4.1 |
| terms, 2.14 | fast Fourier transform, 2.27.59.24 |
| ensemble average, 3.7.5 | sequence search, 2.27.34.3 |
| entropy of alignment, 2.28.124.5 | fasta, 5.5.2 |
| atom, 2.27.18.4 | feature table, 2.28.146.8 |
| enumerate, 2.27.29, 2.27.30, 2.27.31 | in sequences, 2.27.81.23 |
| chiral, 2.27.29 | ffMethod, 2.19.11 |
| library, 2.27.31 | field name, 2.28.87.2 |
| tautomer, 2.27.30 | file, 2.27.102.23 |
| enumeration, 2.28.26 | exists, 2.28.43 |
| eps files, 2.18.23 | list, 2.28.52 |
| error SOAP services, 2.28.42 | length, 2.28.48 |
| ignoring, 2.18.25 | object origin, 2.28.48 |
| error/warning bits cleanup, 2.27.10 | permissions, 2.28.48 |
| errorAction, 2.19.9 | time modified, 2.28.48 |
| vrestraint vs_var, 2.27.81.70 | type, 2.28.48 |
| evalSidechainFlex, 2.29.87 | files, 2.30 |
| evol tree intro, 1.4.3.5 | filter, 2.27.34.10, 2.27.57.3 |
| evolutionary tree intro, 1.4.3.5 | functions, 5.5.4 |
| find, 2.27.34 | expansion, 2.28.134.3 |
| alignment, 2.27.34.1 | gapExtension, 2.16.15 |
| and replace a chemical pattern, 2.27.63.1 | gapFunction, 2.22.3 |
| chemical fragment, 2.27.63 | gapOpen, 2.16.16 |
| chemical, 2.27.34.5 | gcMethod, 2.19.12 |
| pattern, 2.27.63 | generate intermediate conformers, 2.29.38 |
| substructure, 2.28.62.1 | generating movie images, 3.9.2.1 |
| database, 2.16.2, 2.27.34.2 | genomics, 1.4.3.1 |
| fast, 2.27.34.3 | clustering, 2.27.41.2 |
| family of commands, 2.27.34 | intro, 1.4.3.1 |
| in sarray, 2.28.62.7 | geometry optimization, 2.27.60.1 |
| molcart, 2.27.34.9, 3.5 | started, 1.7 |
| molecule, 2.27.34.4 | getting data from outside, 2.25 |
| pattern, 2.27.34.8 | started, 1.7 |
| pdb, 2.27.34.6 | global, 2.27.39 |
| pharmacophore, 2.27.34.11 | glossary, 5 |
| prosite, 2.27.34.7 | goto, 2.27.40 |
| table, 2.27.34.10 | term, 2.16.17, 2.27.81.61 |
| findFuncMin, 2.29.33, 2.29.34 | gpWeights, 2.16.17 |
| findFuncZero, 2.29.35 | graph matching, 2.28.121 |
| findSymNeighbors, 2.29.16 | graphical box, 2.27.23.7 |
| find_related_sequences, 2.29.33 | row selection, 2.28.62.4 |
| finding long covalent bonds, 2.28.125.1 | selection, 2.28.125.5 |
| to density, 2.19.7 | graphics, 2.27.81.3, 2.28.173, 3.2, 5.3.3 |
| fix, 2.27.35 | card, 2.21.5.44 |
| fixed branches, 2.28.125.2 | controls, 2.3, 2.30.15, 5.4.2 |
| flattening 3D molecule, 2.29.17 | exists, 2.28.43 |
| flow control, 2.12 | intro, 1.4.1, 1.4.1.4 |
| fog, 2.16.14, 2.27.13.7, 2.27.23.24, 5.4.2 | learning, 3.2.1 |
| color, 2.16.14 | attributes, 2.16.4 |
| fogStart, 2.16.14 | fogStart, 2.16.14 |
| fold search, 5.9.4 | view vector, 2.27.81.68 |
| foldbank.db, 2.30.3 | greedy matching, 2.9.1.4 |
| folding procedure, 3.14.1 | grid potentials, 2.27.59.25 |
| font, 2.27.53.1 | grob, 5.5.3 |
| size, 2.27.81.31.1, 2.30.14 | coloring, 2.27.13 |
| specification, 2.27.81.31.1 | files, 2.30.10 |
| for, 2.27.36 | inside-out flip, 2.27.81.35 |
| fork, 2.27.37 | normal directions, 2.27.81.35 |
| formal charge, 2.21.5.15, 5.3.2 | translate, 2.27.95 |
| formatdb, 2.27.102.24 | group, 2.27.41 |
| fprintf, 2.27.38 | by column, 2.27.41.4 |
| fractional coordinates, 2.28.177.3 | column, 2.27.41.4 |
| to abs coordinates, 2.28.16 | replacement, 2.27.62 |
| fragmented molecule, 2.27.18.2 | sequence, 2.27.41.1 |
| frame, 2.27.86, 2.27.102.30 | unique, 2.27.41.2 |
| fullscreen, 2.27.81.73 | table, 2.27.41.3 |
| function, 2.27.58 | grouping table by a column, 2.27.81.21 |
| selecting in objects, 2.8.10 | gui, 2.27.42, 5.10.2.4 |
| gamess, 5.6 | exists, 2.28.43 |
| panels, 2.27.97 | hydration, 2.28.7 |
| programming, 2.26, 2.27.42, 2.27.81.21 | parameters, 2.30.13 |
| gzip files, 2.27.15.3 | hydrogen bond, 2.21.5.19, 2.21.5.20, 2.27.59.17, 5.6.1 |
| hash table, 2.21 | bonding parameters, 2.30.12 |
| haze, 2.16.14 | cutoff, 2.16.18 |
| hb, 2.16.18 | bonds, 2.28.90.3 |
| hbCutoff, 2.16.18 | display, 2.21.5.26 |
| hbond, 2.21.5.19, 2.21.5.20, 2.27.22.6, 5.6.1 | placement, 2.27.81.22 |
| color, 2.27.23.14 | hydrophobicity profile, 3.3.12 |
| display, 2.21.5.21, 2.21.5.22 | iProc, 2.15.4 |
| energy, 2.27.23.14 | iSee, 5.9.14 |
| list, 2.28.146.9 | i_out, 2.15.3 |
| show, 2.27.82.20 | iarray, 2.27.22.6, 2.28.49.1, 2.28.59.2, 2.28.62.7, 5.7.1 |
| hbondMinStrength, 2.21.5.19 | making, 2.28.59.1 |
| faq, 3.3.4 | icb files, 5.9.14 |
| how to, 3.3.4 | algorithms, 4.3 |
| header, 2.27.1.1 | application refs, 4.4 |
| helical axis, 2.29.36 | literature, 4.3 |
| helicity, 3.7.6 | archive, 2.27.76.2 |
| content calculation, 3.7.6 | arguments, 2.28.52 |
| help, 2.27.43, 2.27.43.1, 2.27.43.2 | binary, 2.28.96 |
| browser, 2.27.43.1 | branching, 2.12.2 |
| commands, 2.27.43.3 | commands, 2.27 |
| functions, 2.27.43.4 | controls, 2.12 |
| getting, 3.1.1 | flags, 2.1 |
| word, 2.27.43.2 | functions, 2.28 |
| getting, 3.1.1 | graphics, 3.2 |
| hidden blocks, 5.1.1.1 | history, 1.2 |
| display, 2.27.23.3 | jumps, 2.12.3 |
| hydrogens, 2.21.5.26 | learning, 3.1.4 |
| stack in object, 2.27.86.2 | loops, 2.12.1 |
| hierarchical, 2.10 | macros, 2.29 |
| highEnergyAction, 2.19.13 | main refs, 4.2 |
| his-tags, 2.28.165 | menus, 2.21.10.1 |
| histogram, 2.27.59.31 | method literature, 4.4 |
| 2D, 2.28.79 | molecules, 2.13 |
| history, 2.27.44, 2.27.102.39 | object file, 2.30.18 |
| delete, 2.27.22.10 | session, 2.19.10 |
| of ICM, 1.2 | shell, 3.1 |
| homodel, 2.29.41 | support, 1.3 |
| homology modeling, 1.4.2.2, 2.27.7.4, 2.27.81.58, 2.29.1, 3.14.4 | table, 2.20 |
| faq, 3.14.4 | ali, 2.30.31 |
| intro, 1.4.2.2 | all, 2.30.32 |
| output, 2.27.7.4.3 | bbt, 2.30.5 |
| steps, 2.27.7.4.1 | bst, 2.30.6 |
| to export a molcart table, 3.14.6.2 | cfg, 2.30.14 |
| html, 2.27.42, 2.28.87.4, 5.6.2 | clr, 2.30.15 |
| document order, 2.27.81.33 | cmp, 2.30.33 |
| tag removal, 2.28.114.3 | cn, 2.30.9 |
| html-formatted text, 5.6.2 | cnf, 2.30.7 |
| cod, 2.30.4 | entry, 2.28.123.1 |
| col, 2.30.24 | sdf-file path, 2.28.96 |
| gro, 2.30.10 | indices of labeled table rows, 2.28.62.5 |
| hbt, 2.30.12 | selected table rows, 2.28.62.4 |
| hdt, 2.30.13 | infinity, 2.28.154 |
| htm, 2.30.11 | info, 2.27.46 |
| iar, 2.30.35 | molcart, 2.27.46.1 |
| map, 2.30.16 | inner join, 2.27.48 |
| mat, 2.30.37 | insert rows, 2.27.1.4 |
| ob, 2.30.18 | integer, 5.7.2 |
| pdb, 2.30.28 | array, 2.28.59, 5.7.1 |
| prf, 2.30.34 | shell variables, 2.15 |
| rar, 2.30.38 | interaction cutoff, 2.17.27 |
| res, 2.30.20 | lists, 2.17.27, 2.21.14.2 |
| rs, 2.30.23 | interactive docking, 1.4.2.8 |
| rst, 2.30.22 | interface comparison, 2.27.14.3 |
| sar, 2.30.36 | residues, 3.3.5 |
| se, 2.30.30 | torsions, 3.3.7 |
| seq, 2.30.29 | view, 2.29.28 |
| tab, 2.30.25 | intermolecular bond, 2.27.65.3 |
| tot, 2.30.26 | internal coordinate file, 2.30.21 |
| trj, 2.30.17 | coordinates, 2.8.9 |
| var, 2.30.21 | interpolate, 2.28.28.1 |
| vwt, 2.30.27 | interpolation, 2.28.28.1 |
| icmCavityFinder, 2.29.14 | interruptAction, 2.19.14 |
| icmMacroShape, 2.29.85 | inverting array order, 2.28.59.2, 2.28.110.2 |
| icmPmfProfile, 2.29.23 | italic, 2.27.81.31.1 |
| icmPocketFinder, 2.29.86 | iterative overlay, 2.27.89 |
| icmscript, 2.27.76.3 | superposition, 2.21.14, 2.27.90 |
| arguments, 2.28.52 | join, 2.27.48 |
| if, 2.27.45 | tables, 2.27.48 |
| ignoring swiss secondary structure, 2.22.9 | keep, 2.27.47 |
| image, 3.2.6 | kernel models quality, 2.28.124.2 |
| annotation, 3.2.5 | mapping, 2.30.15 |
| center, 3.2.8 | kmz, 5.5.3 |
| format, 5.10.3 | l_antiAlias, 2.17.1 |
| high quality, 3.2.2 | l_autoLink, 2.17.2 |
| parray, 5.8.3.3 | l_bpmc, 2.17.3 |
| resolution, 3.2.2 | l_breakRibbon, 2.17.4 |
| rotation, 3.2.3 | l_bufferedOutput, 2.17.5 |
| imposing tether, 2.27.81.58 | l_bug, 2.17.6 |
| place, 2.11.4 | l_caseSensitivity, 2.17.7 |
| ops, 2.11.4 | l_commands, 2.17.8 |
| incidence, 2.28.79.12 | l_confirm, 2.17.9 |
| increasing the number of shell variables, 2.30.14 | l_easyRotate, 2.17.10 |
| increment charge, 2.27.81.9 | l_info, 2.17.11 |
| index expressions, 2.6 | l_minRedraw, 2.17.12 |
| in array, 2.28.62.3 | l_neutralAcids, 2.17.13 |
| substring, 2.28.62.2 | l_out, 2.17.14 |
| table, 2.27.102.23 | l_print, 2.17.15 |
| l_readMolArom, 2.17.17 | database, 2.27.55 |
| l_showAccessibility, 2.17.18 | font, 2.27.53.1 |
| l_showMC, 2.17.19 | html documents, 2.28.87 |
| l_showMinSteps, 2.17.20 | molcart, 2.27.56 |
| l_showResCodeInSelection, 2.17.21 | database, 2.27.56 |
| l_showSites, 2.17.23 | of files, 2.28.123 |
| l_showSpecialChar, 2.17.22 | updates, 2.27.60 |
| l_showSstructure, 2.17.24 | listUpdateThreshold, 2.16.20 |
| l_showTerms, 2.17.26 | literature, 4.1 |
| l_showWater, 2.17.25 | load, 2.27.57 |
| l_updateLists, 2.17.27 | conf, 2.27.57.1 |
| l_warn, 2.17.28 | frame, 2.27.57.2 |
| l_wrapLine, 2.17.29 | molcart, 2.27.57.3 |
| l_writeStartObjMC, 2.17.30 | object, 2.27.57.6 |
| l_xrUseHydrogen, 2.17.31 | solution, 2.27.57.4 |
| label, 2.27.23.22, 5.7.3 | stack object, 2.27.57.5 |
| fonts, 2.30.15 | loadEDS, 2.29.42 |
| latent, 2.28.90.6 | loadEDSweb, 2.29.43 |
| learn, 2.27.49 | local, 3.5.1 |
| atom, 2.27.49.1 | logarithm, 2.28.74 |
| left join, 2.27.48 | logical, 5.7.4 |
| triangle of a matrix, 2.28.79.3 | operations, 2.11.3 |
| library to replacement groups, 2.27.59.27, 2.27.84.2 | variables, 2.17 |
| ligand binding, 2.29.28 | logical_ops, 2.11.3 |
| dock faq, 3.13.2 | logicals, 2.17 |
| docking, 3.13, 3.13.1, 3.13.2 | long axes, 2.28.149 |
| intro, 1.4.2.6 | loop database rebuilding, 2.27.102.27 |
| editing, 1.4.2.8 | interrupt, 2.16.44 |
| editor, 2.29.37 | modeling, 1.4.2.3 |
| fit, 3.13 | intro, 1.4.2.3 |
| setting, 3.13.2 | search, 2.27.7.4.2 |
| view, 2.21.5.25 | resolution shape, 2.29.85 |
| light, 2.21.5.28 | ma29, 3.11 |
| limits, 2.30.14 | macro, 2.27.58, 5.7.5 |
| line thickness in 2D chemicals, 2.21.9.14 | macro_def, 5.7.5 |
| lineWidth, 2.16.19 | main ICM references, 4.2 |
| linear chemical notation, 2.24 | concepts, 3.10.1 |
| regression, 2.28.73 | make, 2.27.59 |
| group, 2.27.50 | 3d label, 2.27.59.15 |
| internal variables of molecular object, 2.27.51 | angle, 2.27.59.18 |
| ms2ali, 2.27.52 | background, 2.27.59.1 |
| sequences to 3D objects, 2.27.52 | bond, 2.27.59.2 |
| to alignment, 2.27.52 | chain, 2.27.59.3 |
| variable, 2.27.51 | multi, 2.27.59.3 |
| variables, 2.27.51 | boundary, 2.27.59.4 |
| linked alignment, 2.28.87 | directory, 2.27.59.5 |
| sequence, 2.28.87 | distance, 2.27.59.16 |
| linux shell, 2.27.91, 5.11.2 | disulfide bond, 2.27.59.6 |
| list, 2.27.53 | drestraint, 2.27.59.7 |
| binary, 2.27.54 | factor, 2.27.59.8 |
| chem_array, 2.27.59.9 | transformations, 2.28.134.4 |
| grob, 2.29.36 | trimming, 2.28.21 |
| from image, 2.27.59.11 | value sigma, 2.28.121 |
| matrix, 2.27.59.12 | contouring, 2.27.59.14 |
| image, 2.27.59.11 | mapAtomMargin, 2.16.22 |
| map, 2.27.59.10 | mapSigmaLevel, 2.16.21 |
| matrix, 2.27.59.12 | mapping properties to sequence, 2.28.110.4 |
| potential, 2.27.59.13 | and factors, 3.11 |
| skin, 2.27.59.14 | mass-spectrometry functions, 2.27.29, 2.27.30, 2.27.31 |
| hbond, 2.27.59.17 | matching chemicals, 2.28.62.1 |
| image, 2.27.59.20 | hydrogens, 2.27.81.59 |
| key, 2.27.59.21 | matrix, 5.7.7 |
| map, 2.27.59.22 | new, 2.28.79.1 |
| cell, 2.27.59.23 | map value, 2.28.80 |
| factor, 2.27.59.24 | maxColorPotential, 2.15.5 |
| potential, 2.27.59.25 | maxMemory, 2.15.6 |
| xray, 2.27.59.30 | movie, 3.9.2 |
| molcart, 2.27.59.26 | mcBell, 2.16.23 |
| molsar, 2.27.59.27 | mcJump, 2.16.24 |
| pca, 2.27.59.28 | mcShake, 2.16.25 |
| peptide bond, 2.27.59.29 | mcStep, 2.16.26 |
| plot, 2.27.59.31 | memorizing positions, 3.2.4 |
| reaction, 2.27.59.32 | menu, 2.27.61 |
| sequence, 2.27.59.34 | script, 3.1.3 |
| alignment, 2.27.59.33 | merge PDB, 2.29.89 |
| from alignment, 2.27.59.33 | arrays to table, 2.27.41.3 |
| torsion, 2.27.59.19 | continuation lines, 2.27.76.37 |
| tree, 2.27.59.35 | objects, 2.27.65.2 |
| unique, 2.27.59.36 | parts of molecule, 2.27.65.3 |
| makeAxisArrow, 2.29.36 | pdb, 3.4.4 |
| makeIndexChemDb, 2.29.44 | sarray into string, 2.28.144 |
| makeIndexSwiss, 2.29.45 | stacks, 3.7.7 |
| makePdbFromStereo, 2.29.46 | tables, 2.27.4.3, 2.27.48 |
| makePharma, 2.29.84 | merge2, 3.8.7 |
| makeSimpleDockObj, 2.29.47 | mergePdb, 2.29.89 |
| makeSimpleModel, 2.29.48 | several chemical, 2.28.144.1 |
| making predictive models, 2.27.49 | merging into one molecule, 2.27.65.3 |
| manual style, 1.5 | mesh, 2.28.174 |
| map, 2.16.22, 2.21.5.9, 5.7.6 | score, 3.13.3.3 |
| aa property to sequence, 2.28.110.1 | mfMethod, 2.19.15 |
| averaging, 2.28.134.4 | mfWeight, 2.16.27 |
| calculation, 2.27.59.24 | mimel, 5.7.8 |
| conversion, 2.27.59.30 | mimelDepth, 2.16.28 |
| file, 2.30.16 | mimelMolDensity, 2.16.29 |
| fitting, 2.19.7 | minNumGrad, 2.27.60 |
| format, 5.7.6 | minTetherWindow, 2.15.7 |
| mean value, 2.28.82 | minimization exit criteria, 2.27.60 |
| min value, 2.28.83 | minimize, 2.15.9, 2.27.60 |
| name, 2.28.75 | cartesian, 2.27.60.1 |
| operations, 5.7.6 | loop, 2.27.60.2 |
| tether, 2.15.7, 2.27.60.4 | properties, 2.27.81.29 |
| drop, 2.16.13 | rotation, 3.2.3 |
| minimizeMethod, 2.19.16 | translation, 3.2.3, 3.2.4 |
| missing bonds, 2.27.65.3 | create, 1.7.2 |
| loop, 2.21.5.6, 2.21.5.7 | intro, 1.7.2, 2.7 |
| residues, 2.28.47.1 | sort/reorder, 2.27.83.4 |
| triangles, 2.28.174 | selecting, 2.8.6 |
| mkUniqPdbSequences, 2.29.49 | montecarlo, 2.15.10, 2.15.12, 2.15.13, 2.15.14, 2.15.18, 2.19.6, 2.27.64 |
| mm26, 3.8 | command, 2.27.64 |
| mmcif, 5.7.10 | local, 2.15.15 |
| mmff, 5.7.9 | trajectory, 2.27.23.17 |
| type, 2.28.167 | moprphing, 2.29.38 |
| show atom types, 2.27.82.10 | more, 5.7.13 |
| mnSolutions, 2.15.8 | morph, 2.27.23.6 |
| mncalls, 2.15.9 | to tether target, 2.29.38 |
| mncallsMC, 2.15.10 | morph2tz, 2.29.38 |
| mnconf, 2.15.11 | morphing, 2.27.23.6, 2.27.81.58, 2.27.86.3 |
| mnhighEnergy, 2.15.12 | mouse controls, 2.3 |
| mnreject, 2.15.13 | file, 2.27.102.30 |
| mnvisits, 2.15.14 | move, 2.27.65 |
| model reliability, 2.29.23 | alignment sequence, 2.27.65.6 |
| modify, 2.27.62 | atoms, 2.27.81.2 |
| and reroot, 2.27.18.4 | bonding, 2.27.65.3 |
| chem, 2.27.63 | column, 2.27.65.5 |
| charge, 2.27.63.2 | element, 2.27.65.4 |
| delete salt, 2.27.63.3 | file, 2.18.28, 2.27.77.3 |
| normalize, 2.27.63.4 | fragments together, 2.27.65.3 |
| chemical find replace, 2.27.63.1 | molecule, 2.27.65.1 |
| molcart, 2.27.63.5 | ms_molecule, 2.27.65.1 |
| modifyGroupSmiles, 2.29.37 | multiple molecules, 2.27.65.2 |
| modules, 1.4.4 | object, 2.27.65.2 |
| mol, 2.27.76.45, 2.27.76.46, 2.27.102.11, 2.27.102.23, 5.7.11 | sequence, 2.27.65.6 |
| file, 2.28.142.2 | table column, 2.27.65.5 |
| to icm, 2.27.18.3 | movie, 2.27.86.3 |
| translation, 3.2.4 | images by frame, 3.9.2.2 |
| mol-file to chem-table element, 2.28.97 | molecular simulation, 3.9.2 |
| mol2, 5.7.12 | rotate view, 3.9.1 |
| molcart, 2.27.16.1, 3.5 | zooming, 3.9.1 |
| connection options, 3.5.2 | moving selection to another object, 2.28.125.8 |
| molecular, 2.28.51, 5.8.3.1 | mpeg, 2.27.102.30 |
| arrays, 5.8.3 | ms_, 2.8.6 |
| manipulations, 3.8 | multi center drestraint, 2.19.5 |
| modifications, 3.8.5 | multi-part molecule, 2.27.18.2 |
| object, 5.8.1 | multiple NMR models, 2.21.14.3 |
| objects, 2.13 | alignment, 2.27.3.2 |
| surface, 2.27.82.8, 5.9.7 | to pairwise similarities, 2.29.8 |
| views, 1.4.1.1 | conformation storage, 5.9.9 |
| volume, 2.28.102 | mol as text, 2.28.142.2 |
| molecule, 2.7 | object file, 2.27.76.2 |
| create, 3.8.4 | sequence alignment intro, 1.4.3.4 |
| mutate residue, 2.27.62 | openGL window, 2.27.97 |
| mutating residue, 3.8.5 | operating system, 2.27.91, 2.28.173, 5.11.2 |
| mute, 5.7.15 | optimal chemical superposition, 3.14.5.1 |
| mysql, 2.27.16.1 | optimize Hbond, 2.29.88 |
| nLocalDeformVar, 2.15.15 | hydrogen bond, 2.29.88 |
| nProc, 2.15.17 | optimizeHbonds, 2.29.88 |
| nSsearchStep, 2.15.16 | or, 2.11.3 |
| name, 2.28.70 | order, 2.27.65.6 |
| atom fields, 2.27.81.29 | os_, 2.8.5 |
| naming compounds, 2.27.81.40 | other variables, 2.22 |
| nearest sequence, 2.28.83 | output, 2.15.3 |
| nested script, 5.9.2 | overlay by atom pairs, 2.27.89 |
| nice, 2.29.39 | chemical substructure, 2.29.22 |
| image, 3.2.2 | overview, 1.4 |
| non-redundant, 3.4.3 | pK shift, 3.7.3 |
| normal distribution, 2.28.109 | packing density, 3.3.8 |
| normalize chemicals, 2.27.63.4 | pair-distances, 2.27.22.6 |
| defined, 2.28.154 | pairdistance parray, 2.21.5.18 |
| nota, 1.5 | panel layout, 2.21.8.5 |
| notational conventions, 1.5 | paragraphs, 2.27.102.23 |
| nucleotides, 2.18.24 | parallelization, 2.15.4, 2.15.17 |
| number of dots, 2.21.5.47 | parray, 2.27.22.6, 5.8.3 |
| elements, 2.28.90 | parrayTo3D, 2.29.81 |
| hydrogen bonds, 2.27.82.20 | parrayToMol, 2.29.80 |
| molecules in objects, 2.28.125.4 | parse SOAP message, 2.28.171 |
| occurrences, 2.28.90 | parsing, 2.28.78 |
| residues in molecules, 2.28.125.4 | web pages, 2.27.76.43 |
| van der Waals contacts, 2.27.82.11 | partial least squares, 2.27.49 |
| transfer from sequence, 2.27.3.1 | slide display, 2.27.23.21 |
| nvis, 2.28.59.6 | sum, 2.28.68 |
| object, 2.27.13.1, 5.8.1 | passing arguments, 5.9.2 |
| parray, 5.8.3.1 | by reference, 2.27.58 |
| properties, 2.27.81.29 | pattern, 5.8.4 |
| stack, 5.9.9 | search, 2.27.34.2 |
| to chemarray, 2.28.26 | pause, 2.27.66 |
| user fields, 2.28.47.1 | pdb, 5.7.10, 5.8.6 |
| assign comment, 2.27.81.14 | file creation time, 2.28.35 |
| source file, 2.28.48 | files, 2.30.28 |
| translate, 2.27.95 | format, 2.27.76.44 |
| merge, 3.8.6 | merge, 3.4.4 |
| selecting, 2.8.5 | sequence generation, 3.4.3 |
| obsolete, 2.16.51 | pdbDirStyle, 2.19.17 |
| occlusion shading, 2.27.13 | peptide, 5.8.7 |
| octanol transfer, 2.28.102 | docking, 3.12.5 |
| off, 2.27.76.21 | folding, 1.4.2.1 |
| format, 5.5.3 | intro, 1.4.2.1 |
| oligonucleotide melting, 2.28.150 | personal gui controls, 3.1.2 |
| on-line help, 2.27.43.1, 2.27.43.2 | setup, 3.1.2 |
| third, 2.28.34 | ph30, 3.12 |
| only, 5.8.2 | ph4, 5.8.8 |
| pharmacophore, 2.27.12, 3.5, 5.8.8 | prediction model, 2.28.73 |
| faq, 3.6 | quality, 2.28.124 |
| grid type definitions, 2.27.81.61 | score, 2.28.124 |
| object, 3.6.1 | preference, 2.19 |
| objects, 3.6 | preferences, 3.1.2.3 |
| pharmacophores, 3.6 | prepSwiss, 2.29.61 |
| psi plot, 2.29.57 | previous atom, 2.28.89.1 |
| pipe, 2.27.76.40 | principal axes, 2.28.149 |
| planar angle, 2.27.59.18 | component analysis, 3.3.9 |
| plot, 2.27.67 | inertia moments, 2.28.77 |
| 3D 2Dfunction, 3.12.3 | print, 2.27.69 |
| shape, 3.12.4 | bar, 2.27.70 |
| area, 2.27.68 | image, 2.27.72 |
| histogram, 3.12.2 | to string, 2.27.85 |
| how to, 3.12 | printMatrix, 2.29.62 |
| simple, 3.12.1 | printPostScript, 2.29.63 |
| plot2DSeq, 2.29.50 | printTorsions, 2.29.64 |
| plotBestEnergies, 2.29.53 | printf, 2.27.71 |
| plotCluster, 2.29.55 | profile, 5.8.9 |
| plotFlexibility, 2.29.54 | program overview, 1.4 |
| plotMatrix, 2.29.56 | progress bar, 2.27.70 |
| plotRama, 2.29.57 | progression, 2.27.70 |
| plotRose, 2.29.58 | project setup, 3.13.2.2 |
| plotSeqDotMatrix, 2.29.51 | projected alignment, 2.28.87.3 |
| plotSeqDotMatrix2, 2.29.52 | projecting surface charge, 3.7.2 |
| plotSeqProperty, 2.29.59 | property, 2.27.81.44, 2.27.81.45 |
| 3d, 1.4.3.7 | grids, 2.16.17 |
| plotting van der Waals, 3.7.1 | map, 2.27.81.61 |
| faq, 3.7.1 | superposition, 2.27.81.61 |
| pls, 2.27.49 | prosite, 5.8.10 |
| column contributions, 2.28.146.7 | pattern, 5.8.4 |
| model, 2.28.146.7 | protein docking, 2.28.177.2 |
| weights, 2.28.146.7 | intro, 1.4.2.5 |
| pmf, 2.19.15 | grid docking, 3.14.2 |
| residue profile, 2.29.23 | health, 2.29.57 |
| pmf-file, 2.30.19 | psa, 5.8.12 |
| pmffile, 2.30.19 | purple box, 2.28.20 |
| png, 2.27.102.35, 5.8.5 | quantum mechanics, 2.27.76.20, 2.27.102.17 |
| pocket, 2.29.28, 2.29.86, 3.13.1.1 | query, 3.14.6.1 |
| point coordinates, 2.28.177.1 | molcart, 2.27.73 |
| pointer array, 5.8.3 | question mark operator, 2.28.142.6 |
| polar hydrogens, 2.21.5.26 | quit, 2.27.74 |
| surface area, 2.28.102 | property transfer via alignment, 2.28.110.3 |
| polarization charge, 3.7.2, 5.8.13 | r_2out, 2.16.31 |
| postscript, 2.18.23 | r_out, 2.16.30 |
| potential surface coloring, 5.8.13 | radii.electrostatic, 2.28.108 |
| pov-ray, 2.27.102.37 | van der Waals, 2.28.108 |
| pow, 2.28.34 | rainbow, 2.28.28.1 |
| precision, 2.28.124.2 | ramachandran faq, 3.3.3 |
| predictSeq, 2.29.60 | how to, 3.3.3 |
| order, 2.28.127 | profile, 2.27.76.34 |
| randomSeed, 2.15.18 | prosite, 2.27.76.35 |
| randomize, 2.15.18, 2.27.75 | rarray, 2.27.76.36 |
| angles, 2.27.75.1 | sarray, 2.27.76.37 |
| coordinates, 2.27.75 | sequence, 2.27.76.7, 2.27.76.38 |
| torsions, 2.27.75 | database, 2.27.76.38.1 |
| rarray, 2.27.22.6, 2.28.49.1, 2.28.110.2, 5.8.11 | smiles, 2.27.76.42 |
| properties, 2.28.110.4 | stack, 2.27.76.39 |
| rdBlastOutput, 2.29.67 | string, 2.27.76.40 |
| rdSeqTab, 2.29.68 | table, 2.27.76.41 |
| reaction, 2.27.59.32 | csv, 2.27.76.41 |
| group file, 2.27.50 | html, 2.27.76.43 |
| read, 2.27.76 | mmcif, 2.27.76.44 |
| FILTER, 2.27.76.5 | mol, 2.27.76.46 |
| alignment, 2.27.76.11 | mol2, 2.27.76.45 |
| all, 2.27.76.6 | trajectory, 2.27.76.30 |
| binary, 2.27.76.2 | and save a fragment, 2.27.76.30.1 |
| color, 2.27.76.12 | write, 2.27.76.30.1 |
| column, 2.27.76.47 | unix, 2.27.76.9 |
| comp_matrix, 2.27.76.13 | cat, 2.27.76.10 |
| conf, 2.27.76.14 | variable, 2.27.76.48 |
| csd, 2.27.76.15 | view, 2.27.76.49 |
| csv, 2.27.76.41 | vrestraint, 2.27.76.50 |
| database, 2.27.76.16 | type, 2.27.76.51 |
| drestraint, 2.27.76.17 | with filter, 2.27.76.5 |
| type, 2.27.76.18 | readMolNames, 2.22.10 |
| entries from database, 2.27.76.7 | readcomp_matrix, 2.27.76.13 |
| factor, 2.27.76.19 | reading external tool output, 2.27.59.1 |
| from file, 2.27.76.1 | from standard input, 2.27.76.40 |
| string, 2.27.76.4 | pdb from ftp, 2.18.18 |
| fromstring, 2.27.76.4 | web, 2.18.19 |
| ftp http, 2.27.76.8 | restraint, 2.27.76.50 |
| gamess, 2.27.76.20 | real, 5.8.14 |
| grob, 2.27.76.21 | array, 5.8.11 |
| html, 2.27.76.3 | shell variables, 2.16 |
| file, 2.27.76.3 | space refinement, 2.27.59.30 |
| iarray, 2.27.76.22 | reals, 2.16 |
| index, 2.27.76.23 | rebel, 2.15.5, 5.8.13 |
| table, 2.27.76.7 | rebuild molcart index, 2.27.7.9 |
| library, 2.27.76.24 | recalculate dependent values, 2.27.7.2 |
| mmff, 2.27.76.25 | values, 2.27.1.1.1 |
| librarymmff, 2.27.76.25 | receptor, 3.13.1.1 |
| map, 2.27.76.26 | preparation, 3.13.1.1 |
| matrix, 2.27.76.27 | redefine hydrogen coordinates, 2.27.81.22 |
| mol, 2.17.13, 2.27.76.7, 2.27.76.28 | references, 4 |
| mol2, 2.27.76.7, 2.27.76.29 | refineModel, 2.29.65 |
| object, 2.27.76.31 | reflections, 2.21.5.27 |
| parray, 2.27.76.31.1 | refresh view, 2.27.23.2 |
| pdb, 2.21.14.3, 2.27.76.32 | refs, 4.1 |
| sequence, 2.27.76.33 | regexp, 2.9, 2.28.78 |
| syntax, 2.9.1 | number, 2.28.59.5 |
| regression, 2.27.49 | table, 2.28.146.3 |
| regul, 2.29.66 | property averaging, 2.28.134.2 |
| regular expression, 2.9, 2.28.62.3, 2.28.78 | calculation, 2.28.56 |
| filter, 2.27.76.1 | proximity, 2.28.79.7 |
| expression, 2.28.114.3 | ranges, 2.8.11 |
| regularization, 2.15.7, 2.27.60.4, 5.8.15 | selection, 2.17.21 |
| procedure, 3.8.3 | as string, 2.28.142.7 |
| rejectAction, 2.19.18 | function, 2.28.115 |
| relational database, 2.28.135 | table, 3.14.4.1 |
| relative accessible area of atoms, 2.19.1 | tethering, 2.27.81.58 |
| release notes, 1.1 | user field, 2.28.47.1 |
| remarkObj, 2.29.69 | residue_selections, 2.8.11 |
| remove expression tags, 2.28.165 | selecting, 2.8.7 |
| file, 2.27.22.9 | resizing, 2.28.61 |
| trailing blanks, 2.28.164 | restraints, 2.14, 2.27.81.58 |
| removing html tags, 2.27.76.43 | torsion, 2.27.81.69 |
| outliers, 2.28.164 | return, 2.27.78 |
| rename, 2.27.77 | reverse complement, 2.28.126.1 |
| chemicals, 2.27.81.40 | lighting, 2.27.81.35 |
| file, 2.27.77.3 | normals, 2.27.81.35 |
| molcart, 2.27.77.2 | reversing order, 2.28.59.2 |
| object, 2.27.77.1 | rgb, 5.8.17 |
| system, 2.27.77.3 | matrix, 2.28.28 |
| atom, 2.27.77.1 | ribbon, 5.8.18 |
| molecule, 2.27.77.1 | bullets, 2.21.5.6 |
| residue, 2.27.77.1 | ribbonColorStyle, 2.19.20 |
| reorder, 2.27.65.6 | ribbonStyle, 2.19.21 |
| alignment sequences, 2.27.102.1 | right join, 2.27.48 |
| array, 2.28.127 | rigid chemical superposition, 2.27.89 |
| objects, 2.27.83.3 | ring, 2.28.118 |
| replace matching array element, 2.28.114.1 | sampling, 3.13.2.3 |
| without interpretation, 2.28.114.2 | templates, 2.27.81.7 |
| replacing scaffold in a library, 2.27.63.1 | rocking, 2.27.23.5 |
| reproducible randomness, 2.15.18 | root mean square deviation, 2.28.124.2 |
| reroot, 2.27.18.4 | rotate, 2.27.79 |
| selections, 3.3.6 | grob, 2.27.79.2 |
| resLabelShift, 2.16.32 | object, 2.27.79.1 |
| resLabelStyle, 2.19.19 | view, 2.27.79.3 |
| reserved names, 2.22 | rotation, 2.27.23.5 |
| residue, 2.27.13.1, 5.8.16 | angle, 2.28.17 |
| alignment, 2.27.81.58 | rounding a real, 2.28.142 |
| conservation, 2.28.110.5 | output, 2.27.82.41 |
| contact area matrix, 2.28.79.7 | rsWeight, 2.16.33 |
| areas, 2.28.7.1 | rs_, 2.8.7 |
| field, 2.27.81.29 | run script, 2.27.8 |
| gap, 2.21.5.6, 2.21.5.7 | running a docking job, 3.13.2.7 |
| label, 2.27.3.1 | dock job, 3.13.2.5 |
| library file, 2.30.20 | script, 3.13.2.6 |
| name, 2.28.70 | script from html, 5.9.2 |
| s_alignment_rainbow, 2.18.1 | inside ICM, 5.9.2 |
| s_blastdbDir, 2.18.2 | name, 5.9.2 |
| s_editor, 2.18.3 | image generation, 2.27.23.3 |
| s_entryDelimiter, 2.18.4 | scripting molecular movements, 3.2.4 |
| s_errorFormat, 2.18.5 | sdf, 2.27.102.23 |
| s_fieldDelimiter, 2.18.6 | file, 2.27.76.45, 2.27.76.46, 2.27.81.40, 2.27.102.11, 2.28.142.2, 5.8.3 |
| s_helpEngine, 2.18.7 | to chem-table, 2.28.97 |
| s_icmPrompt, 2.18.10 | search for chemical pattern, 2.28.49.3 |
| s_icmhome, 2.18.8, 3.1.2.1 | pdb headers, 3.4.5 |
| s_imageViewer, 2.18.11 | prosite, 3.4.1 |
| s_inxDir, 2.18.9 | sequence pattern, 2.27.34.8 |
| s_javaCodeBase, 2.18.12 | searchObjSegment, 2.29.72 |
| s_labelHeader, 2.18.13 | searchPatternDb, 2.29.70 |
| s_lib, 2.18.14 | searchPatternPdb, 2.29.71 |
| s_logDir, 2.18.15 | searchSeqDb, 2.29.73 |
| s_out, 2.18.16 | searchSeqFullPdb, 2.29.75 |
| s_pdbDir, 2.18.17 | searchSeqPdb, 2.29.74 |
| s_pdbDirFtp, 2.18.18 | searchSeqProsite, 2.29.76 |
| s_pdbDirWeb, 2.18.19 | searchSeqSwiss, 2.29.77 |
| s_printCommand, 2.18.21 | searches and alignments, 3.4 |
| s_projectDir, 2.18.20 | second moments, 2.28.149 |
| s_prositeDat, 2.18.22 | secondary structure derivation from 3D, 2.27.5.1 |
| s_psViewer, 2.18.23 | segMinLength, 2.15.19 |
| s_reslib, 2.18.24 | segment, 5.9.4 |
| s_skipMessages, 2.18.25 | select, 2.27.80 |
| s_sysCp, 2.18.26 | atoms by number of bonded atoms, 2.28.125.3 |
| s_sysLs, 2.18.27 | of the fixed torsions, 2.28.125.2 |
| s_sysMv, 2.18.28 | by bfactor, 2.28.125.7 |
| s_sysRm, 2.18.29 | center of mass, 2.28.125.14 |
| s_tempDir, 2.18.30 | coordinates, 2.28.125.7 |
| s_translateString, 2.18.31 | iarray, 2.28.125 |
| s_userDir, 2.18.32 | length, 2.28.125.13 |
| s_usrlib, 2.18.33 | occupancy, 2.28.125.7 |
| s_webEntrezLink, 2.18.34 | user field, 2.28.125.7 |
| s_webViewer, 2.18.35 | chemical, 2.27.80.1 |
| s_xpdbDir, 2.18.36 | lines, 2.27.76.1 |
| sa23, 3.3 | tether partners, 2.28.125.12 |
| sampling grid, 2.28.177.2 | vw partners, 2.28.125.12 |
| sarray, 2.27.22.6, 5.9.1 | selectMinGrad, 2.16.34 |
| transformation in place, 2.27.94.1 | selectSphereRadius, 2.16.35 |
| save print, 3.2.6 | selected stack conformations, 2.27.22.16 |
| sdf file, 2.27.102.11 | selecting by b-factor, 2.28.125 |
| saving graphics to album, 2.27.59.20 | y z, 2.28.125 |
| image, 2.27.102.35 | columns, 5.10.1 |
| scaffolds, 2.27.50 | from clusters, 3.14.6.3 |
| scoring, 3.13.1.4 | neighboring elements, 2.28.89 |
| screen X, 2.28.175 | residues, 3.3.6 |
| coordinates, 2.28.175 | saving, 2.28.59.4 |
| script, 2.28.87.4, 5.9.2 | selection, 2.8, 2.28.125, 2.28.125.6 |
| file name, 2.28.48 | elements, 2.8.4 |
| functions, 2.8.10 | sequenceLine, 2.15.21 |
| gap patching, 2.28.125, 2.28.125.11 | sequences, 3.4 |
| level, 2.8, 2.28.167 | not in alignments, 2.27.22.22 |
| levels, 2.8.2 | set, 2.27.81 |
| simplification, 2.28.125.11 | alternative atom, 2.27.81.15 |
| transfer, 2.28.125, 2.28.142.7 | area, 2.27.81.1 |
| type, 2.8 | atom, 2.27.81.2 |
| types, 2.8.1 | background image, 2.27.81.3 |
| variable, 2.22.11 | bfactor, 2.27.81.4 |
| atoms, 2.8.8 | biological symmetry, 2.27.81.54 |
| functions, 2.8.10 | bond topology, 2.27.81.6 |
| molecules, 2.8.6 | type, 2.27.81.5 |
| objects, 2.8.5 | and formal charges, 2.27.81.6 |
| output, 2.22.14 | cartesian, 2.27.81.7 |
| residues, 2.8.7 | chain, 2.27.81.8 |
| torsions, 2.8.9 | charge, 2.27.81.9 |
| variables, 2.8.9 | formal, 2.27.81.10 |
| selections, 2.27.81.29 | mmff, 2.27.81.11 |
| in molecular objects, 2.8 | chargemmff, 2.27.81.11 |
| seq_ali_project, 2.28.142.5 | chiral, 2.27.81.12 |
| sequence, 2.28.158, 2.28.159, 5.9.3 | color, 2.27.81.13 |
| alignment, 2.28.5.1, 2.29.2 | comment, 2.27.81.14, 2.27.81.15 |
| intro, 1.4.3.3 | sequence, 2.27.81.16 |
| analysis intro, 1.4.3 | comp_matrix, 2.27.81.17 |
| assembly, 2.27.41.2 | current map, 2.27.81.38 |
| belongs to alignment, 2.28.62 | object, 2.27.81.41 |
| conservation, 2.28.124.5 | directory, 2.27.81.18 |
| distance, 2.28.125 | drestraint, 2.27.81.19 |
| matrix from alignment, 2.28.79.8 | type, 2.27.81.20 |
| dotplot, 1.4.3.2 | electrostatic radii, 2.27.81.67 |
| from pdb, 2.27.59.34 | error, 2.27.81.28 |
| identity, 2.29.8 | field, 2.27.81.29 |
| intro, 1.4.3 | name, 2.27.81.30 |
| modification, 2.28.165 | font, 2.27.81.31 |
| neighbor, 2.28.87.3 | grob, 2.27.81.32 |
| parray, 5.8.3.2 | foreground, 2.27.81.33 |
| pattern, 5.8.4 | format, 2.27.81.34 |
| position correspondence, 2.28.146.3 | grob, 2.27.81.35 |
| positional weights, 2.27.81.1 | coordinates, 2.27.81.35 |
| redundancy removal, 2.27.41.2 | label, 2.27.81.35 |
| search, 2.27.34.2 | group, 2.27.81.53 |
| selection, 2.27.22.22 | column, 2.27.81.21 |
| structure alignment, 2.29.1 | hydrogen, 2.27.81.22 |
| to alignment transfer, 2.28.110.3 | key, 2.27.81.36 |
| type, 5.9.3 | label, 2.27.81.37 |
| sequence-alignment mapping, 2.28.142.4, 2.28.142.5 | 3d label, 2.27.81.37.4 |
| sequence-structure alignment, 2.28.5.1 | chemical, 2.27.81.37.3 |
| output format, 2.15.20, 2.15.21 | distance, 2.27.81.37.1 |
| sequenceBlock, 2.15.20 | table, 2.27.81.37.2 |
| sequenceColorScheme, 2.19.22 | map, 2.27.81.38 |
| molecular variables, 2.27.81.71 | setResLabel, 2.29.78 |
| name, 2.27.81.40 | setcomp_matrix, 2.27.81.17 |
| sequence, 2.27.81.40.1 | setting conf properties, 2.27.81.51 |
| object, 2.27.81.41 | setvs_var, 2.27.81.71 |
| occupancy, 2.27.81.42 | sfWeight, 2.16.36 |
| plane, 2.27.81.43 | sh24, 3.4 |
| property, 2.27.81.44, 2.27.81.45 | shadows, 2.21.5.28 |
| chemical view, 2.27.81.45 | shell, 3.1, 5.9.5 |
| radii graphical, 2.27.81.74 | intro, 1.7.1 |
| randomSeed, 2.27.81.46 | progression, 2.27.70 |
| randomize, 2.27.81.46 | warning message, 2.28.176 |
| resolution, 2.27.81.47 | shineStyle, 2.19.23 |
| site, 2.27.81.23 | shininess, 2.16.37 |
| residue, 2.27.81.25 | show, 2.27.82, 2.27.82.35 |
| slide, 2.27.81.26 | alias, 2.27.82.6 |
| sstructure backbone, 2.27.81.49 | aliases, 2.27.82.6 |
| sequence, 2.27.81.50 | alignment, 2.27.82.7 |
| to sequence, 2.27.81.50 | area, 2.27.82.8 |
| stack, 2.27.81.51 | atom, 2.27.82.9 |
| energy, 2.27.81.51, 2.27.86.1 | type, 2.27.82.10 |
| stereo, 2.27.81.48 | atoms, 2.27.82.9 |
| swiss, 2.27.81.52 | clash, 2.27.82.11 |
| name, 2.27.81.52 | color, 2.27.82.12 |
| symmetry, 2.27.81.55 | column, 2.27.82.13 |
| bio, 2.27.81.54 | comp_matrix, 2.27.82.14 |
| crystal, 2.27.81.53 | database, 2.27.82.15 |
| group, 2.27.81.53 | drestraint, 2.27.82.16 |
| to a torsion, 2.27.81.55 | type, 2.27.82.17 |
| table, 2.27.81.56 | energy, 2.27.82.18 |
| terms, 2.27.81.57 | gradient, 2.27.82.19 |
| tether, 2.27.81.58 | hbond, 2.27.82.20 |
| append, 2.27.81.59 | exact, 2.27.82.21 |
| texture, 2.27.81.27 | hbondexact, 2.27.82.21 |
| type, 2.27.81.60 | html, 2.27.82.22 |
| mmff, 2.27.81.65 | iarray, 2.27.82.23 |
| molecule, 2.27.81.63 | integer, 2.27.82.24 |
| object, 2.27.81.62 | key, 2.27.82.3 |
| property, 2.27.81.61 | label, 2.27.82.25 |
| sequence, 2.27.81.64 | library, 2.27.82.26 |
| variable grid, 2.27.81.72 | link, 2.27.82.27 |
| variablegrid, 2.27.81.72 | logical, 2.27.82.28 |
| view, 2.27.81.68 | map, 2.27.82.4 |
| vrestraint, 2.27.81.69 | mol, 2.27.82.29 |
| vrestraintvs_var, 2.27.81.70 | mol2, 2.27.82.30 |
| radii, 2.27.81.66 | molecule, 2.27.82.31 |
| vwelradii, 2.27.81.67 | molecules, 2.27.82.5 |
| vwradii, 2.27.81.66 | object, 2.27.82.32 |
| window, 2.27.81.73 | pdb, 2.27.82.33 |
| xstick, 2.27.81.74 | pharmacophore type, 2.27.82.49 |
| radii, 2.27.81.74 | preferences, 2.27.82.34 |
| residue, 2.27.82.36 | to chem-table element, 2.28.97 |
| type, 2.27.82.37 | smooth alignment, 2.28.134.3 |
| residuetype, 2.27.82.37 | interpolation, 2.27.86.3 |
| segment, 2.27.82.38 | map, 2.28.134.4 |
| sequence, 2.27.82.39 | rarray, 2.28.134.1 |
| shell variable, 2.27.82.2 | surface, 2.29.85 |
| site, 2.27.82.1 | soap, 2.25 |
| stack, 2.27.82.40 | soft trim, 2.28.164 |
| svariable, 2.27.82.2 | solubility, 2.28.102 |
| table, 2.27.82.41 | solvation, 2.19.24 |
| as database, 2.27.82.15 | energy, 2.16.36, 2.19.24 |
| term, 2.27.82.42 | solvent accessible area, 2.15.22 |
| tethers, 2.27.82.43 | surface, 2.21.5.47, 2.21.5.48, 2.27.82.8 |
| version, 2.27.82.44 | sort, 2.27.83, 2.27.83.3 |
| volume, 2.27.82.47 | array, 2.27.83.1 |
| map, 2.27.82.48 | arrays, 2.27.83.1 |
| volumemap, 2.27.82.48 | molecules, 2.27.83.4 |
| vrestraint, 2.27.82.45 | object, 2.27.83.3 |
| type, 2.27.82.46 | stack, 2.27.83.5 |
| vrestraints, 2.27.82.45 | table, 2.27.83.2 |
| showcomp_matrix, 2.27.82.14 | sortSeqByLength, 2.29.79 |
| showing weak hydrogen bonds, 2.21.5.19 | space transformations, 2.28.162 |
| side chain, 2.29.87 | sparse atoms, 2.21.14.2 |
| flexibility, 2.29.87 | spawn background job, 2.27.59.1 |
| sigma level, 2.21.7.5 | special values, 2.28.154 |
| signal recognition measure, 2.29.21 | specificity, 2.28.124.2 |
| similar chains, 2.28.125.13 | split, 2.27.84 |
| similarity, 2.27.34.9, 2.27.34.10 | column values, 2.27.84.4 |
| simple expressions, 2.9.1.1 | grob, 2.27.84.1 |
| string substitution, 2.28.114.2 | group, 2.27.84.2 |
| simplify mesh structure, 2.27.15.1 | object, 2.27.84.5 |
| simulation duration, 2.16.44 | to molecules, 2.27.84.5 |
| temperature, 2.16.43 | table, 2.27.84.3 |
| intro, 1.4.2 | cell, 2.27.84.4 |
| site, 2.27.11.2, 5.9.6 | to columns, 2.27.84.3 |
| arrows, 2.27.81.23 | tree, 2.27.84.6 |
| table, 2.28.146.8 | splitting selection, 2.8.11 |
| by residue selection, 2.27.22.23 | sprintf, 2.27.85 |
| sequences, 2.28.146.8 | sql, 2.27.73, 2.27.81.39, 2.28.43.1, 2.28.87.10, 2.28.90.5, 2.28.167.2 |
| sixthe power, 2.19.5 | sqlite, 3.5.1 |
| skin, 5.9.7 | sqrt, 2.28.34 |
| intro, 1.4.1.2 | square matrix to element pairs, 2.28.146.5 |
| slide, 2.27.1.3, 2.28.132, 5.9.14 | ssThreshold, 2.16.38 |
| transition time, 2.27.23.21 | ssWeight, 2.16.39 |
| slides, 2.28.175 | ssbond, 5.4.5 |
| slideshow, 2.27.1.3, 2.27.23.21, 2.28.132 | ssearch, 2.15.16, 2.27.87 |
| sln, 5.9.8 | ssearchStep, 2.16.40 |
| smallest set of smallest rings, 2.28.118 | ssign sstructure segment, 2.27.5.2 |
| smarts, 2.28.62.1 | stack, 2.15.11, 2.15.12, 2.15.14, 2.19.6, 2.27.81.51, 2.27.86, 2.27.86.1, 2.28.59.6, 2.28.146.6, 5.3.11, 5.9.9 |
| smiles, 2.24 | bin size, 2.27.14 |
| extension, 2.27.4.2 | minimize, 2.27.90 |
| multiplication, 2.27.4.2 | support, 1.3 |
| merge, 3.7.7 | suppressing view changes, 2.27.23.21 |
| standard chemical form, 2.27.63.4 | surface, 5.9.15 |
| deviation, 2.28.121 | accessibility, 2.27.82.8 |
| standardize chemical, 2.27.63 | area, 2.29.3, 5.9.15 |
| startup, 3.1.2.3 | charge, 5.8.13 |
| static RMSD, 2.28.141 | color, 2.27.81.13 |
| and dynamic hbonds, 2.21.5.18 | dot density, 2.21.5.47 |
| stereo, 2.21.5.44, 2.27.29, 2.27.81.48 | energy, 2.19.24 |
| reconstruction, 3.8.9 | mesh, 2.28.177.2 |
| stereoisomer, 2.27.29 | point selection, 2.28.177 |
| stereoisomers, 2.17.16 | term, 2.16.36 |
| stick, 5.9.10 | surfaceAccuracy, 2.15.22 |
| store, 2.27.86 | surfaceMethod, 2.19.24 |
| conf, 2.27.86, 2.27.86.1 | surfaceTension, 2.16.41 |
| frame, 2.27.86.3 | svariable, 5.9.12 |
| image, 2.27.59.20 | swapping protein fragments, 3.8.7 |
| stack object, 2.27.86.2 | swiss, 2.27.81.52 |
| torsion type, 2.27.86 | swissFields, 2.22.9 |
| strength of hydrogen bond, 2.27.23.14 | swissprot, 2.27.81.23 |
| string, 5.9.11 | symmetrization of a matrix, 2.28.79.3 |
| array, 2.28.123, 5.9.1 | symmetry, 2.28.162 |
| filtering, 2.28.164 | faq, 3.10 |
| inversion, 2.28.142.1 | group, 2.15.2 |
| label, 2.27.23.12 | sys, 2.27.91 |
| matching, 2.9, 2.28.78 | system, 5.11.2 |
| variables, 2.18 | command, 2.27.91 |
| strings, 2.18 | copy, 2.18.26 |
| strip, 2.27.88 | file move, 2.18.28 |
| struct, 2.28.87.2 | list file, 2.18.27 |
| structural alignment, 2.27.3.4, 2.28.5.2 | remove, 2.18.29 |
| optimization, 2.27.34.1 | table, 2.27.22.4, 2.27.81.44, 2.27.81.45, 5.10.1 |
| superposition, 2.27.3.4 | actions, 5.10.2.4 |
| analysis, 3.3 | column, 2.28.87 |
| comparison, 2.28.22.2 | format, 2.27.81.34 |
| factors, 3.11.1 | plot, 2.27.59.31 |
| structure, 3.11.1 | transformations, 2.28.92 |
| sub-alignment to selection, 2.28.116 | creation, 2.27.41.3 |
| sub-matrix, 2.28.79.2 | display style, 5.10.1 |
| subalignment, 2.28.5.3 | expression, 5.10.2 |
| submap, 2.28.75 | from matrix, 2.28.146.4 |
| subroutine, 2.27.58 | grid view, 5.10.1 |
| subset, 2.6 | of atoms and distances, 2.28.146.9 |
| substring, 2.28.78, 2.28.142, 2.28.142.1 | operations, 5.10.2.1 |
| substructure, 2.27.34.9, 2.27.34.10 | plot, 5.10.2.3 |
| search, 2.27.34.4 | principal component analysis, 2.27.59.28 |
| superimpose, 2.21.14, 2.27.89 | print, 2.27.82.41 |
| faq, 3.3.1 | row, 2.27.65.4 |
| how to, 3.3.1 | label mark, 2.27.81.37.2 |
| selected row numbers, 2.28.62 | transforming points, 2.28.177.4 |
| subset, 5.10.2.2 | translate, 2.27.95 |
| show html, 2.27.100.1 | transparency, 2.27.81.35, 5.5.3 |
| targa, 5.10.3 | background, 2.27.102.35 |
| tautomer, 2.27.30 | grob, 2.27.23.11 |
| tempCycle, 2.16.43 | grobs, 2.21.5.49 |
| tempLocal, 2.16.42 | tree, 2.27.59.35, 2.28.87.5 |
| temperature, 2.16.43 | cluster, 2.10 |
| variations in optimizer, 2.16.43 | delete, 2.27.22.33 |
| template docking, 3.13.2.8 | label format, 2.28.87.5 |
| tensor product of two vectors, 2.28.79 | representatives, 2.10.1 |
| terminal font, 2.30.14 | trim string array, 2.27.94.1 |
| window, 2.27.42 | trimming grid map values, 2.28.164 |
| terms, 2.14 | true positives, 2.28.124.2 |
| hydrogen bonding, 2.16.18 | truncate alignment, 2.27.59.33 |
| test, 2.27.92 | values, 2.28.164 |
| binary, 2.27.92.1 | tsv table format, 2.27.76.41 |
| testing if argument exists, 2.28.52 | two alignments, 2.28.38.11 |
| tether, 2.27.102.9, 5.10.4 | txdoc browser, 2.27.76.3 |
| text, 2.28.78 | type, 2.28.167.1 |
| search in tables, 2.28.49.2 | tzMethod, 2.19.25 |
| to script, 5.9.2 | tzWeight, 2.16.47 |
| texture, 5.5.3 | uncharge functional groups, 2.27.63.2 |
| tga, 5.10.3 | unclip, 2.27.23.2 |
| then, 2.27.93 | underline, 2.27.81.31.1 |
| thread to template, 2.27.60.4 | undisplay, 2.27.96 |
| threading, 2.28.5.1 | graphics, 2.27.97 |
| letter code, 2.28.158, 2.28.159 | window, 2.27.97 |
| thumbnails, 2.28.61 | unfix, 2.27.98 |
| tif, 5.10.5 | unique, 2.27.13.1, 5.11.1 |
| time, 2.28.35 | atomic order, 2.27.59.36 |
| timeLimit, 2.16.44 | column values, 2.27.41.4 |
| tolFunc, 2.16.46 | names, 2.28.87 |
| tolGrad, 2.16.45 | new object name, 2.28.87 |
| topological psa, 5.8.12 | smiles, 2.27.59.36 |
| torsion rmsd comparison, 2.27.14.2 | unix, 2.27.91, 5.11.2 |
| torsions, 2.28.90.3 | grep, 2.27.76.1 |
| tpsa, 5.8.12 | unlink alignments, 2.27.22.20 |
| trajectory, 2.27.57.2, 2.27.86, 2.27.86.3, 5.7.14 | sequences, 2.27.22.20 |
| file, 2.30.17 | variables, 2.27.22.20 |
| frame writing, 2.27.23.17 | update database, 2.27.63.5 |
| smoothing, 2.27.23.17 | updates, 1.1 |
| transform, 2.27.94, 2.27.94.2 | updating atom pairs, 2.17.27 |
| general, 2.27.94 | url string parsing, 2.28.146 |
| grob coordinates, 2.27.94.2 | user atom display, 2.21.5.2 |
| molecules, 2.27.94.2 | environment, 3.1.2.2 |
| sarray, 2.27.94.1 | menu, 2.21.10.1 |
| transformation, 5.10.6 | user-defined properties, 2.27.81.29 |
| vector, 5.10.6 | solvation parameters, 2.28.7 |
| and symmetry, 3.10 | user_startup, 3.1.2.4 |
| guide, 3 | vwMethod, 2.19.28 |
| v_, 2.8.1 | vwSoftMaxEnergy, 2.16.52 |
| van der Waals surface, 2.21.5.48 | wait, 2.27.99 |
| varLabelStyle, 2.19.26 | warning, 2.21.14.2 |
| variable restraint, 2.27.81.69 | message, 2.28.176 |
| selection, 2.8.9 | suppression, 2.17.28 |
| vector, 2.28.90.6 | water.dielectric constant, 2.16.12 |
| dot product, 2.28.172.1 | waterRadius, 2.16.53 |
| length, 2.28.91 | wavefront format, 2.27.59.11 |
| product, 2.28.172.1 | web, 2.27.100 |
| transformation, 2.28.92 | table, 2.27.100.1 |
| vertex, 2.27.13.4.2 | webEntrezOption, 2.19.29 |
| connectivity, 2.28.79.12 | weighted rmsd, 2.21.14 |
| vertexes, 2.27.13.4.2 | while, 2.27.101 |
| vertical alignment block, 2.27.59.33 | whole string, 2.28.114.1 |
| workspace, 2.21.8.5 | window averaging, 2.28.134.1 |
| vertices, 2.27.13.4.2 | layout, 2.28.142.8 |
| vicinity, 2.16.48 | width and height, 2.28.175 |
| video, 2.27.102.30 | windowSize, 2.15.23 |
| view point, 2.28.175 | movie, 2.27.102.30 |
| restoration, 2.28.65 | wire, 5.11.7 |
| transition, 2.27.81.68 | wireBondSeparation, 2.16.54 |
| views, 5.9.14 | wireStyle, 2.19.30 |
| virtual, 5.11.3 | workspace, 2.27.97 |
| chemistry, 2.27.63, 2.28.90.4 | write, 2.27.102 |
| field, 2.27.7.2 | album, 2.27.102.21 |
| ligand screening, 3.13, 3.13.1, 3.13.2, 3.13.3 | alignment, 2.27.102.1 |
| intro, 1.4.2.7 | array, 2.27.102.8 |
| visitsAction, 2.19.27 | table, 2.27.102.8 |
| vls, 3.13, 3.13.1, 3.13.2, 3.13.3 | binary, 2.27.102.2 |
| cluster, 3.13.3.6 | blast, 2.27.102.24 |
| faq, 3.13.3 | column, 2.27.102.12 |
| intro, 1.4.2.7 | database, 2.27.102.13 |
| job queueing, 3.13.3.6 | drestraint, 2.27.102.14 |
| overview, 3.13.1 | type, 2.27.102.15 |
| parallelization, 3.13.3.5 | factor, 2.27.102.16 |
| results, 3.13.3.8 | gamess, 2.27.102.17 |
| scores storage, 3.13.3.7 | grob, 2.27.102.18 |
| threshold, 3.13.3.2 | html, 2.27.102.19 |
| vls_intro, 3.13.3.1 | iarray, 2.27.102.3 |
| volume, 5.11.4 | image, 2.27.102.20 |
| vrestraint, 5.11.5 | chemical, 2.27.102.22 |
| file, 2.30.23 | parray, 2.27.102.21 |
| type, 5.11.6 | index, 2.27.102.23 |
| file, 2.30.22 | blast, 2.27.102.24 |
| vs_, 2.8.9 | library, 2.27.102.25 |
| vs_out, 2.22.14 | map, 2.27.102.26 |
| vwCutoff, 2.16.49 | matrix, 2.27.102.6 |
| vwExpand, 2.16.50 | model, 2.27.102.27 |
| vwExpandDisplay, 2.16.51 | mol, 2.27.102.28 |
| molcart, 2.27.102.7 | |
| movie, 2.27.102.30 | |
| object, 2.27.102.31 | |
| parray, 2.27.102.33 | |
| simple, 2.27.102.32 | |
| pdb, 2.27.102.34 | |
| png, 2.27.102.35 | |
| postscript, 2.27.102.36 | |
| pov, 2.27.102.37 | |
| povray, 2.27.102.37 | |
| project, 2.27.102.2 | |
| rarray, 2.27.102.4 | |
| sarray, 2.27.102.5 | |
| sequence, 2.27.102.38 | |
| session, 2.27.102.39 | |
| several array, 2.27.102.8 | |
| simple object, 2.27.102.32 | |
| stack, 2.27.102.40 | |
| table, 2.27.102.10 | |
| mol, 2.27.102.11 | |
| with links, 2.27.102.19 | |
| tether, 2.27.102.9 | |
| tethers, 2.27.102.9 | |
| trajectory, 2.27.23.17 | |
| vs_var, 2.27.102.41 | |
| writevs_var, 2.27.102.41 | |
| xml, 2.28.78 | |
| xplor format, 2.27.76.26 | |
| xrMethod, 2.19.31 | |
| xrWeight, 2.16.55 | |
| xray density to rectangular energy map, 2.27.59.30 | |
| xstick, 5.11.8 | |
| xyz morphing, 3.8.8 | |
| zega, 5.11.9 | |
| intro, 1.4.3.6 | |
| |, 2.11.3 | |
|