ICM Manual v.3.7
by Ruben Abagyan,Eugene Raush and Max Totrov Copyright © 2013, Molsoft LLC May 16 2013
|
Index
| &, 2.12.3 | CCP4, 5.6.6 |
| 2D labels, 2.27.54.1 | CONSENSUS, 2.21.1 |
| to 3D, 3.16 | CONSENSUSCOLOR, 2.21.2 |
| trees, 2.27.61.36 | CONSENSUS_strength, 2.17.9 |
| smooth, 2.28.139.2 | Cad, 2.28.23, 2.28.23.1, 2.28.23.2 |
| 3D chemical builder, 1.4.2.8 | Cad1, 2.28.23.1 |
| font size, 2.27.23.12 | Cadalign, 2.28.23.2 |
| label, 2.27.23.12, 2.27.85.36 | Ceil, 2.28.24 |
| labels, 2.27.54.1 | Cell, 2.28.25 |
| mol file, 2.29.84 | Charge, 2.28.26 |
| plots intro, 1.4.3.7 | Chemical, 2.28.27 |
| smoothing, 2.28.139.3 | Cluster, 2.28.28 |
| superposition, 2.29.22 | Collada, 5.5.3 |
| transformations, 2.27.98.2 | Collection, 2.28.28.1 |
| tree, 2.27.61.36 | Color, 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, 5.5.3 | Connolly surface, 5.8.7 |
| =, 2.12.1 | Consensus, 2.28.30 |
| A, 5.1 | Corr, 2.28.31 |
| APF distance, 2.28.129 | Cos, 2.28.32 |
| Abs, 2.28.1 | Cosh, 2.28.33 |
| Acc, 2.28.2 | Count, 2.28.34 |
| Acos, 2.28.3 | CubicRoot, 2.28.35 |
| Acosh, 2.28.4 | D, 5.4 |
| Adobe, 2.19.23 | DAE, 5.5.3 |
| Align, 2.28.5 | DE, 2.27.34.2 |
| sequence, 2.28.5.1 | DNA 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, 2.28.7.1 | Date, 2.28.36 |
| Asin, 2.28.8 | Deletion, 2.28.37 |
| Asinh, 2.28.9 | Descriptor, 2.28.38 |
| Ask, 2.28.10 | Det, 2.28.39 |
| Askg, 2.28.11 | Disgeo, 2.28.40 |
| Atan, 2.28.12 | Distance, 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, 2.21.5.6 | GRID, 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, 2.21.5.13 | GROB, 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, 2.26 | I_out, 2.22.4 |
| plot, 2.27.61.31 | Iarray, 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, 2.28.55 | Icm Options, 2.1 |
| Getenv, 2.28.56 | IcmSequence, 2.28.63 |
| Gradient, 2.28.57 | Image, 2.28.64 |
| Graphics, 1.4.1 | collection, 3.9.2.1 |
| Grob, 2.28.58 | frame by frame, 3.9.2.2 |
| Group, 2.28.59 | Index, 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, 5.8.5 | Indexx, 2.28.66 |
| intro, 1.7.1 | Info, 2.28.68 |
| script, 2.27.8 | image, 2.28.69 |
| ICMFF force field, 2.29.78 | model, 2.28.70 |
| ICMHOME, 3.1.2.1 | Insertion, 2.28.67 |
| shell variable, 3.1.2.1 | Integer, 2.28.71 |
| IMAGE, 2.21.9 | Integral, 2.28.72 |
| bondLength2D, 2.21.9.15 | Interrupt, 2.28.73 |
| color, 2.21.9.8 | Introduction, 1 |
| compress, 2.21.9.9 | JSON, 2.27.80.55 |
| gammaCorrection, 2.21.9.7 | LIBRARY, 2.21.10 |
| generateAlpha, 2.21.9.10 | men, 2.21.10.1 |
| lineWidth, 2.21.9.3 | res, 2.21.10.2 |
| lineWidth2D, 2.21.9.14 | Label, 2.28.74 |
| orientation, 2.21.9.16 | Laplacian, 2.28.75 |
| paperSize, 2.21.9.17 | Latent, 2.28.179.3 |
| previewResolution, 2.21.9.13 | LatentVector, 2.28.179.3 |
| previewer, 2.21.9.12 | Length, 2.28.76 |
| printerDPI, 2.21.9.2 | LinearFit, 2.28.77 |
| quality, 2.21.9.1 | LinearModel, 2.28.78 |
| rgb2bw, 2.21.9.18 | Log, 2.28.79 |
| LogS, 2.28.107 | Next, 2.28.94, 2.28.94.1 |
| M_out, 2.22.5 | covalent neighbors, 2.28.94.1 |
| Mac, 3.14.6.2 | Nof, 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, 2.28.84.9 | Norm, 2.28.96 |
| grob connectivity, 2.28.84.12 | Normalize, 2.28.97 |
| histogram, 2.28.84.11 | NotInList, 2.28.98 |
| new, 2.28.84.1 | R, 5.7 |
| residue areas, 2.28.84.7 | OBJECT, 2.21.11 |
| comparison, 2.28.84.4 | Obj, 2.28.99 |
| stack, 2.28.84.10 | Occupancy, 2.28.100 |
| sub, 2.28.84.2 | PBS, 3.13.3.6 |
| symmetrical, 2.28.84.3 | PLOT, 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, 2.20.5 | PLS, 2.28.95.6 |
| Name, 2.28.92 | error, 2.28.129.3 |
| chemical, 2.28.92.6 | models, 2.28.129.3 |
| property, 2.28.92.1 | Parray, 2.28.102 |
| close sequence, 2.28.92.3 | Parray-object, 2.28.102 |
| conf, 2.28.92.7 | Path, 2.28.101 |
| image, 2.28.92.11 | Pattern, 2.28.103 |
| molcart, 2.28.92.12 | Pi, 2.28.104 |
| object parray, 2.28.92.10 | Polar Surface Area, 5.7.12 |
| sequence, 2.28.92.8 | Potential, 2.28.105 |
| soap, 2.28.92.2 | Power, 2.28.106 |
| string, 2.28.92.4 | Predict, 2.28.107 |
| tree, 2.28.92.5 | Probability, 2.28.108 |
| Namex, 2.28.93 | Profile, 2.28.109 |
| image, 2.28.93.2 | Property, 2.28.110 |
| sequence, 2.28.93.1 | Putarg, 2.28.111 |
| Newick tree format, 2.28.149.4 | Putenv, 2.28.112 |
| REBEL, 3.7.2 | SSSR, 2.28.123 |
| faq, 3.7.2 | S_out, 2.22.8 |
| file, 2.27.51 | Sarray, 2.28.128 |
| RNA topology, 2.21.5.13 | index, 2.28.128.1 |
| R_2out, 2.22.7 | Score, 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, 2.28.115.3 | Select, 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, 2.28.119.4 | Select_by atom numbers, 2.28.130.10 |
| exact, 2.28.119.1 | Select_by_sequence, 2.28.130.13 |
| regexp, 2.28.119.3 | Select_by_text, 2.28.130.9 |
| simple, 2.28.119.2 | Select_lists, 2.28.130.12 |
| Res, 2.28.120, 2.28.121 | Select_patching, 2.28.130.11 |
| Resali, 2.28.121 | Select_projection, 2.28.130.8 |
| Resolution, 2.28.122 | Sequence, 2.28.131 |
| Rfactor, 2.28.124 | array, 2.28.131.2 |
| Rfree, 2.28.125 | Sequence(dna reverse), 2.28.131.1 |
| Ring, 2.28.123 | Shuffle, 2.28.132 |
| Rmsd, 2.28.126 | Sign, 2.28.133 |
| of subset, 2.21.14 | Simulations, 1.4.2 |
| Rot, 2.28.127 | Sin, 2.28.134 |
| S, 5.8 | Sinh, 2.28.135 |
| SAR analysis, 2.27.61.27, 2.27.88.2 | Site, 2.28.136 |
| SC, 2.27.34.2 | Slide, 2.28.137 |
| SEQUENCE.restoreOrigNames, 2.21.12.15 | Smiles, 2.28.138 |
| SITE, 2.21.13 | Smooth, 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, 2.21.13.3 | Smoothrs, 2.28.139.3 |
| labelStyle, 2.21.13.4 | SoapMessage, 2.28.145 |
| labelWrap, 2.21.13.5 | SolveQuadratic, 2.28.140 |
| showSeqSkip, 2.21.13.6 | SolveQubic, 2.28.141 |
| wrapComment, 2.21.13.7 | Sort, 2.28.146 |
| SLN notation, 2.28.149.10 | Sphere, 2.21.14.3, 2.28.144 |
| SMARTS, 2.24, 2.27.10, 2.28.95.2 | Split, 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, 2.28.147.1 | Tointeger, 2.28.159 |
| Sql, 2.28.142 | Tolower, 2.28.160 |
| Sqrt, 2.28.143 | Toreal, 2.28.161 |
| Srmsd, 2.28.148 | Torsion, 2.28.162 |
| Sstructure, 2.28.150 | Tostring, 2.28.163 |
| String, 2.28.149, 2.28.149.8 | Toupper, 2.28.164 |
| alternative, 2.28.149.7 | Tr123, 2.28.165 |
| date, 2.28.149.2 | Tr321, 2.28.166 |
| mol, 2.28.149.3 | Trace, 2.28.167 |
| selection, 2.28.149.8 | Trans, 2.28.168 |
| slide gui, 2.28.149.9 | Transform, 2.28.169 |
| substring, 2.28.149.1 | Transpose, 2.28.170 |
| chemical formula, 2.28.149.10 | Trim, 2.28.171 |
| Sum, 2.28.151 | sequence, 2.28.172 |
| chemical, 2.28.151.1 | Turn, 2.28.173 |
| image, 2.28.151.2 | Type, 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, 2.21.14 | Unique, 2.28.175 |
| edsDir, 2.21.14.1 | Unix, 2.28.176 |
| membrane, 2.21.14.2 | Uppsala, 2.29.42 |
| minSphereCubeSize, 2.21.14.3 | server, 2.29.43 |
| pdbReadNmrModels, 2.21.14.4 | V_, 2.8.1 |
| smilesXyzSeparator, 2.21.14.5 | Value, 2.28.177 |
| superimposeMaxDeviation, 2.21.14.8 | soap, 2.28.178 |
| superimposeMaxIterations, 2.21.14.6 | Vector, 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, 2.21.14.10 | Vectorproduct, 2.28.179.1 |
| tsWeight, 2.21.14.11 | Vectorsymmetrytransformation, 2.28.179.2 |
| writePdbRenameRes, 2.21.14.12 | Version, 2.28.180 |
| Table, 2.28.153 | View, 2.28.182 |
| alignment numbers, 2.28.153.3 | Volume, 2.28.181 |
| distance, 2.28.153.9 | WEBAUTOLINK, 2.21.16 |
| matrix, 2.28.153.4 | WEBLINK, 2.21.15 |
| model, 2.28.153.7 | Warning, 2.28.183 |
| chem, 2.28.153.8 | Wavefront format, 2.27.80.21 |
| pairs, 2.28.153.5 | XML, 2.10 |
| stack, 2.28.153.6 | Xyz, 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, 2.28.41.6 | ZEGA, 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, 2.30.2 | alignMethod, 2.20.2 |
| icm, 2.30.2 | alignMinCoverage, 2.17.2 |
| a_, 2.8.1 | alignMinMethod, 2.17.2 |
| abbr, 1.6 | alignOldStatWeight, 2.17.3 |
| abbreviations, 1.6 | alignSS, 2.29.1 |
| absolute to cell x y z, 2.28.184.3 | alignTwoSequences, 2.29.2 |
| accFunction, 2.22.2 | aligned residues, 2.28.121 |
| acceptor, 3.6.1 | alignment, 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, 2.29.13 | alignment_as_text, 2.28.149.4 |
| in place, 2.12.4 | aliphatic amines, 2.27.66.2 |
| to slideshow, 2.27.1.3 | all, 5.1.2 |
| admet selection, 3.13.3.4 | torsions table, 3.3.11 |
| advanced chemical search, 3.6 | alpha, 2.21.5.54, 2.27.85.39, 5.1.3 |
| operations, 2.12.6 | channel, 2.21.9.10 |
| ops, 2.12.6 | alternative flag, 2.27.85.17 |
| ali_seq_project, 2.28.149.5 | amber, 5.1.4 |
| alias, 2.27.2 | amino acid, 2.19.24, 2.28.165, 2.28.166 |
| align, 2.27.3 | labels, 2.27.3.1 |
| 3D, 2.27.3.4 | and, 2.12.3 |
| faq, 3.3.2 | angles, 2.28.95.3 |
| heavy, 2.27.3.5 | angular hbond dependence, 2.21.5.23 |
| how to, 3.3.2 | animated story, 5.8.15 |
| chemical, 2.27.84.1 | animation, 2.27.23.5, 2.27.23.6, 3.9 |
| fragments, 2.27.3.3 | annotation, 2.27.85.25 |
| append, 5.1.5 | atomSingleStyle, 2.20.4 |
| a tables, 2.27.1.4 | atomic 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, 2.27.1.1 | attenuation by occupancy, 2.27.61.25 |
| an element, 2.12.4 | auc enrichment, 2.29.21 |
| menu items, 2.21.10.1 | auto saving log, 2.20.10 |
| representations to a slide, 2.27.23.21 | autoSavePeriod, 2.16.1 |
| rows to matrix, 2.27.1.2 | avi, 2.27.106.30 |
| area under curve, 2.29.21 | axis, 5.1.8 |
| arguments, 2.27.60 | axisLength, 2.17.4 |
| arithmetic operations, 2.12.2 | background, 2.28.29.2 |
| arithmetics, 2.12 | ball, 2.27.85.2, 5.2.2 |
| array, 2.27.68.4, 5.1.6, 5.7.3.1 | base, 5.2.1 |
| assignment, 2.12.1 | pair diagram, 2.21.5.13 |
| derivative, 2.28.139.1 | basis set, 2.27.80.20, 2.27.106.17 |
| overlap, 2.28.129.1 | batch chemical processing, 3.1.2.5 |
| parray, 2.27.22.29 | docking, 3.13.2.5 |
| size, 2.28.95 | beta, 5.2.3 |
| subset, 2.6 | bfactor circles, 2.21.5.2 |
| arrow from selection, 2.29.36 | biased probability monte carlo, 2.27.67 |
| length, 2.27.85.25 | binary 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, 2.22.12 | binding 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, 2.27.5.1 | biological 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, 5.1.7 | blast files, 2.27.106.24 |
| code file, 2.30.4 | blast-formatted database, 2.27.34.3, 2.27.106.24 |
| coordinates, 2.28.184.1 | blending, 2.27.106.30 |
| flickering, 2.27.85.3 | images, 2.28.151.2 |
| label font, 2.30.15 | blob, 5.8.11 |
| labels, 2.27.85.2 | bold, 2.27.85.35.1 |
| name, 2.28.74 | bond 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, 2.28.174 | bonded atoms, 2.28.94.1 |
| user field, 2.28.50.1 | born radii, 2.27.86.9 |
| atomLabelStyle, 2.20.3 | boundary element, 5.2.4 |
| box, 2.28.21 | chain breaks, 2.21.5.6, 2.21.5.7, 2.28.130.1 |
| break, 2.27.6 | symbol, 2.27.85.9 |
| brightness, 2.21.5.30 | change 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, 2.27.7.2 | changing local stick radii, 2.27.85.82 |
| faq, 3.8.1 | surface dot size, 2.21.5.51 |
| from string, 2.27.7.8 | channel, 2.21.14.2 |
| helix, 3.10.5 | charge, 5.3.2 |
| how to, 3.8.1 | compounds, 2.27.66.2 |
| hydrogen, 2.27.7.9 | change, 2.27.85.10 |
| loop, 2.27.7.6 | chem formula, 2.28.149.10 |
| model, 2.27.7.5, 2.27.106.9 | chemSuper3D, 2.29.22 |
| molcart, 2.27.7.10 | chemical, 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, 2.27.85.20 | chemistry, 2.23, 2.28.27 |
| cell axis vectors, 2.28.184.7 | chiral isomer generation, 2.27.29 |
| specific icm commands, 5.9.2.4 | chirality, 2.18.16, 2.27.29 |
| center, 2.11.1, 2.27.9 | choosing 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, 2.27.10 | column, 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, 2.28.41.7 | combinatorial 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, 2.28.65.9 | combining plots, 2.27.61.31 |
| centers, 2.11.1 | receptor and ligand stacks, 2.27.4.2 |
| selection, 2.28.65.9 | command, 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, 2.20.5 | commands, 2.20.10, 5.1.1 |
| cnWeight, 2.17.6 | communication protocols, 2.25 |
| coil, 5.3.4 | comp, 2.28.98 |
| collection, 2.10, 5.3.6 | comp_matrix, 2.27.85.19, 2.27.86.16, 5.3.11 |
| color, 2.21.5.30, 2.27.11 | compare, 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, 2.16.5 | compareMethod, 2.20.6 |
| hydrophobicity, 3.2.10 | comparing two sarrays, 2.28.98 |
| pharmacophore, 2.27.12 | comparison operations, 2.12.5 |
| potential, 2.29.25 | complete view, 2.28.137 |
| shape depth, 2.27.13 | compound accessibilities, 3.14.4.1 |
| chemical, 2.27.12, 2.27.84.1 | array, 2.23 |
| file, 2.30.15 | compress, 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, 2.27.13.4.1 | compressed table view, 2.27.85.23 |
| label, 2.27.13.5 | conditional buttons, 5.5.5 |
| map, 2.27.13.6 | string, 2.28.149.7 |
| by value, 2.27.23.16 | conf, 2.27.85.57, 2.27.106.40, 2.28.153.6, 5.3.12, 5.8.9 |
| confgen, 3.16 | convertObject, 2.29.13 |
| configuration, 2.30.14 | converting 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, 2.27.15.2 | cool, 2.29.40 |
| file, 2.30.7 | pictures, 2.21.5.27 |
| transition, 2.29.38 | cooling schedule, 2.17.43 |
| conformer storage, 2.27.59.5, 2.27.90.2 | coordinate frame, 2.17.4, 2.27.23.4 |
| conformers, 3.16 | coordinates, 2.21.14.5 |
| connect, 2.27.16 | copy, 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, 2.21.2 | correlation matrix, 2.28.156 |
| definitions, 2.21.1 | covalent bound count, 2.28.130.3 |
| consensusStrength, 2.17.7 | neighbors, 2.28.94.1 |
| conservation, 2.28.115.5, 2.28.129.6 | covalently attached molecule, 2.28.94.1 |
| constant, 2.5 | cpk, 5.3.13 |
| constants, 2.5 | create a covalent bond, 2.27.61.2 |
| contact areas, 2.28.84 | pharmacophore, 2.29.85 |
| continue, 2.27.17 | creating a local patch object, 2.27.18.2 |
| contour surfaces, 2.21.7.5 | credits, 4.5 |
| contouring density, 2.27.61.14 | crypt, 2.27.20 |
| contrast, 2.21.5.30 | crystal 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, 3.13.2 | crystallographic 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, 2.27.92 | crystallography, 2.28.122 |
| and reroot, 2.27.18.4 | csv format, 2.27.80.43 |
| chemical 3D, 2.29.81 | csym, 1.4.2.4 |
| and optmimize geometry, 2.29.82 | cube, 2.21.14.2 |
| comp, 2.27.18.1 | current, 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, 2.29.83 | cursor action, 5.9.2.4 |
| macro, 2.29.13 | custom field, 2.27.85.48 |
| pdb, 3.8.2 | interaction, 2.27.86.37 |
| to 3D, 2.27.85.8 | customization, 3.1.2 |
| ICM object, 2.29.84 | and paste chemicals, 2.21.9.14, 2.21.9.15 |
| iarray, 2.28.159 | cyclic temperature protocol, 2.17.43 |
| icm-object, 2.27.18 | cylinder, 2.21.14.2 |
| integer, 2.28.159 | cz32, 4.5 |
| convert2Dto3D, 2.29.83 | data visualization, 2.27.61.36 |
| convert3Dto3D, 2.29.84 | database, 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, 2.27.22.2 | deleting sites by number, 2.27.22.23 |
| array element, 2.27.22.6 | delphi, 2.29.25 |
| index, 2.27.22.6 | density 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, 2.27.22.14 | densityCutoff, 2.17.10 |
| boundary, 2.27.22.15 | dependent columns, 2.27.1.1.1 |
| chemical, 2.27.22.35 | depth cueing, 2.27.13.7, 5.4.2 |
| fragment, 2.27.22.35 | depth-cueing, 2.17.14 |
| selection, 2.27.22.35 | desolvation, 2.20.24 |
| class, 2.27.22 | detecting bad covalent geometry, 2.27.86.12 |
| conf, 2.27.22.16 | proximity, 2.28.41.7 |
| directory, 2.27.22.8 | dialog 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, 2.27.22.9 | dielConst, 2.17.11 |
| from array, 2.27.22.6 | dielConstExtern, 2.17.12 |
| hydrogen, 2.27.22.11 | dielectric constant, 2.17.11 |
| label, 2.27.22.18, 2.27.22.19 | diff, 2.28.98 |
| chemical, 2.27.22.19 | dihedral angle, 2.27.61.19 |
| link, 2.27.22.20 | calculation, 3.3.10 |
| map, 2.27.22.21 | directory, 2.27.22.8, 2.27.61.5, 2.28.128 |
| molcart, 2.27.22.3 | display, 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, 2.27.23.13 | dots, 2.27.74 |
| label, 2.27.23.15 | dotted surface, 2.21.5.53 |
| map, 2.21.5.10, 2.27.23.16 | double click action, 5.9.2.4 |
| model, 2.27.23.1 | drestraint, 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, 2.27.23.18 | drop, 2.17.13 |
| rotate, 2.27.23.5 | drug, 2.10 |
| site, 2.27.23.19 | ds3D, 2.29.31 |
| skin, 2.27.23.20 | dsCellBox, 2.29.15 |
| slide, 2.27.23.21 | dsChem, 2.29.17 |
| stack, 2.27.23.6 | dsCustom, 2.29.18 |
| string, 2.27.23.22 | dsPocket, 2.29.28 |
| surface, 2.27.23.20 | dsPropertySkin, 2.29.19 |
| area, 2.21.5.2 | dsPrositePdb, 2.29.24 |
| tethers, 2.27.23.23 | dsRebel, 2.16.5, 2.29.25 |
| trajectory, 2.27.23.17 | dsSeqPdbOutput, 2.29.26 |
| volume, 2.27.23.24 | dsSkinLabel, 2.29.27 |
| window, 2.3, 2.27.23.25 | dsStackConf, 2.29.29 |
| distance, 2.21.5.21, 5.4.3 | dsVarLabels, 2.29.30 |
| averaging, 2.20.5 | dsXyz, 2.29.32 |
| contact-based, 2.28.23, 2.28.23.1 | dump database, 2.27.106.7 |
| geometry, 5.4.4 | dynamic gui, 5.5.5 |
| matrix, 2.28.153.5, 2.29.8 | ecepp, 5.5.1 |
| between stack conformations, 2.28.84.10 | edit, 2.27.24 |
| restraint, 5.4.6 | files, 2.21.14.1 |
| file, 2.30.9 | electro intro, 1.4.2.9 |
| type file, 2.30.8 | electroMethod, 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, 5.4.5 | electrostatic 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, 3.13.2.1 | ellipsoid, 2.28.156 |
| result viewing, 2.29.28 | elseif, 2.27.25 |
| simple models, 3.14.3 | endfor, 2.27.26 |
| timing, 3.13.1.3 | endif, 2.27.27 |
| with template, 3.13.2.6 | endmacro, 2.27.28 |
| documents, 5.5.8 | endwhile, 2.27.32 |
| dominant color, 2.28.29.2 | energetics, 3.7 |
| donor, 3.6.1 | function, 2.21.14.3 |
| plot intro, 1.4.3.2 | terms, 2.15 |
| entropy of alignment, 2.28.129.6 | fast Fourier transform, 2.27.61.24 |
| atom, 2.27.18.4 | sequence search, 2.27.34.3 |
| enumerate, 2.27.29, 2.27.30, 2.27.31 | fasta, 2.21.12.15, 5.5.2 |
| chiral, 2.27.29 | format, 2.27.106.1 |
| library, 2.27.31 | feature table, 5.8.6.1 |
| tautomer, 2.27.30 | in sequences, 2.27.85.25 |
| enumeration, 2.28.27 | ffMethod, 2.20.11 |
| eps files, 2.19.23 | field name, 2.28.92.2 |
| error SOAP services, 2.28.45 | file, 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, 2.27.34.10 | files, 2.30 |
| match, 2.28.119.1 | filling volume, 2.21.5.8 |
| example scripts, 3.14 | filter, 2.27.34.10, 2.27.59.3 |
| exit, 2.27.33 | functions, 5.5.4 |
| exitSeslogStyle, 2.20.10 | filtering table rows, 5.5.4 |
| expanding substructure match, 2.27.85.66 | find, 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, 5.8.14 | findFuncMin, 2.29.33, 2.29.34 |
| false negatives, 2.28.129.3 | findFuncZero, 2.29.35 |
| family, 2.27.85.35.1 | findSymNeighbors, 2.29.16 |
| faq, 1.3 | find_related_sequences, 2.29.33 |
| cheminformatics, 3.14.6 | finding long covalent bonds, 2.28.130.1 |
| chemsuper, 3.14.5 | to density, 2.20.7 |
| mac gui preferences, 3.14.6.2 | fix, 2.27.35 |
| molcart dump, 3.14.6.3 | fixed branches, 2.28.130.2 |
| query, 3.14.6.1 | flattening 3D molecule, 2.29.17 |
| multiple chem overlay, 3.14.5.1 | flow control, 2.13 |
| residue table, 3.14.4.1 | fog, 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, 2.27.36 | greedy matching, 2.9.1.4 |
| fork, 2.27.37, 2.28.65.1 | grid energy, 2.27.86.21 |
| formal charge, 2.21.5.17, 5.3.2 | potentials, 2.27.61.25 |
| formatdb, 2.27.106.24 | grob, 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, 2.27.60 | group, 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, 2.22.3 | grouping table by a column, 2.27.85.23 |
| gapOpen, 2.17.16 | gui, 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, 2.29.38 | gvim text editor, 5.8.2 |
| generating movie images, 3.9.2.1 | gzip files, 2.27.15.3 |
| genomics, 1.4.3.1 | hash, 2.10, 5.3.6 |
| clustering, 2.27.42.2 | table, 5.3.6 |
| intro, 1.4.3.1 | haze, 2.17.14 |
| geometry optimization, 2.27.62.1 | hb, 2.17.18 |
| started, 1.7 | hbCutoff, 2.17.18 |
| getting data from outside, 2.25 | hbond, 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, 2.17.17 | hbondMinStrength, 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, 2.28.65.5 | header, 2.27.1.1 |
| selection, 2.28.130.5 | helical 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, 2.30.29 | interactive docking, 1.4.2.8 |
| tab, 2.30.25 | interatomic potential, 2.27.85.48, 2.27.86.37 |
| tot, 2.30.26 | interface 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, 2.29.14 | intermolecular bond, 2.27.68.3 |
| icmMacroShape, 2.29.86 | internal coordinate file, 2.30.21 |
| icmPmfProfile, 2.29.23 | coordinates, 2.8.9 |
| icmPocketFinder, 2.29.87 | positional restraints, 5.9.4 |
| icmscript, 2.27.80.3 | interpolate, 2.28.29.1 |
| arguments, 2.28.55 | interpolation, 2.28.29.1 |
| if, 2.27.46 | interruptAction, 2.20.14 |
| ignoring swiss secondary structure, 2.22.9 | inverting array order, 2.28.62.2, 2.28.115.2 |
| illegal smiles, 2.28.65.2 | italic, 2.27.85.35.1 |
| image, 3.2.6 | iterative overlay, 2.27.93 |
| annotation, 3.2.5 | superposition, 2.21.14, 2.27.94 |
| center, 3.2.8 | join, 2.27.49 |
| format, 5.9.3 | tables, 2.27.49 |
| high quality, 3.2.2 | keep, 2.27.48 |
| parray, 5.7.3.3 | kernel models quality, 2.28.129.3 |
| resolution, 3.2.2 | mapping, 2.30.15 |
| rotation, 3.2.3 | kmz, 5.5.3 |
| implicit continuous solvation, 2.30.13 | l_antiAlias, 2.18.1 |
| solvation, 2.27.85.68 | l_autoLink, 2.18.2 |
| imposing tether, 2.27.85.64, 2.27.85.65 | l_bpmc, 2.18.3 |
| place, 2.12.4 | l_breakRibbon, 2.18.4 |
| ops, 2.12.4 | l_bufferedOutput, 2.18.5 |
| incidence, 2.28.84.12 | l_bug, 2.18.6 |
| increasing the number of shell variables, 2.30.14 | l_caseSensitivity, 2.18.7 |
| increment charge, 2.27.85.10 | l_commands, 2.18.8 |
| index expressions, 2.6 | l_confirm, 2.18.9 |
| in array, 2.28.65.4 | l_easyRotate, 2.18.10 |
| substring, 2.28.65.3 | l_info, 2.18.11 |
| table, 2.27.106.23 | l_minRedraw, 2.18.12 |
| entry, 2.28.128.1 | l_neutralAcids, 2.18.13 |
| sdf-file path, 2.28.101 | l_out, 2.18.14 |
| indices of labeled table rows, 2.28.65.6 | l_print, 2.18.15 |
| selected table rows, 2.28.65.5 | l_racemicMC, 2.18.16 |
| infinity, 2.28.161 | l_readMolArom, 2.18.17 |
| info, 2.27.47 | l_showAccessibility, 2.18.18 |
| molcart, 2.27.47.1 | l_showMC, 2.18.19 |
| inner join, 2.27.49 | l_showMinSteps, 2.18.20 |
| insert rows, 2.27.1.4 | l_showResCodeInSelection, 2.18.21 |
| integer, 5.6.2 | l_showSites, 2.18.23 |
| array, 2.28.62, 5.6.1 | l_showSpecialChar, 2.18.22 |
| output, 2.16.4 | l_showSstructure, 2.18.24 |
| shell variables, 2.16 | l_showTerms, 2.18.26 |
| interaction cutoff, 2.18.27 | l_showWater, 2.18.25 |
| l_warn, 2.18.28 | listUpdateThreshold, 2.17.20 |
| l_wrapLine, 2.18.29 | literature, 4.1 |
| l_writeStartObjMC, 2.18.30 | load, 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, 2.27.50.1 | loadEDS, 2.29.42 |
| left join, 2.27.49 | loadEDSweb, 2.29.43 |
| triangle of a matrix, 2.28.84.3 | local, 3.5.1 |
| library to replacement groups, 2.27.61.27, 2.27.88.2 | logarithm, 2.28.79 |
| ligand based screening, 3.15 | logical, 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, 3.13.2 | logical_ops, 2.12.3 |
| intro, 1.4.2.6 | logicals, 2.18 |
| editing, 1.4.2.8 | long axes, 2.28.156 |
| editor, 2.29.37 | loop 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, 2.21.12.5 | lower case, 2.28.160 |
| in 2D chemicals, 2.21.9.14 | ma29, 3.11 |
| lineWidth, 2.17.19 | macro, 2.27.60, 5.6.5 |
| linear chemical notation, 2.24 | macro_def, 5.6.5 |
| regression, 2.28.78 | main ICM references, 4.2 |
| group, 2.27.51 | concepts, 3.10.1 |
| internal variables of molecular object, 2.27.52 | make, 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, 2.27.61.12 | mapAtomMargin, 2.17.22 |
| potential, 2.27.61.13 | mapSigmaLevel, 2.17.21 |
| skin, 2.27.61.14 | mapping 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, 2.27.61.21 | mass-spectrometry functions, 2.27.29, 2.27.30, 2.27.31 |
| map, 2.27.61.22 | matching chemicals, 2.28.65.2 |
| cell, 2.27.61.23 | hydrogens, 2.27.85.66 |
| factor, 2.27.61.24 | matrix, 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, 2.27.61.27 | maxColorPotential, 2.16.5 |
| pca, 2.27.61.28 | maxMemory, 2.16.6 |
| peptide bond, 2.27.61.29 | movie, 3.9.2 |
| plot, 2.27.61.31 | mcBell, 2.17.23 |
| reaction, 2.27.61.32 | mcJump, 2.17.24 |
| sequence, 2.27.61.34 | mcShake, 2.17.25 |
| alignment, 2.27.61.33 | mcStep, 2.17.26 |
| from alignment, 2.27.61.33 | mean force, 2.27.85.48, 2.27.86.37 |
| torsion, 2.27.61.19 | membrane, 2.21.14.2 |
| tree, 2.27.61.35 | memorizing positions, 3.2.4 |
| object, 2.27.61.36 | menu, 2.27.63 |
| unique, 2.27.61.37 | script, 3.1.3 |
| makeAxisArrow, 2.29.36 | merge 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, 5.6.6 | merge2, 3.8.7 |
| aa property to sequence, 2.28.115.1 | mergePdb, 2.29.90 |
| averaging, 2.28.139.5 | several chemical, 2.28.151.1 |
| calculation, 2.27.61.24 | merging into one molecule, 2.27.68.3 |
| conversion, 2.27.61.30 | mesh, 2.28.181 |
| file, 2.30.16 | point radius, 2.21.5.18 |
| fitting, 2.20.7 | score, 3.13.3.3 |
| format, 5.6.6 | mfMethod, 2.20.15 |
| mean value, 2.28.87 | mfWeight, 2.17.27 |
| min value, 2.28.88 | mimel, 5.6.8 |
| name, 2.28.80 | mimelDepth, 2.17.28 |
| operations, 5.6.6 | mimelMolDensity, 2.17.29 |
| transformations, 2.28.139.5 | minNumGrad, 2.27.62 |
| trimming, 2.28.22 | minTetherWindow, 2.16.7 |
| value sigma, 2.28.126 | minimization exit criteria, 2.27.62 |
| on atoms, 2.27.85.33 | minimize, 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, 2.27.62.4 | molecule, 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, 5.6.10 | monte carlo, 2.27.67 |
| mmff, 5.6.9 | montecarlo, 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, 2.16.8 | moprphing, 2.29.38 |
| mncalls, 2.16.9 | more, 5.6.13 |
| mncallsMC, 2.16.10 | morph, 2.27.23.6 |
| mnconf, 2.16.11 | to tether target, 2.29.38 |
| mnhighEnergy, 2.16.12 | morph2tz, 2.29.38 |
| mnreject, 2.16.13 | morphing, 2.27.23.6, 2.27.85.64, 2.27.85.65, 2.27.90.3 |
| mnvisits, 2.16.14 | mouse controls, 2.3 |
| model reliability, 2.29.23 | file, 2.27.106.30 |
| modify, 2.27.64 | move, 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, 3.2.4 | movie, 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, 3.5.2 | moving selection to another object, 2.28.130.8 |
| molecular, 2.28.54, 5.7.3.1 | mpeg, 2.27.106.30 |
| arrays, 5.7.3 | ms_, 2.8.6 |
| manipulations, 3.8 | multi center drestraint, 2.20.5 |
| modifications, 3.8.5 | multi-part molecule, 2.27.18.2 |
| object, 5.7.1 | multicore, 2.28.65.1 |
| objects, 2.14 | multiline input, 2.27.80.4 |
| surface, 2.27.86.9, 5.8.7 | multiple 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, 2.28.149.3 | obsolete, 2.17.51 |
| object file, 2.27.80.2 | occlusion shading, 2.27.13 |
| sequence alignment intro, 1.4.3.4 | octanol transfer, 2.28.107 |
| smiles file format, 2.27.80.44 | off, 2.27.80.21 |
| multiprocessor, 2.27.37 | format, 5.5.3 |
| mutate residue, 2.27.64 | oligonucleotide melting, 2.28.157 |
| mutating residue, 3.8.5 | on-line help, 2.27.44.1, 2.27.44.2 |
| mute, 5.6.15 | third, 2.28.35 |
| mysql, 2.27.16.1 | only, 5.7.2 |
| nLocalDeformVar, 2.16.15 | openGL window, 2.27.101 |
| nProc, 2.16.17 | operating system, 2.27.95, 2.28.180, 5.10.2 |
| nSsearchStep, 2.16.16 | optimal chemical superposition, 3.14.5.1 |
| name, 2.28.74 | optimization, 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, 2.28.88 | optimizeHbonds, 2.29.89 |
| neighbor joining, 2.27.61.36 | or, 2.12.3 |
| nested script, 5.8.2 | order, 2.27.68.6 |
| real array, 2.28.115 | original sequence names, 2.21.12.15 |
| nice, 2.29.39 | os_, 2.8.5 |
| image, 3.2.2 | other variables, 2.22 |
| non-redundant, 3.4.3 | out-of density atoms, 2.27.86.21 |
| normal distribution, 2.28.114 | output, 2.16.3 |
| normalize chemicals, 2.27.66.4 | overlay by atom pairs, 2.27.93 |
| defined, 2.28.161 | chemical substructure, 2.29.22 |
| nota, 1.5 | overview, 1.4 |
| notational conventions, 1.5 | pK shift, 3.7.3 |
| nproc, 2.27.37 | packing density, 3.3.8 |
| nucleotides, 2.19.24 | pair-distances, 2.27.22.6 |
| number, 2.16.17 | pairdistance parray, 2.21.5.21 |
| of dots, 2.21.5.52 | pairwise interactions, 2.27.85.48 |
| elements, 2.28.95 | panel layout, 2.21.8.5 |
| hydrogen bonds, 2.27.86.23 | paragraphs, 2.27.106.23 |
| molecules in objects, 2.28.130.4 | parallel, 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, 2.27.86.13 | parallelization, 2.28.65.1 |
| transfer from sequence, 2.27.3.1 | parameter list file, 3.14.6.2 |
| nvis, 2.28.62.6 | parray, 2.27.22.6, 5.7.3 |
| object, 2.27.13.1, 5.7.1 | parrayTo3D, 2.29.82 |
| parray, 5.7.3.1 | parrayToMol, 2.29.81 |
| properties, 2.27.85.32 | parse SOAP message, 2.28.178 |
| stack, 5.8.9 | parsing, 2.28.83 |
| to chemarray, 2.28.27 | web pages, 2.27.80.45 |
| user fields, 2.28.50.1 | partial 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, 2.27.99 | passing 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, 5.7.6 | pmf, 2.20.15 |
| file creation time, 2.28.36 | residue profile, 2.29.23 |
| files, 2.30.28 | pmf-file, 2.30.19 |
| format, 2.27.80.46 | pmffile, 2.30.19 |
| merge, 3.4.4 | png, 2.27.106.35, 5.7.5 |
| sequence generation, 3.4.3 | pocket, 2.29.28, 2.29.87, 3.13.1.1 |
| pdbDirStyle, 2.20.17 | point coordinates, 2.28.184.1 |
| peptide, 5.7.7 | size, 2.21.5.18 |
| docking, 3.12.5 | pointer array, 5.7.3 |
| folding, 1.4.2.1 | polar hydrogens, 2.21.5.29 |
| intro, 1.4.2.1 | surface area, 2.28.107 |
| personal gui controls, 3.1.2 | polarization charge, 3.7.2, 5.7.13 |
| setup, 3.1.2 | positional constraint, 2.21.14.10 |
| ph30, 3.12 | postscript, 2.19.23 |
| ph4, 5.7.8 | potential surface coloring, 5.7.13 |
| object faq, 3.6.1 | pov-ray, 2.27.106.37 |
| pharmacophore, 2.27.12, 3.5, 5.7.8 | pow, 2.28.35 |
| faq, 3.6 | precision, 2.28.129.3 |
| grid type definitions, 2.27.85.69 | predict, 2.27.72 |
| object, 3.6.1 | predictSeq, 2.29.60 |
| objects, 3.6 | prediction model, 2.28.78 |
| pharmacophores, 3.6 | quality, 2.28.129 |
| psi plot, 2.29.57 | score, 2.28.129 |
| pipe, 2.27.80.42 | preference, 2.20 |
| planar angle, 2.27.61.18 | preferences, 3.1.2.3 |
| plot, 2.27.70 | prepSwiss, 2.29.61 |
| 3D 2Dfunction, 3.12.3 | previous atom, 2.28.94.1 |
| shape, 3.12.4 | principal 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, 3.12.2 | print, 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, 2.29.53 | printMatrix, 2.29.62 |
| plotCluster, 2.29.55 | printPostScript, 2.29.63 |
| plotFlexibility, 2.29.54 | printTorsions, 2.29.64 |
| plotMatrix, 2.29.56 | printf, 2.27.75 |
| plotRama, 2.29.57 | problem, 3.14.6.2 |
| plotRose, 2.29.58 | processors, 2.16.17 |
| plotSeqDotMatrix, 2.29.51 | profile, 5.7.9 |
| plotSeqDotMatrix2, 2.29.52 | program overview, 1.4 |
| plotSeqProperty, 2.29.59 | progress bar, 2.27.74 |
| 3d, 1.4.3.7 | progression, 2.27.74 |
| plotting van der Waals, 3.7.1 | project setup, 3.13.2.2 |
| faq, 3.7.1 | projected alignment, 2.28.92.3 |
| pls, 2.27.50 | projecting surface charge, 3.7.2 |
| column contributions, 2.28.153.7, 2.28.153.8 | property, 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, 2.27.80.50 | rename, 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, 2.27.80.42 | renaming, 2.21.12.15 |
| pdb from ftp, 2.19.18 | reorder, 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, 5.7.11 | replace matching array element, 2.28.119.1 |
| shell variables, 2.17 | without interpretation, 2.28.119.2 |
| space refinement, 2.27.61.30 | replacing scaffold in a library, 2.27.66.1 |
| reals, 2.17 | reproducible randomness, 2.16.18 |
| rebel, 2.16.5, 5.7.13 | reroot, 2.27.18.4 |
| rebuild molcart index, 2.27.7.10 | selections, 3.3.6 |
| recalculate dependent values, 2.27.7.2 | resLabelShift, 2.17.32 |
| values, 2.27.1.1.1 | resLabelStyle, 2.20.19 |
| receptor, 3.13.1.1 | reserved names, 2.22 |
| preparation, 3.13.1.1 | residue, 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, 2.28.171 | residue_selections, 2.8.11 |
| removing html tags, 2.27.80.45 | selecting, 2.8.7 |
| outliers, 2.28.171 | resizing, 2.28.64 |
| preference, 2.27.81.4 | s_inxDir, 2.19.9 |
| restraining molecules to shapes, 2.21.14.10 | s_javaCodeBase, 2.19.12 |
| restraints, 2.15, 2.27.85.64, 2.27.85.65 | s_labelHeader, 2.19.13 |
| torsion, 2.27.85.77 | s_lib, 2.19.14 |
| return, 2.27.82 | s_logDir, 2.19.15 |
| reverse complement, 2.28.131.1 | s_out, 2.19.16 |
| lighting, 2.27.85.39 | s_pdbDir, 2.19.17 |
| normals, 2.27.85.39 | s_pdbDirFtp, 2.19.18 |
| reversing order, 2.28.62.2 | s_pdbDirWeb, 2.19.19 |
| rgb, 5.7.17 | s_printCommand, 2.19.21 |
| matrix, 2.28.29 | s_projectDir, 2.19.20 |
| ribbon, 5.7.18 | s_prositeDat, 2.19.22 |
| bullets, 2.21.5.6 | s_psViewer, 2.19.23 |
| diagram, 2.21.5.39, 2.21.5.40 | s_reslib, 2.19.24 |
| ribbonColorStyle, 2.20.20 | s_skipMessages, 2.19.25 |
| ribbonStyle, 2.20.21 | s_sysCp, 2.19.26 |
| right join, 2.27.49 | s_sysLs, 2.19.27 |
| rigid chemical superposition, 2.27.93 | s_sysMv, 2.19.28 |
| ring, 2.28.123 | s_sysRm, 2.19.29 |
| sampling, 3.16 | s_tempDir, 2.19.30 |
| templates, 2.27.85.8 | s_translateString, 2.19.31 |
| rocking, 2.27.23.5 | s_userDir, 2.19.32 |
| root mean square deviation, 2.28.129.3 | s_usrlib, 2.19.33 |
| roots, 2.28.140, 2.28.141 | s_webEntrezLink, 2.19.34 |
| rotate, 2.27.83 | s_webViewer, 2.19.35 |
| grob, 2.27.83.2 | s_xpdbDir, 2.19.36 |
| object, 2.27.83.1 | sa23, 3.3 |
| view, 2.27.83.3 | sampling grid, 2.28.184.2 |
| rotation, 2.27.23.5 | sarray, 2.27.22.6, 5.8.1 |
| angle, 2.28.17 | transformation in place, 2.27.98.1 |
| rounding, 2.28.115 | save print, 3.2.6 |
| a real, 2.28.149 | sdf file, 2.27.106.11 |
| output, 2.27.86.45 | saving graphics to album, 2.27.61.20 |
| rsWeight, 2.17.33 | image, 2.27.106.35 |
| rs_, 2.8.7 | scaffolds, 2.27.51 |
| run script, 2.27.8 | scoring, 3.13.1.4 |
| running a docking job, 3.13.2.5 | screen X, 2.28.182 |
| dock job, 3.13.2.4 | coordinates, 2.28.182 |
| script from html, 5.8.2 | script, 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, 2.19.4 | scripting molecular movements, 3.2.4 |
| s_errorFormat, 2.19.5 | sdf, 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, 2.19.10 | search 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, 2.28.156 | selections, 2.27.85.32 |
| secondary structure derivation from 3D, 2.27.5.1 | in molecular objects, 2.8 |
| schematic, 2.21.5.39 | selftether, 2.21.14.10, 5.9.4 |
| segMinLength, 2.16.19 | seq_ali_project, 2.28.149.6 |
| segment, 5.8.4 | sequence, 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, 2.28.62.4 | sequence-alignment mapping, 2.28.149.5, 2.28.149.6 |
| selection, 2.8, 2.28.130, 2.28.130.6 | sequence-structure alignment, 2.28.5.1 |
| elements, 2.8.4 | output format, 2.16.20, 2.16.21 |
| examples, 2.8.3 | sequenceBlock, 2.16.20 |
| functions, 2.8.10 | sequenceColorScheme, 2.20.22 |
| gap patching, 2.28.130, 2.28.130.11 | sequenceLine, 2.16.21 |
| level, 2.8, 2.28.174 | sequences, 3.4 |
| levels, 2.8.2 | not in alignments, 2.27.22.22 |
| simplification, 2.28.130.11 | set, 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, 2.27.86.16 | showcomp_matrix, 2.27.86.16 |
| database, 2.27.86.17 | showing weak hydrogen bonds, 2.21.5.22 |
| drestraint, 2.27.86.18 | side chain, 2.29.88 |
| type, 2.27.86.19 | flexibility, 2.29.88 |
| energy, 2.27.86.20 | sigma level, 2.21.7.5 |
| atom, 2.27.86.21 | signal recognition measure, 2.29.21 |
| gradient, 2.27.86.22 | similar chains, 2.28.130.13 |
| hbond, 2.27.86.23 | similarity, 2.27.34.9, 2.27.34.10 |
| exact, 2.27.86.24 | simple expressions, 2.9.1.1 |
| hbondexact, 2.27.86.24 | string substitution, 2.28.119.2 |
| html, 2.27.86.25 | simplified representation, 2.21.5.13 |
| iarray, 2.27.86.26 | mesh structure, 2.27.15.1 |
| integer, 2.27.86.27 | simulation duration, 2.17.44 |
| key, 2.27.86.4 | temperature, 2.17.43 |
| label, 2.27.86.28 | intro, 1.4.2 |
| library, 2.27.86.29 | site, 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, 2.27.86.33 | sixthe power, 2.20.5 |
| intro, 1.4.1.2 | sprintf, 2.27.89 |
| slide, 2.27.1.3, 2.28.137, 5.8.15 | sql, 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, 2.27.23.21 | sqlite, 3.5.1 |
| slides, 2.28.182 | sqrt, 2.28.35 |
| slideshow, 2.27.1.3, 2.27.23.21, 2.28.137 | square matrix to element pairs, 2.28.153.5 |
| sln, 5.8.8 | ssThreshold, 2.17.38 |
| smallest set of smallest rings, 2.28.123 | ssWeight, 2.17.39 |
| smart, 2.21.14.5 | ssbond, 5.4.5 |
| smarts, 2.28.65.2 | ssearch, 2.16.16, 2.27.91 |
| smiles, 2.21.14.5, 2.24 | ssearchStep, 2.17.40 |
| to chem-table element, 2.28.102 | ssign sstructure segment, 2.27.5.2 |
| smooth alignment, 2.28.139.4 | stack, 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, 2.28.171 | standard chemical form, 2.27.66.4 |
| solid sphere, 2.21.5.8 | deviation, 2.28.126 |
| solubility, 2.28.107 | standardization, 2.27.22.11 |
| solvation, 2.20.24, 2.21.14.2 | chemical, 2.27.66 |
| energy, 2.17.36, 2.20.24 | startup, 3.1.2.3 |
| solvent accessible area, 2.16.22 | static 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, 2.27.87.3 | stereo, 2.21.5.49, 2.27.29, 2.27.85.54 |
| array, 2.27.87.1 | reconstruction, 3.8.9 |
| arrays, 2.27.87.1 | stereo-specific hydrogens, 2.27.22.11 |
| molecules, 2.27.87.4 | stereoisomer, 2.27.29 |
| object, 2.27.87.3 | stereoisomers, 2.18.16 |
| stack, 2.27.87.5 | stick, 5.8.10 |
| table, 2.27.87.2 | store, 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, 2.28.161 | strength of hydrogen bond, 2.27.23.14 |
| specificity, 2.28.129.3 | string, 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, 2.27.88.4 | strings, 2.19 |
| table, 2.27.88.3 | strip, 2.27.92 |
| cell, 2.27.88.5 | struct, 2.28.92.2 |
| to columns, 2.27.88.3 | structural 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, 5.7.13 | targa, 5.9.3 |
| color, 2.27.85.15 | target coordinates, 5.9.4 |
| dot density, 2.21.5.52 | tautomer, 2.27.30 |
| energy, 2.20.24, 2.27.85.68 | tempCycle, 2.17.43 |
| mesh, 2.28.184.2 | tempLocal, 2.17.42 |
| point selection, 2.28.184 | temperature, 2.17.43 |
| term, 2.17.36 | variations in optimizer, 2.17.43 |
| surfaceAccuracy, 2.16.22 | template docking, 3.13.2.6 |
| surfaceMethod, 2.20.24 | tensor product of two vectors, 2.28.84 |
| surfaceTension, 2.17.41 | terminal font, 2.30.14 |
| svariable, 5.8.13 | window, 2.27.43 |
| swapping protein fragments, 3.8.7 | terms, 2.15 |
| swiss, 2.27.85.58 | hydrogen bonding, 2.17.18 |
| swissFields, 2.22.9 | test, 2.27.96 |
| swissprot, 2.27.85.25 | binary, 2.27.96.1 |
| symmetrization of a matrix, 2.28.84.3 | testing if argument exists, 2.28.55 |
| symmetry, 2.28.169 | tether, 2.21.14.10, 2.27.106.9, 5.9.4, 5.9.5 |
| faq, 3.10 | text, 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, 5.8.2 | texture, 5.5.3 |
| sys, 2.27.95 | tga, 5.9.3 |
| system, 5.10.2 | then, 2.27.97 |
| command, 2.27.95 | thread to template, 2.27.62.4 |
| copy, 2.19.26 | threading, 2.28.5.1 |
| file move, 2.19.28 | letter code, 2.28.165, 2.28.166 |
| list file, 2.19.27 | thumbnails, 2.28.64 |
| remove, 2.19.29 | tif, 5.9.6 |
| table, 2.27.22.4, 2.27.85.49, 2.27.85.50, 2.27.85.51, 5.9.1 | time, 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, 5.7.12 | unix, 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, 2.30.17 | unlink 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, 2.27.98.2 | update database, 2.27.66.5 |
| general, 2.27.98 | speadsheet, 2.27.1.1.1 |
| grob coordinates, 2.27.98.2 | updates, 1.1 |
| molecules, 2.27.98.2 | updating atom pairs, 2.18.27 |
| sarray, 2.27.98.1 | upper case, 2.28.164 |
| transformation, 2.28.115, 5.9.7 | url string parsing, 2.28.153 |
| vector, 5.9.7 | user 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, 2.27.99 | user-defined properties, 2.27.85.32 |
| transparency, 2.27.85.39, 5.5.3 | solvation parameters, 2.28.7 |
| background, 2.27.106.35 | user_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, 2.28.92.5 | v_, 2.8.1 |
| cluster, 2.11 | van der Waals surface, 2.21.5.53 |
| delete, 2.27.22.34 | varLabelStyle, 2.20.26 |
| label format, 2.28.92.5 | variable restraint, 2.27.85.77 |
| representatives, 2.11.1 | selection, 2.8.9 |
| trim string array, 2.27.98.1 | vector, 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, 2.21.14.10 | vertex, 2.27.13.4.2 |
| table format, 2.27.80.43 | connectivity, 2.28.84.12 |
| two alignments, 2.28.41.11 | vertexes, 2.27.13.4.2 |
| dimensional plot, 2.28.139.2 | vertical alignment block, 2.27.61.33 |
| txdoc browser, 2.27.80.3 | workspace, 2.21.8.5 |
| type, 2.28.174.1 | vertices, 2.27.13.4.2 |
| tzMethod, 2.20.25 | vicinity, 2.17.48 |
| tzWeight, 2.17.47 | video, 2.27.106.30 |
| uncharge functional groups, 2.27.66.2 | view 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, 2.27.100 | views, 5.8.15 |
| graphics, 2.27.101 | virtual, 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, 2.27.106.1 | writevs_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 | |
|