Oct 21 2010 Feedback.
Contents
 
Introduction
How To Guide
Getting Started
Molecular Graphics
Slides and Documents
ActiveICM
Movie Making
Sequences & Alignments
Protein Structure Analysis
Protein Superposition
Crystallographic Analysis
Homology & Modeling
3D Predict
Molecular Mechanics
Cheminformatics
Chemsitry Menu
Docking
Ligand Editor
Tables
Local Databases
FAQs
Tutorials
 
Index

Index

2D, 4.4.9, 15.2.21, 15.2.26, 16.7, 16.8, 16.14Docking, 21.3.27
     to 3D, 16.6Editor, 3.5.1.15.2
     depiction, 16.8FILTER.Z, 3.5.1.15.2
3D, 4.4.9, 15.2.21, 15.2.26, 15.2.29, 16.8, 22.3     gz, 3.5.1.15.2
     ligand editor.add substituent, 22.12.13     uue, 3.5.1.15.2
               atomic energy circles, 22.12.7Filter.zip, 3.5.1.15.2
               begin edit, 22.12.11Formula, 21.6.12, 21.6.15
               center ligand, 22.12.10Frequently Asked Questions, 21
               display, 22.12.4GAMESS, 3.5.15.11, 14.11
               dock, 22.12.20GIF, 3.5.1.14, 7, 7.1
               dock-tether, 22.12.21GRAPHIC.store Display, 3.5.1.15.3
               edit 2D, 22.12.15     NtoC Rainbow, 3.5.1.15.4
               fragment linkers, 22.12.23     alignment Rainbow, 3.5.1.15.4
               hydrogen atoms, 22.12.8     atomLabelShift, 3.5.1.15.7
                    bond, 22.12.6     ballStickRatio, 3.5.1.15.1
               ligand setup, 22.12.1     center Follows Clipping, 3.5.1.15.3
               minimization, 22.12.19     clash Style, 3.5.1.15.3
               multiple substituent, 22.12.14     clashWidth, 3.5.1.15.3
               preferences, 22.12.3     clip Grobs, 3.5.1.15.3
               purple box, 22.12.18          Skin, 3.5.1.15.3
               receptor setup, 22.12.2          Static, 3.5.1.15.3
               save spreadsheet, 22.12.17     discrete Rainbow, 3.5.1.15.4
               screen substituents, 22.12.22     displayLineLabels, 3.5.1.15.7
               surface, 22.12.5     displayMapBox, 3.5.1.15.3
               undo redo, 22.12.12     distance Label Drag, 3.5.1.15.1
               unsatisfied hydrogen bonds, 22.12.9     dnaBallRadius, 3.5.1.15.9
     object, 3.6.5.5     dnaRibbonRatio, 3.5.1.15.9
     predict, 13     dnaRibbonWidth, 3.5.1.15.9
          helices strands, 13.1     dnaRibbonWorm, 3.5.1.15.9
          local flexibility, 13.3     dnaStickRadius, 3.5.1.15.9
          protein health, 13.2     dnaWormRadius, 3.5.1.15.9
          tools identify ligand binding pocket, 13.5     font Scale, 3.5.1.15.7
               oda, 13.4     fontColor, 3.5.1.15.7
4D, 22.19     fontLineSpacing, 3.5.1.15.7
64, 21.1.2     grobLineWidth, 3.5.1.15.3
APF, 16.24.5     hbond Ball Period, 3.5.1.15.1
     template, 16.24.4               Style, 3.5.1.15.1
ActiveICM, 3.5.1.11     hbondAngleSharpness, 3.5.1.15.1
Area, 21.3.27     hbondMinStrength, 3.5.1.15.1
Atom Single Style, 3.5.1.15.3     hbondStyle, 3.5.1.15.1
Bad Groups, 21.6.12, 21.6.15     hbondWidth, 3.5.1.15.1
Blast, 21.3.26     hetatmZoom, 3.5.1.15.1
BlastDB Directory, 3.5.1.15.2     hydrogenDisplay, 3.5.1.15.1
     alphas, 4.4.3     light, 3.5.1.15.3
COLLADA, 3.5.1.6     lightPosition, 3.5.1.15.3
CPK, 3.6.1, 4.1.3     mapLineWidth, 3.5.1.15.3
Clash Threshold, 3.5.1.15.10     occupancy Radius Ratio, 3.5.1.15.3
DNA, 3.5.1.1.4, 8, 8.2.3     occupancyDisplay, 3.5.1.15.3
Display, 21.3.27     quality, 3.5.1.15.3
Dock Directory, 3.5.1.15.2     rainbow Bar Style, 3.5.1.15.4
     resize Keep Scale, 3.5.1.15.3     generateAlpha, 3.5.1.15.6
     ribbonRatio, 3.5.1.15.9     lineWidth, 3.5.1.15.6
     ribbonWidth, 3.5.1.15.9     lineWidth2D, 3.5.1.15.6
     ribbonWorm, 3.5.1.15.9     orientation, 3.5.1.15.6
     rocking, 3.5.1.15.4     paper Size, 3.5.1.15.6
          Range, 3.5.1.15.4     previewResolution, 3.5.1.15.6
          Speed, 3.5.1.15.4     previewer, 3.5.1.15.6
     selectionStyle, 3.5.1.15.3     print, 3.5.1.15.6
     site Label Drag, 3.5.1.15.7     printerDPI, 3.5.1.15.6
               Shift, 3.5.1.15.7     scale, 3.5.1.15.6
     siteArrow, 3.5.1.15.7     stereoAngle, 3.5.1.15.6
     stereoMode, 3.5.1.15.3     stereoBase, 3.5.1.15.6
     stickRadius, 3.5.1.15.1     stereoText, 3.5.1.15.6
     surfaceDotDensity, 3.5.1.15.3ISIS, 21.6.8
     surfaceDotSize, 3.5.1.15.3IUPAC, 15.7
     surfaceProbeRadius, 3.5.1.15.3Icm Prompt, 3.5.1.15.10
     transparency, 3.5.1.15.3Inx Directory, 3.5.1.15.2
     wire Width, 3.5.1.15.1JPEG, 3.5.1.14
     wormRadius, 3.5.1.15.9KMZ, 3.5.1.6
     xstick Backbone Ratio, 3.5.1.15.1Log Directory, 3.5.1.15.2
          Hydrogen Ratio, 3.5.1.15.1LogP, 19.5
          Style, 3.5.1.15.1LogS, 19.5
          Vw Ratio, 3.5.1.15.1MOL, 15, 15.1.1, 15.2.1, 15.2.21, 15.2.22, 15.2.23, 15.2.24, 17.4.3, 19.2
GROB.arrowRadius, 3.5.1.15.3MOL2, 15.1.1, 17.4.3
     atomSphereRadius, 3.5.1.15.3MOLT, 20.1
     contourSigmaIncrement, 3.5.1.15.3MOVIE.frame Grab Mode, 3.5.1.15.4
     relArrow Size, 3.5.1.15.3Map Atom Margin, 3.5.1.15.10
     relArrowHead, 3.5.1.15.3     Sigma Level, 3.5.1.15.10
GUI, 1Markush, 16.22.1
     auto Save, 3.5.1.15.4     create, 16.20.1
               Interval, 3.5.1.15.4Max_Fused_Rings, 16.1
     autoSave, 21.3.34Mnconf, 3.5.1.15.10
     autoSaveInterval, 21.3.34MolIPSA, 21.6.12, 21.6.15
     max Sequence Length, 3.5.1.15.4MolLogP, 21.6.12, 21.6.15
     table Row Mark Colors, 3.5.1.15.4MolLogS, 21.6.12, 21.6.15
     workspace Folder Style, 3.5.1.15.4MolPSA, 16.1
     workspaceTabStyle, 3.5.1.15.4MolVol, 16.1
HBA, 21.6.12, 21.6.15Molcart, 15.8.3
HBD, 21.6.12, 21.6.15MoldHf, 16.1, 21.6.12, 21.6.15
How To Guide, 2Movie.fade Nof Frames, 3.5.1.15.4
Html, 3.6.4.8     quality, 3.5.1.15.4
Hydrogen.bond, 3.5.1.15.5          Auto, 3.5.1.15.4
ICM, 1NCBI, 21.3.26
     Browser How To, 2.1NMR, 3.6.4.1
          Pro How To, 2.2Nof_Atoms, 16.1
     graphics crash, 21.9.1Nof_Chirals, 16.1
IMAGE.bondLength2D, 3.5.1.15.6Nof_HBA, 16.1
     color, 3.5.1.15.6Nof_HBD, 16.1
     compress, 3.5.1.15.6Nof_Rings, 16.1
     gammaCorrection, 3.5.1.15.6Nof_RotBonds, 16.1
ODA, 21.3.27Real Format, 3.5.1.15.10
Optimal, 21.3.27Receptor Setup, 17.1.5
Output Directory, 3.5.1.15.2     Label Shift, 3.5.1.15.7
PBS, 17.4.6          Style, 3.5.1.15.7
PCA, 19.5.1, 19.5.3RotB, 21.6.12, 21.6.15
PDB, 3.5.4.3, 3.6.4.7, 3.6.4.8, 3.6.4.9, 8.1, 11.3, 15.4SAR, 19.5
     Directory, 3.5.1.15.2     table, 16.22.1
          Style, 3.5.1.15.2SCORE, 21.5.7, 21.5.18
     Search, 3.5.2.12, 3.5.2.13, 3.5.2.14, 3.5.2.15, 3.5.2.16SDF, 15, 15.1.1, 15.2.21, 15.2.22, 15.2.23, 15.2.24, 17.4.3, 19.2
          Field, 3.5.2.13SEQUENCE.site Colors, 3.5.1.15.4
          Homology, 3.5.2.15SITE.label Style, 3.5.1.15.7
          Identity, 3.5.2.14     labelOffset, 3.5.1.15.7
          Sequence, 3.5.2.16     wrap Comment, 3.5.1.15.7
     convert, 3.6.4.9, 22.4.2SLIDE.ignore Background Color, 3.5.1.15.4
     pattern, 3.6.4.4          Fog, 3.5.1.15.4
     query, 3.6.4.2, 3.6.4.4SMILES, 15.3.11, 15.5.2
     search, 3.6.4.1, 3.6.4.2, 3.6.4.4, 3.6.4.5, 3.6.4.6, 22.4.1Select Min Grad, 3.5.1.15.10
     sensitive search, 3.6.4.5Show Res Code In Selection, 3.5.1.15.7
     sequence, 3.6.4.4Smiles, 21.6.12, 21.6.15, 21.6.17
     similarity, 3.6.4.5Swissprot, 3.5.1.6
PFAM, 3.5.1.6     Dat, 3.5.1.15.2
PLOT.Yratio, 3.5.1.15.8Temp Directory, 3.5.1.15.2
     color, 3.5.1.15.8UNIX, 17.4.6
     date, 3.5.1.15.8VLS, 17.4, 17.4.1, 17.4.2, 17.4.6, 17.4.10
     draw Tics, 3.5.1.15.8     preferences, 17.4.4
     font, 3.5.1.15.8Var Label Style, 3.5.1.15.7
     fontSize, 3.5.1.15.8Volume, 21.6.12, 21.6.15
     labelFont, 3.5.1.15.8Water Radius, 3.5.1.15.10
     lineWidth, 3.5.1.15.8Wire Style, 3.5.1.15.1
     logo, 3.5.1.15.8X-ray, 3.6.4.1, 17.1.1
     markSize, 3.5.1.15.8XPDB Directory, 3.5.1.15.2
     orientation, 3.5.1.15.8Xstick, 3.6.1, 4.1.3
     paper Size, 3.5.1.15.8a-bright, 3.6.2
     previewer, 3.5.1.15.8acceptor, 15.3.5
     rainbowStyle, 3.5.1.15.8acid, 3.5.1.1.4
     seriesLabels, 3.5.1.15.8active, 6, 21.3.36
PLS, 19.5.1activeICM, 6.1
PNG, 3.1.19, 3.5.1.14, 7, 7.1activeicm, 6, 6.4, 6.6, 6.6.1
Projects Directory, 3.5.1.15.2     advanced, 6.6
Prosite Dat, 3.5.1.15.2     control, 6.5
Protein, 21.3.27activityy, 19.5
     Viewer, 3.5.1.15.2add image album, 4.11.4
QSAR, 19.5, 19.5.1adding fragment, 15.3.4
     build model, 22.15.1          in editor, 15.3.4
     predict, 22.15.2administration, 15.12.4
R, 15.11, 16.22advanced alignment selectioection, 8.5.12
     and S, 21.5.22album, 4.11.4
R-group, 15.10alias, 15.3.3
RMSD, 10.2align, 3.1.15, 3.3.5, 8.4.1, 16.14
Ramachandran Plot, 9.9     color 2D scaffold, 16.14
     multiple sequences, 8.4.4angle, 3.5.6.7, 3.5.6.8, 4.4.5, 4.5, 4.8.6, 9.7, 9.8, 21.3.17, 21.4.16
     two sequences, 8.4.2angstrom, 3.4.9, 21.4.7
     DNA to protein, 8.2.7, 8.4.3animate, 3.5.3.15
     multiple, 8.4.4     view, 3.5.3.15
     sequence, 8.4, 8.4.5animation, 5.1, 5.1.1, 5.1.2, 5.1.3, 5.1.4
     two sequences, 8.2.5, 8.4.2     store, 5.1.4
alignment, 3.3.6, 21.4.12, 22.6, 22.6.2animations, 5
     comment, 8.5.3annotate, 16.3
     editing, 8.5.1     by substructure, 16.3
     editor, 8.5antialias, 3.5.1.14, 3.5.3.10
     example, 8.2.14     lines, 3.5.3.17
     font size, 21.3.1     lines, 3.5.3.17
     format, 8.5.8apf, 21.6.18
     gaps, 8.5.8     super, 16.24.4
     introduction, 8.4.1     alignment, 16.24.5
     reorder, 8.2.12apf3Dqsa, 21.6.18
     search, 8.5.9append.rows, 3.5.9.6
     selection, 8.5.10applying prediction models, 19.5.2
     view options, 8.5.7area, 3.5.5.4, 3.5.6.3, 9.3, 13.4, 17.6, 17.6.1, 17.6.2
     box, 8.5.6aromatic, 15.2.26
     color, 8.5.5, 8.5.6arrange, 3.1.18
     comment, 8.5.3     window, 3.1.18
     consensus, 8.5.5, 8.5.12     graph, 21.3.8
     cut, 8.2.11as_graph, 21.3.8
     delete, 8.5.2asparagine, 3.5.15.2, 14.2
     display title, 8.5.7assign, 4.1.6
     editor, 8.5     2D coordinates, 16.8
     extract, 8.2.10     helices, 3.5.5.1, 13.1
     gaps, 8.5.8     strands, 3.5.5.1, 13.1
     horizontal scroll, 8.5.7atom, 3.5.1.15.5, 15.2.26, 21.3.4, 21.3.5, 21.3.8, 21.3.15, 21.3.16, 21.4.10, 22.2.1, 22.2.2
     linked, 22.7.2     charge, 21.4.21
     multiple, 8.2.8atomLabelStyle, 3.5.1.15.7
     options, 8.5.7attachment, 15.3.2, 15.8.1
     print, 8.5.2     point, 16.21
     rename, 8.5.7auto play slide, 6.5
     reorder, 8.2.12autofit, 17.5
     ruler, 8.5.7autosave, 21.3.34
     save, 8.5.2ave, 19.6
     search, 8.5.9avi, 7, 7.1, 7.2
     selection, 8.5.10, 8.5.11, 8.5.12axes, 19.3.11
     sequence offset, 8.5.7axis, 19.3.7
     shade, 8.5.6     options, 19.3.6
     table, 8.5.7     grid, 19.3.6
     view, 8.5.7     range, 19.3.6
alignments, 3.3, 8.4, 22.5     title, 19.3.6
alpha, 3.6.2b-factor, 3.5.5.3, 13.3, 17.1.1, 22.8.2
     channel, 3.5.1.15.6backbone, 21.3.12
ambient, 3.6.2background, 4.2.2
amino, 3.5.1.1.4     color shortcut, 21.3.2
analysis, 8.2     image, 4.2.2
bad, 16.1ccp4, 21.3.28, 21.3.29
     groups, 15.3.5cell, 3.5.4.2, 11.2
ball, 3.5.1.15.5center, 3.1.2, 3.5.3.20, 4.8, 4.8.5, 19.1.31, 21.4.22
     and stick, 3.6.1, 4.1.3     and representative members, 19.6.1
bank, 3.6.4.1chain.breaks, 21.3.35
basic alignment selection, 8.5.11chains, 3.5.6.1
basicsel, 3.2.3chair, 21.5.21
batch, 17.1.10, 17.4.6, 17.6.8chair-boat, 21.5.3
beep, 21.3.37change selection, 3.2.4
begin docking simulation, 17.1.8     speed range, 5.1.2
best, 15.2.32changing font in alignment editor, 8.5
binding, 3.4.7, 21.3.13, 21.5.2, 21.5.11charge, 3.4.3, 3.4.4, 3.4.5, 3.5.3.21, 4.4.2, 15.3.2, 15.8.1, 16.9.1, 16.9.2, 16.9.3, 21.4.1
     pocket, 22.6chem convert, 21.6.10
bioinfo align dna protein, 8.2.7     save, 15.5
          multiple, 8.2.8          editor, 15.5.2
          two sequences, 8.2.5          image, 15.5.4
     links, 8.2.9          table, 15.5.1
     secondary structure, 8.2.2          workspace, 15.5.3
     translation, 8.2.3     super, 16.24
biological, 3.5.4.3, 11.3     view, 15.2.26
biomolecule, 3.5.4, 3.5.4.3, 11.3, 22.8, 22.8.4chemical, 15, 15.2.25, 15.2.26, 15.2.28, 15.2.29, 15.2.32, 15.2.33, 15.3.6, 15.11, 15.12.3, 16.8, 16.11, 16.21, 16.23, 16.24, 19.6, 21.6.9, 21.6.10, 21.6.12, 21.6.13, 21.6.14, 21.6.15
bit, 21.1.2     clustering, 16.15
blast, 8.3     dictionary, 15.3.3
boat, 21.5.21     draw load, 15.1
bond, 3.4.3, 3.4.8, 12.9, 15.3.6, 21.4.1, 21.6.12, 21.6.15, 22.6.3     editor, 15.3, 15.3.4
     covalent, 21.4.2          not starting, 21.9.3
     type, 3.4.4, 3.4.5, 16.9.1, 16.9.2, 16.9.3     find replace, 15.10
bonding, 4.1.10     fragments, 15.2.31
     preferences, 3.5.1.15.1     group, 15.3.3
box, 3.5.1.1.8, 3.5.1.15.7, 4.4.16, 21.5.10     groups, 15.3.3, 15.3.4
bpmc, 22.7.3     right click, 15.3.2
break, 3.1.10     search, 15.8
browse, 15.2.29, 17.1.12          filter, 15.8.2
     mode, 15.2.29          text, 15.8.4
     molt, 20.2     smiles, 15.1.2
     stack, 3.5.15.10, 14.10     spreadsheet, 21.6.19
bugs, 21.9          compare, 15.2.19
build, 5.1.1     spreadsheets, 15.2
     homology model, 12.3     structure, 15
     hydrogens, 3.5.15.5, 14.5     superimpose.apf, 22.13.2
buttons, 6.6          rigid flexible, 22.13.1
bye, 3.5.1.18     table, 21.6.17
cache, 6.6.1          display, 15.2.1
calculate, 3.4.9, 21.5.2     tables, 19.2
     properties, 16.1     2D, 16.9
     startup, 21.8.2     3D, 16.9
carbon, 21.3.4, 21.3.5     append, 15.3.7
cartesian, 16.10     clustering, 16.15, 16.15.1
cavities, 9     convert, 3.4.3, 3.4.4, 3.4.5, 3.5.15.1, 14.1, 16.9, 16.9.1, 16.9.2, 16.9.3, 21.4.1
     closed, 3.5.6.4, 9.4     display.fit, 21.6.19
     duplicates, 15.2.18     chemical, 15.2.33
     edit, 15.3.8, 22.9.2     display mesh, 3.6.5.7
     editor, 15.5, 15.5.1, 15.5.2, 15.5.3, 15.5.4     faq, 21.3.21
     load, 15.1, 15.1.1     table, 15.2.24
     merge, 16.17     2D sketch, 15.9.5
     name, 15.7     background, 3.5.3.18
     new, 15.3.1     distance, 4.4.11
     properties, 15.2.17     mesh, 3.6.5.7
     query, 15.3.2, 15.8.1, 15.8.3     table, 15.2.24
     read, 15.1, 15.1.1coloring, 4.2.1
     redo, 15.3.12column, 19, 19.1.20, 19.1.30, 19.1.31, 19.3, 19.3.1, 21.6.12
     save, 15.3.7, 15.5, 15.5.1, 15.5.2, 15.5.3, 15.5.4     row width, 19.1.20
     search, 15.3.2, 15.8, 15.8.1, 15.8.3, 22.10.1, 22.10.2     statistics, 19.1.24
     similarity, 15.3.2, 15.8, 15.8.1, 15.8.3, 22.10.1, 22.10.2     color, 19.1.8
     smiles, 15.1.2     hide, 15.2.6
     spreadsheet, 15.2, 15.5, 15.5.1, 15.5.2, 15.5.3, 15.5.4     show, 15.2.6
     structure, 15.1.1, 15.3.7, 15.3.8combinatorial.library, 16.21.1
     substructure, 22.10.2combine, 3.5.9.4
     superimpose, 16.24.1, 16.24.2, 16.24.3     display style, 3.5.1.15.9
     superposition, 16.24.4, 16.24.5command, 21.5.17
     table, 15.2, 19.2, 22.9.1, 22.9.2     line, 21.3.33
     undo, 15.3.12commands, 3.5.1.1.5, 21.8.1
cheminformatics, 15.2, 21.6compare, 15.2.27, 16.16, 16.17
chemistry, 16.11, 21.6     table, 15.2.19
     menu, 16     tables, 16.16
     smiles, 16.6compatible, 3.5.1.9
     duplicates, 16.19compound, 16.11, 19.2
     remove.redundant, 16.19compounds, 21.6.3
chemlib.so, 21.1.2compress, 3.5.1.15.6
chi, 4.4.5, 21.3.17conditions, 15.8.2
chiral, 16.13     gen, 16.10
chirality, 16.13conformation, 16.10, 17.2.2
clash, 3.5.1.15.5, 4.4.15conformations, 21.7.2
classes, 15.2.26conformers, 16.10
clear display and planes, 3.5.3.2connect, 3.6.5.6, 4.8, 4.8.7
     planes, 3.5.3.2     object, 4.8.7
click, 3.1.16, 4.7, 4.8connectivity, 15.3.2, 15.8.1
clip, 3.6.5.8, 4.9.1, 21.3.10consensus, 3.5.6.1
clipboard, 4.11.2, 19.6.2conservation, 22.6
clipping, 21.3.20construct, 3.5.1.1, 3.5.1.1.1, 5.1.1
     planes, 3.1.3, 4     DNA, 3.5.1.1.3
     tool, 4.9     RNA, 3.5.1.1.3
     tools, 4.9     chemical, 3.5.1.1.2
closed cavities, 3.5.5.5, 3.5.6.4, 13.5     compound, 3.5.1.1.2
cluster, 17.4.6, 19.6     molecule, 3.5.1.1
     representative.center, 16.15.2     nucleic, 3.5.1.1.4
clustering, 19.5.4     object, 3.5.1.1
collada, 3.6.5, 3.6.5.4     protein, 3.5.1.1.4
color, 3.5.5.2, 4.2, 4.2.1, 4.4.2, 4.4.3, 13.2, 15.2.33, 16.14, 19.1.34, 19.6.3, 21.3.4, 21.3.5, 21.3.15, 21.3.21, 22.6     sequence, 3.5.1.1.4
     alignment, 8.5.5contact, 3.5.6.3, 9, 9.3
contour, 3.5.4.6, 3.5.4.7, 11.6, 11.7     label, 4.4.9
     map, 3.5.4.6     rotation, 4.8.2
convert, 3.4.2, 3.6.4.9, 16.12, 21.6.10cut, 19.1.26
     2D to 3D.conformer generator, 22.11.3     vertical alignment block, 8.2.11
                    from table, 22.11.2damaged skin, 21.9.2
                    molecule editor, 22.11.1dash, 21.3.11
     chemical, 15.2.21data, 3.6.4.1
          2D 3D, 16.9databank, 3.4.1
     local database, 3.5.1.5database, 8.3, 15.12, 16.21, 17.1.2, 17.4.3, 17.4.5, 20.1
     pdb chem, 16.9.1     file format, 17.4.3
     smiles to 2D, 21.6.17     seach and alignment, 8.3
     local.database, 3.5.1.5databases, 21.6.3
     smiles, 16.6, 16.7decompose.library, 16.22.1
convert2grid, 3.5.4.7decomposition, 16.21, 16.22
converting pdb, 3.6.4.9default, 3.1.17
copy, 15.2.22, 15.3.13, 15.9.2, 19.1.26delete, 3.5.2.1, 5.6.7, 21.4.9
     cell, 19.1.27     column row, 19.1.29
     chemical, 15.2.22     label, 4.4.10
     paste row, 19.1.26     all, 3.5.2.2
          structure, 15.3.10     angle.label, 4.5.4
     row, 19.1.27     column, 19.1.29
     selection to table, 19.1.28     distance.label, 4.5.4
     chemical, 15.2.14     label, 4.4.10
cpk, 4.1.8, 21.3.22     row, 19.1.29
crash, 3.5.2.11     selection, 3.5.2.1
creat, 5.6.1     tether, 3.5.15.5, 14.5
create, 19.1.1deleteall, 3.5.2.2
     modify markush, 16.20density, 3.5.4.4, 3.5.4.6, 3.5.4.7, 11.4, 11.6, 11.7, 21.3.28, 21.3.29
cross, 21.3.9depth, 3.6.5.10
     section, 4.9deselect, 21.3.7
crystal, 3.5.4.2, 11.2deviation, 21.4.7
crystallographic analysis, 11dialog, 5.6.5
          biomolecule, 11.3diffuse, 3.6.2
          contour map, 11.6dihedral, 3.5.6.8, 4.4.5, 9.8, 21.3.17
          convert2grid, 11.7     angle, 9
          crystallographic cell, 11.2dimensional, 21.6.11
          load eds, 11.4directories preferences, 3.5.1.15.2
          maps cell, 11.5directory, 3.5.1.15
          symmetry packing, 11.1disappearing labels, 21.9.2
          tools, 22.8display, 3.1.7, 3.1.18, 3.4.8, 3.5.1.15, 4.4.15, 4.10, 15.2.25, 16.13, 21.3.4, 21.3.5, 21.3.8, 21.3.9, 21.3.10, 21.3.16, 21.3.22, 21.3.31, 21.3.33, 21.4.10, 21.4.11, 21.4.20, 21.6.9, 22.2, 22.6.1, 22.6.3
     cell, 3.5.4.2     chemical, 15.2.25
     cell, 3.5.4     delete distances, 4.5.4
     neigbor, 3.5.4.1, 11.1     dihedral, 4.5.3
     neighbors, 3.5.4     distance restraints, 4.4.14
crystallography, 3.5.4.4, 3.5.4.6, 3.5.4.7, 11.4, 11.6, 11.7, 21.3.28, 21.3.29     distance2, 4.5.1
csv, 19.1.2, 19.1.3, 19.1.19          angles, 4.5
current, 21.3.23     formal charge, 4.1.2
     slide, 6.5     gradient, 4.4.17
custom, 4.8, 15.2.1, 16.24     hydrogen, 4.1.1
     fragments, 16.3     mesh, 3.6.5.2
     structure, 3.1.8     batch, 17.1.10
     tab, 3.6.1, 21.3.15     binding, 17.1.6
     tether, 4.4.13     conformations, 21.5.21
     toggle, 4.4.16     flexible.rings, 21.5.21
     CPK, 4.1.8     hitlist, 17.1.14
     angle, 4.5.2     interactive, 17.1.9
     chemical, 15.2.1     maps, 17.1.7
     dihedral.angle, 4.5.3     preparation, 17.1.3
     distace, 4.4.11     procedure, 17.1.8
     distance, 4.4.14, 4.5.1     project name, 17.1.4
     electrostatic, 3.5.3.21     rank, 17.1.14
     energy.gradient, 4.4.17     receptor setup, 17.1.5
     hydrogen, 4.1.1     results, 17.1.11, 17.1.12, 17.1.13, 17.1.14
          polar, 4.1.1     sampling, 21.5.21
     macroshape, 3.6.5.3     score, 17.1.14
     meshes, 3.6.5.2     stack, 17.1.13
          and display.macroshape, 3.6.5     template, 17.3
     molecule, 15.2.21document, 3.5.1.1.6, 5.6.4, 5.6.5
     origin, 4.4.12     navigation, 5.6.6
     potential, 3.5.3.21documents, 4.11.4, 21.3.19
     representations, 3.6.1, 4.1.3dollar, 21.8.3
     restraints, 4.4.14donator, 15.3.5
     ribbon, 4.1.6     envelope, 3.6.1, 4.1.3
     skin, 4.1.7     surface, 3.5.1.15.5
     status, 21.3.33dots, 3.1.10
     surface, 3.6.5.1, 4.1.9dotted lines, 3.1.10, 21.3.35
     surfaces, 3.6.5double, 15.3.6
     table, 15.2.1download, 21.6.3
     tethers, 4.4.13drag, 3.1.15, 3.3.6, 3.5.1.15.7, 4.4.3, 5.6.4, 8.4.5, 21.4.5
     wire, 4.1.4     and drop sequences, 8.4.5
     xstick, 4.1.5     residue label, 3.5.3.16
distance, 3.4.9, 3.5.6.6, 4.4.11, 4.5, 9, 9.6, 16.16, 21.3.11, 21.4.8, 21.4.10draganddrop, 3.1.15
     faq, 21.4.10draw, 15.3.13, 16.23, 21.6.7
     label, 3.5.1.15.7     chemical, 15.3.1
distances, 3.6.3drop, 3.1.15, 3.3.6, 5.6.4, 8.4.5, 21.4.5
disulfide, 12.9drug, 16.1, 21.6.12, 21.6.14
diverse set, 19.5.4druglikeness, 15.3.5
dock, 17, 17.1, 17.1.2, 17.5, 21.5.3, 21.5.4, 21.5.5, 21.5.6, 21.5.8, 21.5.9, 21.5.11, 21.5.12, 21.5.13, 21.5.14, 21.5.15, 21.5.16, 21.5.17, 21.5.22, 22.17.1, 22.17.2, 22.19dsPocket, 3.1.12
     command, 21.5.17easy rotate, 3.5.3.12
docking, 3.4.2, 3.5.5.4, 13.4, 17, 17.1.3, 17.1.15, 17.2, 17.2.1, 17.2.2, 17.4, 17.4.1, 17.4.2, 17.4.5, 17.6, 17.6.1, 17.6.2, 17.6.3, 17.6.4, 17.6.5, 17.6.7, 17.6.8, 17.6.9, 21.5, 21.5.1, 21.5.10, 21.5.18, 21.5.19, 22.16, 22.16.1, 22.16.2, 22.18, 22.20edit, 21.6.8
     explicit group, 22.20     alignment, 8.5.1
               docking explicit, 22.20.5     chemical, 15.3.8
                    project, 22.20.3          moledit, 15.2.23
               receptor setup, 22.20.1     ligand, 18.5
               rotate hydroxyls, 22.20.2          editor preferences, 18.2
               run docking, 22.20.4          tools, 3.5.2.17
     start, 17.1.3     menu, 3.5.2
     template, 17.3     molecular document, 5.6.1
     adjust, 17.1.6     molecule, 15.3
     background, 21.5.20     molt, 20.3
     selection, 3.5.2.5     icb, 3.5.1.4
     table row, 19.1.22     phrarmacophore, 15.9.4
     molecule, 15.2.23faq, 21, 21.2, 21.3, 21.3.12, 21.4, 21.5, 21.7, 21.8, 21.8.2
     movie, 7.3.7     ISISdraw, 21.6.8
     structure, 15.2.23     activeicm, 21.3.36
editor, 21.4.12, 22.6.2     apf model, 21.6.18
editpdbsearch, 3.5.2.12     atom charge, 21.4.21
eds, 3.5.4.4, 3.5.4.6, 3.5.4.7, 11.4, 11.6, 11.7          display, 21.3.16
electron, 3.5.4.4, 3.5.4.6, 3.5.4.7, 11.4, 11.6, 11.7, 21.3.28, 21.3.29     autosave, 21.3.34
     denisty map, 3.5.4.5, 11.5     backbone, 21.3.12
     densitry map.contour, 3.5.4     background color, 21.3.2
          map, 3.5.1.6, 3.5.4, 17.5          job, 21.5.20
electrostatic, 3.4.7     beep, 21.3.37
     potential, 3.5.3.21     binding energy, 21.5.2
electrostatics, 17.6.7     blend transition, 21.3.32
element, 15.3.6     breaks, 21.3.35
embed browser, 6.3     change torsion, 21.4.16
     powerpoint03, 6.1     chem table display, 21.6.9
     powerpoint07, 6.2     chemical monitor, 21.6.15
     activeicm, 6.5          query2, 21.6.5
          script, 6.5     cheminformatics, 21.6
     browser, 6, 6.3     clipping plane, 21.3.10
     firefox, 6, 6.3     closest, 21.4.22
     internet.explorer, 6, 6.3     color carbon, 21.3.4
     microsoft, 6          skin, 21.3.15
     powerpoint, 6, 6.1, 6.2     command line display, 21.3.33
enantiomer, 21.5.22     convert chemical from pdb, 21.4.1
energy, 3.4.2, 3.5.5.2, 4.4.15, 13.2, 17.1.13, 21.3.19, 21.5.1, 21.5.2, 21.7.2     covalent bond, 21.4.2
     mesh, 21.3.19     delete, 21.4.9
     terms, 3.5.15.12, 14.12     deselect, 21.3.7
enumerate.reaction, 16.23.1     dihedral, 21.3.17
enumeration, 16.21     dock probe, 21.5.14
eps, 15.5.4          racemic, 21.5.22
epsilon, 21.4.15          repeat, 21.5.6
errno, 21.1.2     docking, 21.5
error, 21.1.2, 21.3.37     docktime, 21.5.12
escaping, 3.1.3     dollar, 21.8.3
exact, 16.16     druglikeness, 21.6.14
excel, 15.6     energy, 21.5.1
exclude fragment, 15.8.2     extract ligand, 21.6.13
exit, 3.5.1.18     flexible dock, 21.5.16
explicit, 15.2.26, 17.2.1          ring docking, 21.5.21
     flex, 17.2.1     font size, 21.3.1
     groups, 22.20     foreground table, 21.8.4
export, 3.5.6.9, 9.10     gl failure, 21.9.1
     excel, 15.6     gui, 21.3
extract, 3.3.4, 8.1, 21.4.12, 21.6.13, 22.6.2     guided dock, 21.5.4
     icb, 3.5.1.4     hardware, 21.2
     sub alignment, 8.2.10     hitlist, 21.5.8
     2D chemical sketch, 15.4     iSee, 21.3.31
     insert column, 21.6.12fasta, 3.3, 3.3.2
     installation, 21.1file, 3.5.1.2, 3.6.4.7
     interactions, 21.3.11     close, 3.5.1.12
     ligandbox, 21.5.10     compatible, 3.5.1.9
     merge, 21.4.5     export, 3.5.1.11
     molcart 64bit, 21.1.2     load, 3.5.1.6
          query, 21.6.6     menu, 3.5.1
          sdf, 21.6.4     password, 3.5.1.10
          text search, 21.6.16     quick image, 3.5.1.13
     molecule c, 21.3.5     icb, 3.1.14
     moledit, 21.6.7     recent, 3.5.1.16
     movie planes, 21.3.20     bak, 3.5.2.11
     newscript, 21.8.1filter, 20.2, 21.3.4
     nmr, 21.4.18     selection, 3.2.5
     nvidia error, 21.1.1          tut, 22.2.4
     origin, 21.3.9find, 3.5.6.1
     pmf score, 21.5.7     chemical, 15.2.30
     pockets, 21.3.13     related chains, 3.5.6.1
     preserve coordinates, 21.6.11finding dihedral angle, 3.5.6.8
     quad buffer, 21.2.3     planar angle, 3.5.6.7
     receptor selection, 21.5.15fingerprint, 21.6.5, 21.6.6
     reload dock, 21.5.5fit, 15.2.32, 17.5, 21.5.16
     remove select, 21.3.6fitting, 17.5, 19.3.12
     renumber, 21.4.4flex super, 16.24.3
     ringflex dock, 21.5.3flexibility, 3.5.5.3, 13.3
     rmsd, 21.4.7flexible, 16.24, 17.2, 17.2.1, 17.2.2, 21.5.16, 22.19
     rmsdtips, 21.4.8     rings, 21.5.3
     rotate chemical, 21.6.19fog, 3.5.3.5, 4
     scanScoreExternal, 21.5.18font, 3.5.1.15, 3.5.1.15.7, 4.4.2, 4.4.3, 15.2.26, 19.1.31, 19.6.3
     scanScoreExternal2, 21.5.19     preferences, 3.5.1.15.7
     score, 21.5.9     size, 8.5, 21.3.1
     script, 21.8form, 15.2.4
     sgi, 21.1.3     view, 19.1.5
     simulations, 21.7formal, 3.4.3, 21.4.21
     smiles, 21.6.17     charge, 4.1.2
     solvent accessible surface table, 21.4.19format, 19.1.2, 19.1.31
     ss, 21.4.17formula, 15.3.5, 16.1
     structure, 21.4fragment, 15.2.33, 16.22
     superimpose, 21.4.6fragments, 15.11
     thoroughness, 21.5.13frame, 8.2.3
     transparent ribbon, 21.3.3frequency, 15.2.33
     truncate mesh, 21.3.14front, 3.6.5.8, 4.9.1
     view stack, 21.7.2full scene antialias, 3.5.3.10
     weak hydrogen bonds, 21.4.20     screen, 3.5.3.8
     write pdb, 21.4.3function, 19.1.23, 19.1.24
faqcontour, 21.3.29functional.groups, 16.3
faqhbondstrength, 21.3.30general preferences, 3.5.1.15.5
faqmaps, 21.3.28generalselecttools, 3.2.2
faqoda, 21.3.27generator, 3.5.4.3, 11.3, 16.10
faqstereo, 21.9.4getting started, 3
glutamine proline, 3.5.15.2, 14.2     bins, 19.3.3
google, 3.5.1.6     color, 19.3.2
     objects, 3.6.5.4     source, 19.3.2
     3D, 3.6.5, 3.6.5.4     style, 19.3.2
graphical, 1, 21.3.4     title, 19.3.2
     display, 3.4.4, 3.4.5, 16.9.2, 16.9.3hitlist, 17.1.11, 17.1.14, 17.4.8, 17.4.9, 17.4.11, 21.5.8
          tutorial, 22.1homology, 3.5.6.1, 12, 12.1, 12.2, 12.4.1, 12.6, 12.7, 22.7, 22.7.1
               2D3D labels, 22.1.4     loops, 12.5
               annotation, 22.1.2     model introduction, 12.1
               color representation, 22.1.1          start, 12.2
               labels, 22.1.3     3D editor, 22.12
     user interface, 21.3               add substituent, 22.12.13
     card, 21.1.1               begin edit, 22.12.11
     controls, 4               center ligand, 22.12.10
     defects, 21.9.2               default, 22.12.4
     preferences, 3.5.1.15.3               dock, 22.12.20
     tips, 3.1.3                    tether, 22.12.21
     shadow, 3.5.3.13               edit 2d, 22.12.15
grid, 15.2.1, 15.2.4, 16.24, 21.6.9, 22.19               energy circles, 22.12.7
grob, 3.5.1.15.5, 3.5.4.4, 3.5.4.6, 3.5.4.7, 11.4, 11.6, 11.7                    hydrogen, 22.12.8
group, 16.22, 18.7               fragment linkers, 22.12.23
groups, 15.11, 16.1, 16.2               hydrogen bond, 22.12.6
gui, 3.5.1.15.4               minimization, 22.12.19
     menus, 3.5               multiple substituent, 22.12.14
     preferences, 3.5.1.15.4               preferences, 22.12.3
     tabs, 3.6               purple box, 22.12.18
guided docking, 21.5.4               save spreadsheet, 22.12.17
h, 21.3.19               screen substituents, 22.12.22
h-bond, 3.4.8, 21.3.11, 21.3.19, 22.6.3               setup ligand, 22.12.1
hardware, 21.2                    receptor, 22.12.2
     stereo, 3.5.3.7               surface, 22.12.5
hbond, 21.3.30               undo redo, 22.12.12
     strength, 21.3.30               unsatisfied hydrogen bonds, 22.12.9
header, 3.6.4.8, 19.3.5     add columns, 15.2.2
health, 3.5.5.2, 13.2, 22.7.4     change view, 15.2.4
helices strands, 3.5.5.1     chemical 2D 3D, 22.11
helix, 21.3.21                    conformer generator, 22.11.3
hetero, 15.2.26                    from table, 22.11.2
hidden block format, 8.5.8                    molecule editor, 22.11.1
          width, 8.5.8          superimpose, 22.13
hide, 19.1.30               apf, 22.13.2
high, 3.5.1.14               rigid flexible, 22.13.1
     quality, 3.5.3.11     cluster center, 16.15.2
his, 21.4.15     color 2D by ph4, 15.9.5
histidine, 3.5.15.2, 14.2, 21.4.15     copy 2D, 15.2.14
     tautomer, 21.4.15          paste, 15.2.5
histogram, 17.4.10, 17.4.11, 19.3, 19.3.1, 19.3.5, 19.3.7, 19.3.9, 19.3.10, 19.3.11, 19.3.12, 19.3.13, 19.3.14, 19.3.15, 19.3.17, 22.14, 22.14.1     decompose, 16.22.1
     bins, 19.3.3     duplicate chemicals, 15.2.18
     options, 19.3.2     edit table, 15.2.15
     bin.size, 19.3.2          tree, 16.15.4
     extract 2D, 15.4html-doc font size, 21.3.1
          3D ph4, 15.9.4hybridization, 15.3.2, 15.8.1
     filter, 15.2.10hydrogen, 3.4.2, 3.4.8, 4.1.10, 15.3.2, 15.8.1, 21.3.11, 21.3.19, 21.6.12, 21.6.15, 22.6.3
     find replace, 15.2.11     bond, 4.1.10
     histogram, 22.14.1     bond, 15.3.5, 21.4.20
     mark row, 15.2.12hydrogens, 15.2.26
     markush, 16.21.1     remove, 15.2.16
          structure, 16.20.1hyperlink, 5.6.1, 5.6.2
     merge tables, 15.2.20iSee, 3.1.14, 3.5.1.1.6, 3.5.1.4, 3.5.1.11, 4.11.4, 21.3.19, 21.3.31, 21.3.32, 21.3.36, 22.3
     plot, 22.14.2icb, 21.3.31, 21.3.36
     plots, 22.14icm, 21.3.36
     properties, 15.2.17     chemist howto chemical search, 2.4.3
     qsar, 22.15               cluster, 2.4.5
          build model, 22.15.1               combi library, 2.4.7
          predict, 22.15.2               ph4, 2.4.4
     reactions, 16.23.1               plots, 2.4.8
     reorder, 16.15.3               sketch, 2.4.1
     sdf, 15.2.7               spreadsheets, 2.4.2
     show hide, 15.2.6               stereoisomers tautomers, 2.4.6
     smiles, 15.3.11          pro 3D ligand editor, 2.5.1
     sort column, 15.2.3               chem3D, 2.5.2
     standardize, 15.2.16               chemsuper, 2.5.3
     table hyperlinks, 15.2.13               qsar, 2.5.4
          print, 15.2.9               tutorials, 2.5
          activeicm, 2.3          tutorials, 2.4
               create molecular documents, 2.3.3     hanging, 21.9.3
                    slides, 2.3.2icm-crash, 21.9.3
               download, 2.3.1icmFastAlignment, 8.3
               ppt, 2.3.4icmPocketFinder, 3.5.5.5, 13.5, 21.3.13, 21.5.11
               web, 2.3.5image, 3.1.19, 3.5.1.15, 3.5.1.15.5, 4.11.1, 4.11.2, 4.11.3, 4.11.4, 5.6.3, 15.5, 15.5.4, 19.3.16
          chemical clusering, 16.15.1     advanced, 4.11.3
          display, 3.1     clipboard, 4.11.2
          icm browser convert display pocket, 2.1.5     preferences, 3.5.1.15.6
                    distances angles, 2.1.8     multiple, 3.5.1.6
                    get started, 2.1.1     quality, 3.5.3.11
                    graphical display, 2.1.2     quick, 3.5.1.13
                         effects, 2.1.3images, 4.11
                    images, 2.1.6in-a-window, 21.2.3
                    labels annotation, 2.1.4index, 21.6.16
                    pro crystallographic tools, 2.2.6induced, 21.5.16
                         get started, 2.2.1     fit, 17.2, 17.2.1, 22.19
                         graphics, 2.2.2insert, 5.6.4
                         plots, 2.2.8     column, 19.1.23
                         sequence analysis, 2.2.7     image, 5.6.3
                         structure analysis, 2.2.3     row, 19.1.25
                         superimpose, 2.2.5     script, 5.6.4
                         surfaces, 2.2.4install, 1, 15.12.1, 21.1.2, 21.1.4
                    superimpose, 2.1.7installation, 21.1, 21.1.3
hrydrogen.bond, 21.3.30interactio, 21.5.2
html, 3.5.1.1.6, 3.5.1.11, 5.6.1, 5.6.6interaction, 3.5.6.3, 9.3, 21.3.11
     loop, 12.4.3     distances, 4.4.11
     make, 12.4.1     tab, 3.6.3
     modeling, 12.4, 12.4.1landscape, 3.5.1.15.6
     modeling, 12.4lasso, 22.2.1, 22.2.2
interface, 1layer, 4.10
interrupt, 5.1.3layers, 4.10
     animation, 5.1.3learn, 16.4, 16.5, 19.5, 19.5.1, 21.6.18
introduction, 1learning, 19.5
invert selection, 19.1.21     theory, 19.5.3
invisible residue label, 21.9.2least.squares, 19.3.12
isee, 5.6.5library, 16.21
isis, 15.3.13     reaction, 16.23.1
isotope, 15.3.2, 15.8.1license, 21.1.4
iupac, 15.7ligand, 17.1.2, 17.2, 17.6.5, 17.6.6, 21.4.5, 21.4.11, 21.5.2, 21.5.10, 21.6.13, 22.6.1
job, 21.5.20     best replace, 18.7
jobs, 17.4.6     editor, 18
join, 16.17          preferences, 3.5.2.18
jpg, 4.11, 4.11.1     linker, 18.6
     means, 19.6     pocket, 21.4.11
key chemical, 15.3.6     tether, 18.8
keyboard mouse, 4.7     convert, 3.5.15.1, 14.1
keystokes in chem-edit, 15.3.6     editor, 18, 18.1, 18.6
kmz, 3.6.5, 3.6.5.4          binding.re-dock ligand, 18.4
label, 3.4.9, 3.5.1.15.7, 19.6.3, 21.3.16          display, 18.3
     annotation, 4.4.7          edit, 18.5
     atoms, 4.4.2          energy, 18.3
     color, 4.4.8          hydrogen.bond, 18.3
     move, 4.4.4          pocket, 18.3
     residues, 4.4.3          preferences, 18.2
     sites, 4.4.6          restraint, 18.8
     variables, 4.4.5          surface, 18.3
     2D, 3.6.3          tether, 18.8
     3D, 3.6.3, 4.4.1     optimization, 22.18
     annotation, 4.4.7     pocket, 3.1.12
     atom, 4.4.1     receptor.contact, 3.5.6.3, 9.3
     atoms, 4.4.2     surface, 22.12.5
     color, 4.4.8light, 3.6.2
     custom, 4.4.9     tab, 3.6.2
     delete, 4.4.1, 4.4.10lighting, 4.3
     distance, 4.4.11likeness, 16.1, 21.6.14
     drag, 3.5.3.16line, 3.5.1.15.5, 19.6.3, 21.3.11
     move, 3.5.3.16, 4.4.4lineWidth, 3.5.1.15.3
     residue, 4.4.1link, 8.2.9, 22.6
     residues, 4.4.3     structure to alignment, 22.5
     site, 4.4.1linker, 18.6
     sites, 4.4.6links, 3.2.14
     variable, 4.4.1linux, 15.12.1
     variables, 4.4.5, 21.3.17load, 3.3, 3.3.2, 3.5.1.2, 3.5.1.16, 3.5.4.4, 3.5.4.6, 3.5.4.7, 3.6.4.7, 8.1, 11.4, 11.6, 11.7
labeling, 4.4.1     eds, 3.5.4.4
labels, 4.4, 15.2.26     example alignment, 8.2.14
     sequence, 8.1     html, 5.6
          extract pdb, 8.1.3     color, 19.3.10
          from file, 8.1.4map, 3.5.1.15.7, 3.5.4.4, 3.5.4.6, 3.5.4.7, 11.4, 11.6, 11.7
          paste, 8.1.2     cel, 3.5.4.5, 11.5
          swissprot, 8.1.1maps, 17.6.7, 21.3.28, 21.3.29, 21.5.10, 22.19
     libraries, 3.5.15.6, 14.6     cell, 3.5.4.5
     pdb, 3.6.4.3mark, 19.1.34
     sequence, 3.3.1     row, 19.1.34
local, 21.3.25, 21.3.26     shape, 19.3.9
     databases, 20     size, 19.3.9
     flexibility, 3.5.5.3markush, 16.20, 16.22, 22.18
     database.browse, 20.2     docking, 22.18
          edit, 20.3     library, 16.21.1
          query, 20.4mass, 21.4.22
          row, 20.3materials, 3.6.5
localpdb, 21.3.25max, 19.6
localseq, 21.3.26maxColorPotential, 3.5.1.15.10
lock, 3.6.5.8, 4.9.1, 15.2.29mean, 21.4.7
log, 19.3.7menu, 5.6.5
logP, 15.3.5, 16.1     chemistry, 3.5.13
logS, 15.3.5, 16.1     docking, 3.5.14
logarithmic, 19.3.7     homology, 3.5.12
logout, 3.5.1.18     molmechanics, 3.5.15
loop, 12.6, 21.3.21     tools chemical search, 3.5.10
     model, 12.6          molecular editor, 3.5.11
     modeling, 12.4.3     windows, 3.5.16
     model, 3.5.15.8, 14.8merge, 16.17, 21.4.5
     sample, 3.5.15.8, 14.8     two sets, 16.17
mac, 15.12.1mesh, 3.4.6, 3.4.7, 3.5.4.4, 3.5.4.6, 3.5.4.7, 3.6.5.6, 3.6.5.8, 3.6.5.9, 3.6.5.10, 4.9.1, 11.4, 11.6, 11.7, 21.3.19
macros, 6.6     clip, 3.6.5.8
macroshape, 3.5.3.22, 3.6.5.3     options, 3.6.5.5
make, 3.5.1.1.1, 3.5.1.1.7, 5.1.1, 19.1.1     save, 3.6.5.9
     animation, 5.1.1     options, 3.6.5.5
     flat, 21.6.19meshes, 3.6.5
     images, 4.11min, 19.6
     molecular document, 5.6minimize.cartesian, 3.5.15.7, 14.7
     molt, 20.1     global, 3.5.15.7, 14.7
     movie, 7.3     local, 3.5.15.7, 14.7
     receptor maps, 17.1.7mmff, 3.5.15.6, 14.6, 21.3.16, 21.6.10
     selection, 3.2     type, 4.4.2
     DNA, 3.5.1.1.3mnSolutions, 3.5.1.15.10
     RNA, 3.5.1.1.3model, 12, 12.1, 12.2, 12.3, 12.6, 12.7, 22.7, 22.7.1
     bond, 21.4.2     loop, 12.5
     chemical, 3.5.1.1.2modelers view, 12.4.2
     compound, 3.5.1.1.2     view, 12.4.2
     disulfide, 12.9, 21.4.17modeling, 3.5.15.3, 14.3
     molecule, 3.5.1.1modeller view, 12.4
     object, 3.5.1.1mol, 15.5, 15.5.1, 15.5.2, 15.5.3, 15.5.4, 22.17.2
     sequence, 3.5.1.1.4mol2, 15.5, 15.5.1, 15.5.2, 15.5.3, 15.5.4
making molecular slides, 5.2molcart, 15.12, 15.12.1, 15.12.2, 15.12.3, 15.12.4, 20, 21.1.2, 21.6, 21.6.3, 21.6.4, 21.6.5, 21.6.6, 21.6.16
     connect, 21.6.2     impose conformation, 3.5.15.4
     download dbs, 21.6.3     minimize, 3.5.15.7
     hostid, 21.6.1     mmff, 3.5.15.6
     installation, 15.12.1     regularization, 3.5.15.3
     license, 21.1.4     sample loop, 3.5.15.8
     search, 15.12.3     terms, 3.5.15.12
     start, 15.12.2     view stack, 3.5.15.10
     connect, 21.6.2     minimize, 3.5.15.7, 14.7
     hostid, 21.6.1     mmff, 3.5.15.6, 14.6
     license, 21.6.1molt, 20, 20.4
molclart, 21.1.4monitor, 21.6.15
molecular, 15.2.28, 15.2.29, 15.2.32, 15.2.33, 16.10, 21.6.12, 21.6.15monochrome, 15.2.26
     animations slides, 5monte carlo, 22.7.3
          transitions, 5.1montecarlo, 21.7.1
     document, 3.5.1.1.6mouse, 3.1.2, 4.7, 4.8
     documents, 22.3mov, 7, 7.1, 7.2
     editor, 21.6.7move, 3.1.15, 3.1.17, 3.5.3.19, 3.6.5.6, 4.8, 4.8.7, 21.4.5
          copy, 15.3.10     resize mesh, 3.6.5.6
          cut, 15.3.10     slide, 5.4.1
          paste, 15.3.10     structure, 4.8
          redo, 15.3.12     tools, 4
          selections, 15.3.9     rotate, 4.7
          undo, 15.3.12     slab, 4.7
     graphics molecule representation, 4.1     translate, 4.7
     mechaincs gamess, 14.11     z-rotation, 4.7
     mechanics, 14     zoom, 4.7
          convert, 14.1movie, 3.6.6, 7.2, 7.3, 21.3.20, 21.7.1
          edit structure, 14.5     directory, 7.3.1
          generate normal mode stack, 14.9     montecarlo, 21.7.1
          his asn, 14.2     scene, 7.3.2
          impose conformation, 14.4     tab, 3.6.6
          minimize, 14.7     directory, 7.3.1
          mmff, 14.6     edit, 7.3.7
          regularization, 14.3     export, 7.3.8
          sample loop, 14.8     making, 7, 7.1
          terms, 14.12     open, 7, 7.1
          view stack, 14.10     powerpoint, 7.2
     modeling, 12     preview, 7.3.8
     table, 16.8     resolution, 7.3.1
     weight, 15.3.5     rock, 7.3.6
molecule, 21.3.8, 21.6.8     rotate, 7.3.5
     editor, 15.3     scene, 7.3.2
molecules, 3.5.6.1     still, 7.3.3
moledit, 15.3.4     tween, 7.3.4
molmech icmconv, 3.5.15.1mpeg, 7, 7.1, 7.2
molmechaincs gamess, 3.5.15.11mpg, 7, 7.1
molmechanics, 21.7.2multi apf super, 16.24.5
     edit structure, 3.5.15.5multiple, 17.2.2, 22.19
     generate normal mode stack, 3.5.15.9     rec, 17.2.2
     his asn, 3.5.15.2     protein, 21.3.5
mutate, 21.4.15pca, 19.4
     residue, 21.4.13pdb, 3.3.4, 3.4, 3.4.1, 3.4.2, 3.4.3, 3.5.1.6, 3.6.4.1, 16.9.1, 21.3.25, 21.3.26, 21.4.4, 22.4
          N C, 21.4.14     chem gl, 16.9.3
     residue, 22.7.3          iw, 16.9.2
mutation, 21.4.13, 21.4.14     file, 21.4.3
navigate workspace, 3.2.7     html, 3.6.4.8
nearest, 21.4.22     preparation, 22.8.3
neighbors, 22.2.3     sensitive query, 3.6.4.5
new, 3.3, 3.3.3, 3.5.1.1.1, 8.1     convert, 3.5.15.1, 14.1
     compound, 3.5.1.1.2     recent, 3.5.1.17
     dna, 3.5.1.1.3     search, 3.1.1, 3.6.4, 3.6.4.3
     peptide, 3.5.1.1.1     table, 3.6.4.3
     protein, 3.5.1.1.4pdbsearchfield, 3.5.2.13
     table, 19.1.1pdbsearchhomology, 3.5.2.15
     chemical, 3.5.1.1.2pdbsearchidentity, 3.5.2.14
     compound, 3.5.1.1.2pdbsearchresults, 3.6.4.3
     dna, 3.5.1.1.3pdbsearcsequence, 3.5.2.16
     protein, 3.5.1.1.4peptides, 3.5.1.1.1
     rna, 3.5.1.1.3perspective, 3.5.3.9
     script, 3.5.1.1.5ph4, 15.9
     table, 3.5.1.1.7, 19.1.1     draw 2d, 15.9.1
nmr, 21.4.18          3d, 15.9.2
normal modes, 3.5.15.9, 14.9     search, 15.9.3
notations, 1pharmacophore, 15.2.33, 15.9.5
numbers, 15.2.26     2D, 22.10.4
nvidia, 21.1.1     3D, 22.10.3
object, 3.1.15, 3.4.2, 3.5.1.8.1, 3.5.1.8.2, 21.3.8, 22.4     clone, 15.9.2
objects, 3.6.4.9     draw2D, 15.9.1
occlusion, 3.6.5.10     draw3D, 15.9.2
     shading, 3.6.5.10     edit, 15.9.1, 15.9.2
occupancy, 22.8.2     move, 15.9.2
oda, 3.5.5.4, 13.4, 17.6, 17.6.1, 17.6.2     new, 15.9.2
older version, 3.5.1.9     search, 15.9, 15.9.3, 22.10.3, 22.10.4
omega, 4.4.5, 21.3.17phi, 4.4.5, 21.3.17
open, 3.5.1.2, 19.1.2phylogenetic, 8.5.4
     with password, 3.5.1.3phylogeny, 8.5.4
     movie, 7, 7.1pick, 22.2.1, 22.2.2
     password, 3.5.1.3picking, 4
optimal, 3.5.5.4, 13.4, 17.6, 17.6.1, 17.6.2     atoms, 3.1.3
optimize, 3.5.15.2, 14.2, 22.7.3     residues, 3.1.3
origin, 4.4.12, 21.3.9picture, 3.1.19, 3.5.1.13, 5.6.3
other selection, 3.2.13     tips, 3.1.19
outside, 21.5.10planar, 3.5.6.7, 4.4.5, 9.7, 21.3.17
overlay, 21.3.5, 21.4.6     angle, 9
package.activeicm, 6.5     angle, 4.5.2
packing, 3.5.4.1, 11.1plane, 3.6.5.8, 4.9, 4.9.1, 4.10, 21.3.10, 21.3.20, 21.3.22
parallelization, 17.4.7     faq, 21.3.22
password, 15.12.4plot, 3.5.1.15, 3.5.1.15.8, 17.4.10, 19.3, 19.3.1, 19.3.4, 19.3.5, 19.3.7, 19.3.9, 19.3.10, 19.3.11, 19.3.12, 19.3.13, 19.3.14, 19.3.15, 19.3.16, 19.3.17, 22.14, 22.14.2
paste, 15.3.13, 19.1.26     axis, 19.3.7
pbs, 17.4.6     color, 19.3.10
     grid, 19.3.11printer.resolution, 3.5.1.15.6
     header, 19.3.5probe, 21.5.14
     inline, 19.3.17problem, 21.9.4
     logarithmic, 19.3.8problems, 21.9
     mark, 19.3.9     with selection, 21.9.2
     preferences, 3.5.1.15.8project, 3.5.1.4, 17.6.3
     regression, 19.3.12     name, 17.1.4
     selection, 19.3.14     close, 3.5.1.12
     zoom translate, 19.3.13     rename, 3.5.1.8
     axis, 19.3.11properties, 4.4.2, 16.1, 21.6.12
     display, 19.3.11property, 3.4.7, 15.3.5, 21.6.12, 21.6.13, 21.6.14, 21.6.15
     grid, 19.3.11     monitor, 15.3.5
     inline, 19.3.17propogate, 22.2.5
     logarithmic, 19.3.8protect, 5.6.7
pls, 16.4, 16.5, 19.5protein, 3.4.1, 3.4.2, 3.4.7, 8, 21.4.5, 22.7.4
pmf, 21.5.7     health, 3.5.5.2, 13.2
png, 3.5.1.13, 4.11, 4.11.1, 5.6.3, 15.5, 15.5.4     structure analysis, 9
pocket, 3.1.12, 3.4.6, 3.5.5.5, 13.5, 17.1, 21.3.13, 21.4.11, 21.5.11, 22.6.1               closed cavities, 9.4
     conservation, 21.4.12               contact areas, 9.3
     display, 18.3               distance, 9.6
     peptide, 3.1.12               find related chains, 9.1
     properties, 3.1.12               finding dihedral angle, 9.8
     surface, 22.12.5                    planar angle, 9.7
portait, 3.5.1.15.6               rama export, 9.10
postscript, 3.5.1.15.6               ramachandran plot, 9.9
potential mean force, 17.4.4               rmsd, 9.2
powerpoint, 22.3               surface area, 9.5
ppbatch, 17.6.8     superposition, 10
ppepitope, 17.6.6          select superposition, 10.1
ppmaps, 17.6.7          superimpose 3D, 10.3
ppresults, 17.6.9               grid, 10.5
pproc, 17.6.2               multiple proteins, 10.4
ppsetligand, 17.6.5protein-protein, 3.5.5.4, 13.4, 17.6, 17.6.1, 17.6.2, 17.6.3, 17.6.4, 17.6.5, 17.6.7, 17.6.8, 17.6.9
ppsetproject, 17.6.3protein-proteindocking, 17.6.6
ppsetreceptor, 17.6.4     convert, 3.5.15.1, 14.1
ppt, 6.4, 6.6, 21.3.36protonated, 21.4.15
predict, 8.2.2, 16.4, 16.5, 19.5, 19.5.2, 21.6.14, 21.6.18protprot, 17.6
predicting bioassays, 19.5.2psa, 15.3.5
     compound properties, 19.5.2psi, 4.4.5, 21.3.17
preferences, 3.5.1.15, 21.3.25, 21.3.26purple box, 3.5.3.23
presentatio, 5.6.5qs calculate distance, 3.4.9
presentation, 6, 6.4     convert chemical from pdb, 3.4.3
presentations, 5, 21.3.19          protein, 3.4.2
preserve, 21.6.11     ddali, 3.3.6
press-and-hold to rotate, 15.3.4     hydrogen bond, 3.4.8
preview export movie, 7.3.8     pdb chem gl, 3.4.5
principal component analysis, 19.4               iw, 3.4.4
     components, 19.5.3     quick pocket, 3.4.6
print, 19.3.15, 19.6.2     read pdb, 3.4.1
     plot, 19.3.15     selection, 22.2.1
          ali, 3.3receptor, 17.2.2, 17.6.4, 17.6.6, 21.5.2, 21.5.15, 21.5.16, 22.19
          fasta, 3.3.2     from pdb, 17.1.1
          load, 3.3.1     flexibility, 22.20
          new, 3.3.3     surface, 22.12.5
          pdb, 3.3.4recover, 3.5.2.11
     surface, 3.4.7rectangle, 22.2.1, 22.2.2
qsar, 16.4, 16.5redo, 3.5.2.10, 15.3.12
     learn predict, 16.4refine, 12.7, 12.8
     predict, 16.5     side chain, 12.8
quad.buffer, 21.2.3region, 17.6.6
quality, 3.5.1.14, 3.5.1.15.5regresion, 19.3.12
query, 12.3, 21.6.5, 21.6.6, 21.6.16regression, 19.5.1, 19.5.3
     molt, 20.4regul, 12.7
     pdb, 3.6.4.2regularization, 3.5.15.3, 12.7, 14.3
          sequence, 3.6.4.4related, 3.5.6.1
     processing, 15.8.3relationship, 19.5
     setup, 15.8.1release, 1
quick, 3.1.19reload, 3.5.1.8.1, 3.5.1.8.2, 17.1.15, 21.5.5
     start chain breaks, 3.1.10     dock results, 17.1.15
          move structure, 3.1.2reloading object not running, 3.5.1.8.2
          protein, 3.4reloadingobjectrunning, 3.5.1.8.1
          read pdb, 3.1.1remove, 3.1.10, 21.3.6, 21.3.7, 21.3.9
          representation, 3.1.9     explixit.hydrogens, 16.2
          selection, 3.1.4     salt, 16.2
               level, 3.1.5rename project, 3.5.1.8
          sequence alignment, 3.3.5renumber, 21.4.4
          what is selected, 3.1.6replace chemical, 15.2.30
     dispalay.distance, 4.5.1replacement, 18.7
     start color, 3.1.11representation, 3.5.3.19
quit, 3.5.1.18residue, 3.5.1.15.7, 21.3.8, 21.4.15, 21.4.22
     group, 16.21     alternative orientaiton, 22.8.3
racemic, 15.2.26, 16.12, 21.5.22     content, 8.2.1
radius, 22.2.3     propogate, 22.2.5
rainbow, 3.5.1.15.5, 4.4.16, 15.2.33     content, 8.2, 8.2.1
rama export, 3.5.6.9     mutate, 21.4.13, 21.4.14
ramachandran plot, 3.5.6.9, 9, 9.10residues, 3.4.6, 21.3.13
range, 5.1.2resize, 3.6.5.6, 4.11.3
ratio.selection, 3.5.1.15.5restore, 3.5.2.11, 3.6.5.8, 4.9.1
     dock ligand, 18.4     recent backup, 3.5.2.11
reactions, 15.11, 16.23results, 3.6.4.6, 17.6.9
read, 3.4.1, 3.5.1.2, 3.5.1.8.1, 3.5.1.16, 3.6.4.1, 3.6.4.7, 8.1     stack, 17.1.13
     chemical, 15.1.1review and adjust binding site, 17.1.6
     table, 19.1.2rgroup, 16.21
     pdb, 3.1.1, 3.6.4.3ribbon, 3.1.10, 3.5.1.15.9, 3.6.1, 4.1.3, 4.1.6, 21.3.24, 21.3.35
     sequence, 3.3.1     as a mesh object, 21.3.3
     table, 19     faq, 21.3.24
reagent, 16.23     preferences, 3.5.1.15.9
rear, 3.6.5.8, 4.9.1     style, 3.5.1.15.9
recent files, 3.5.1.16     breaks, 4.1.6
     pdb codes, 3.5.1.17     cylinders, 4.1.6
     worm, 4.1.6scan, 17.1.12
ribbonColorStyle, 3.5.1.15.9     hits, 17.1.12
right, 3.1.16scatter, 17.4.10
     click, 3.1.16scatterplot, 17.4.12
rigid, 16.24score, 17.4.8, 21.5.8, 21.5.9, 21.5.19
     super, 16.24.2     threshold, 17.4.4
          table, 16.24.1screen, 22.16, 22.17.1
ring, 15.3.2, 15.8.1screening, 17.4, 17.4.1, 17.4.2
rings, 15.2.26, 16.10, 16.24screenshot, 7, 7.1
rmsd, 3.5.6.2, 9, 9.2, 21.4.7, 21.4.8, 22.7.5     movie, 7.2
rock, 3.5.3.15, 5, 5.1, 5.1.1, 7.3.6script, 3.5.1.1.5, 5.6.4, 5.6.5, 21.4.19, 21.8, 21.8.1, 21.8.2, 21.8.3
     speed, 5.1.2sdf, 15.2.33, 15.5, 15.5.1, 15.5.2, 15.5.3, 15.5.4, 15.12, 20.1, 21.6.3, 21.6.4, 22.17.2
root, 21.4.7search, 15.12, 15.12.3, 20.2, 21.6.16
     mean square deviation, 3.5.6.2, 9.2     filter, 15.8.2
rotate, 3.1.2, 3.5.3.15, 4, 4.8, 4.8.1, 4.8.2, 5, 5.1, 5.1.1, 7.3.5, 15.2.32, 21.6.19     in workspace, 3.5.2.4
     chemical, 15.2.32     in.workspace, 3.5.2.4
     when pasting, 15.3.4secondary structure, 3.5.5.1, 13.1, 21.3.21
     easy, 3.5.3.12     sctructure, 8.2.2
     speed, 5.1.2     structure, 4.1.6, 8.2
rotating fragment in editor, 15.3.4select, 19, 19.1.34, 21.4.22
rotation, 3.1.3, 4.8.1     a tree branch, 19.6.1
row, 19, 19.1.20, 19.1.26, 19.1.34     amino acid, 3.2.9
     flag, 19.1.11     chemical, 15.3.9
     mark, 19.1.11     duplicates, 16.19
     hide, 15.2.6     neighbors, 3.2.10
     show, 15.2.6          graphic, 3.2.11
ruler, 4.4.16     object, 3.2.8
rundock, 21.5.17     superposition, 3.5.7.1
salts, 15.2.16     tree, 19.6.1
sample, 16.24     atom, 3.1.4, 3.1.5, 3.1.6
save, 3.6.5.9, 4.11.1, 5.1.4, 19.3.16, 19.6.2, 21.3.34     graphical, 3.1.4, 3.1.5, 3.1.6
     chemical, 15.3.7     object, 3.1.4, 3.1.5, 3.1.6
     image, 4.11.1     purple.box, 3.5.3.23
          plot, 19.3.16     residue, 3.1.4, 3.1.5, 3.1.6
     object, 3.1.13     workspace, 3.1.4, 3.1.5, 3.1.6
     print delete alignment, 8.5.2selectall, 3.5.2.3
     project icb, 3.1.14selecting.neighbors, 3.2.11
     slide, 5.4selection, 19.3.14, 19.6.1, 19.6.3, 21.3.4, 21.3.6, 21.3.7, 21.3.8, 21.3.12, 21.3.33, 21.4.9, 21.4.10, 21.4.22, 21.5.15, 22.2, 22.2.1, 22.2.2
     table, 19.1.19     clear, 3.5.2.7
     tree, 19.6.2     neighbors, 3.5.2.8
     image, 3.1.19, 3.5.1.14     toolbar, 3.2.1
     object, 3.1.13     alignment, 3.2.13
     password, 3.5.1.10     all, 3.5.2.3
     picture, 3.5.1.14     alter, 3.2.4
     project, 3.1.14, 3.5.1.7, 3.5.1.8, 3.5.1.9     amino, 3.2.9
     table.view, 19.1.6     atom, 3.2.1, 3.5.2.5
saving, 3.5.1.7     basic, 3.2.3
     project, 3.5.1.7     change, 3.2.4
scaffold, 16.14     clear, 3.5.2.7
scale, 3.5.1.15.5     column, 19.1.21
     graphical, 3.2.1, 3.2.11     types, 3.5.15.6, 14.6
     invert, 3.5.2.6, 19.1.21setAPFparams, 21.6.18
     lasso, 3.2.1setup, 17.6.5, 21.5.14
     level, 3.5.3.3     ligand receptor, 18.1
     mode, 3.5.3.4sgi, 21.1.3
     near atoms, 3.5.2.8shade and box, 8.5.6
     neighbors, 3.2.10, 3.2.12, 3.5.2.5, 3.5.2.8shading, 3.6.5.10
     object, 3.2.8shadow, 3.5.3.13
     other, 3.2.13sheet, 21.3.21
     pick, 3.2.1shell preferences, 3.5.1.15.10
     properties, 3.5.2.5shift, 4.4.3
     range, 19.1.21shine, 3.5.1.15.5, 3.6.2
     residue, 3.5.2.5, 22.2.5shineStyle, 3.5.1.15.3
     row, 19.1.21show, 19.1.30
     sphere, 3.2.10     hide column, 19.1.30
     spherical, 3.5.2.8, 22.2.3side, 15.2.27
     superposition, 3.5.7.1, 10.1     by side, 15.2.27
     table, 3.2.13, 19.1.21               stereo, 3.5.3.6
          elements, 19.1.21     chains, 12.8
     toolbar, 3.2.1side-chains, 17.2.1
     tools, 3.2.2, 3.2.3, 3.2.4, 3.2.5sigmaLevel, 3.5.4.6, 3.5.4.7, 11.6, 11.7
     whole, 3.2.8similar, 3.5.6.1
     workspace, 3.2.6, 3.2.12similarity, 16.16
selectioninvert, 3.5.2.6simulation, 21.7.2
selections, 3.2simulations, 21.7
     links, 8.2.9single, 15.3.6
selectneighbors workspace, 3.2.12sketch accents, 3.5.3.14
sequence, 3.3.1, 3.3.2, 3.3.3, 3.3.4, 3.3.6, 8, 8.1, 8.2, 8.2.8, 12.3, 21.4.12, 22.4, 22.5, 22.6, 22.6.2     accents, 3.5.3.14
     analysis, 8.2skin, 3.6.1, 4.1.3, 4.1.7, 21.3.15
     reordering, 8.5.4slab, 3.6.5.8, 4.9.1
     structure, 8.2.6slice, 4.9
     type, 8.2.4slide, 5.1.4, 5.6.1, 21.3.32
     DNA, 8.2.4     effects, 5.5
     alignment, 3.3.5, 8.2.5, 8.4.5     navigation, 5.3.1
     nucleotide, 8.2.4     show, 5.3
     protein, 8.2.4     blend, 5.5
     search, 8.3     effect, 5.5
     structure.alignment, 8.2.6     smooth, 5.5
sequences, 3.3, 3.6.4.1, 8, 21.3.26     transition, 5.5
     unique, 8.2.13slides, 5, 5.2, 5.3, 21.3.31
     extract, 8.2.13smiles, 15.1.1, 15.3.5, 16.1, 16.6, 16.7
     unique, 8.2.13solvent.accessible.area, 21.4.19
set, 15.2.29, 21.4.21sort hitlist, 17.4.9
     bond type, 3.5.15.5, 14.5     table, 16.18
     charges, 3.5.15.6, 14.6sorting, 17.4.9
     chirality, 3.5.15.5, 14.5     compounds, 19.5.4
     disulfide, 12.9, 21.4.17spec, 3.6.2
          bond, 3.5.15.5, 14.5specifications, 21.2.1
     formal charge, 3.5.15.5, 14.5     faq, 21.2.1
     tether, 3.5.15.5, 14.5speed, 5.1.2
spherical, 21.4.9, 21.4.12, 22.6.2     multiple, 3.5.7.3, 10.4
     selection, 22.2.3     rigid, 16.24.1, 16.24.2
split, 16.22     substructure, 16.24.1, 16.24.2, 16.24.3
spreadsheet, 16.8superposition, 16.24
square, 21.4.7surface, 3.4.7, 3.5.1.15.5, 3.6.1, 4.1.3, 4.1.9, 21.3.15
squence.amino acid, 8.2.4     area, 3.5.6.5, 9
stack, 17.1.11, 17.6.9, 21.7.2     area, 3.5.6.5, 9.5
standard table, 19.1surfaces, 3.4.2, 3.6.5.1
standardize, 16.2surrounding, 3.4.6, 21.4.11, 22.6.1
     table, 16.2swissprot, 3.3.1, 8.1
start, 15.12.2symmetry, 3.5.4.1, 3.5.4.3, 11.1, 11.3, 22.8, 22.8.1
     dock, 17.1     packing, 3.5.4.1
startup, 21.8.2tab, 19.1.2, 19.1.19
static, 21.4.8     pdb, 3.6.4
stereo, 3.5.1.15.6, 15.2.26, 21.2.2, 21.2.3, 21.3.18, 21.9.4table, 15.2.21, 15.2.22, 15.2.26, 15.2.28, 15.2.29, 15.2.32, 15.2.33, 16.8, 16.10, 16.24.1, 19, 19.1.26, 19.1.31, 19.1.34, 19.3, 19.3.1, 19.3.4, 19.3.5, 19.3.7, 19.3.9, 19.3.10, 19.3.11, 19.3.12, 19.3.13, 19.3.14, 19.3.15, 19.6, 21.4.19, 21.6.9, 21.6.10, 21.6.12, 21.6.13
     hardware, 3.5.3.7     alignment, 19.1.10
     side-by-side, 3.5.3.6     clone, 19.1.14
stereohard faq, 21.2.2     color, 19.1.8
stereoisomer, 16.12     column format, 19.1.31
stereoisomers, 16.13     copy, 19.1.27, 19.1.28
stick, 3.5.1.15.5     delete, 19.1.15
still, 7.3.3     edit, 19.1.22
stop, 5.1.3     filter, 19.1.33
store, 3.5.3.19, 5.1.4, 21.3.23     find, 19.1.7
     current view, 3.5.3.19          replace, 15.2.30
               faq, 21.3.23     font, 19.1.9
strain, 3.5.5.2, 13.2          size, 21.3.1
strip, 21.4.9     grid, 19.1.5
structure, 3.4, 3.5.4.3, 11.3, 19.5, 21.4, 22.4, 22.6     histogram, 19.3.1
     ensemble, 3.5.15.9, 14.9     insert, 19.1.23
     representation, 4.1.3     layout, 19.1.5
     smiles, 16.7     mark, 19.1.11
     display, 3.1.8          row, 19.1.11
     undisplay, 3.1.8     mouse, 19.1.35
structures, 3.6.4.1, 15, 15.1     navigation, 19.1.4
style, 3.5.1.15.5     new, 3.5.1.1.7
substructure, 15.10, 15.12.3, 16.3, 21.6.5, 21.6.6          column, 19.1.23
     alerts, 16.3     plot, 19.3
suface, 21.4.19     print, 19.1.17
sulfur, 12.9     rename, 19.1.13
superimpose, 3.5.7, 10.2, 21.3.5, 21.4.6, 21.4.7, 21.4.8, 22.6, 22.7.5     rightclick, 19.1.12
     3D, 3.5.7.2     save, 19.1.3
     grid, 3.5.7.4          selection, 19.1.3
     multiple proteins, 3.5.7.3     search, 19.1.7
     3D, 3.5.7.2, 10.3     select, 19.1.21
     Calpha, 3.5.7.2, 10.3     setup, 19.1.16
     arrange.grid, 3.5.7.4, 10.5     sort, 19.1.32
     backbone, 3.5.7.2, 10.3     split fragments, 15.2.31
     flexible, 16.24.3     view, 19.1.5
     heavy atoms, 3.5.7.2, 10.3          save, 19.1.6
     action, 19.1.35     view, 15.2.4, 15.2.27
     alignment, 19.1.10     width, 19.1.4
     append, 19.1.33tables, 16.16, 19
     clone, 19.1.14tautomer, 16.11, 21.4.15
     color, 19.1.8tautomers, 16.11
     column, 15.2.2, 19.1.23, 19.1.24, 19.1.30temperature, 3.5.5.3, 13.3
     columns, 15.2.6template, 12.3, 16.24
     compare, 15.2.19     docking, 21.5.4
     copy, 15.2.5terminal, 15.2.26
     cursor, 19.1.35     font size, 21.3.1
     delete, 19.1.12, 19.1.15text, 3.5.1.15.7, 5.6, 5.6.1, 5.6.6, 15.2.26, 15.12.3, 21.6.16
     display, 21.8.4     search, 15.8.4
     double.click, 19.1.35texture, 3.6.5
     edit, 15.2.15thoroughness, 16.10, 16.24, 21.5.13
     excel, 15.2.8, 19.1.18three, 15.2.21, 21.6.11
     export, 15.6threshold, 3.5.1.15.5
     filter, 15.2.10, 19.1.33tier, 3.1.17
     find-replace, 15.2.11time, 21.5.12
          to screen, 19.1.4tools 3D, 3.5.5
     font, 19.1.9     analysis, 3.5.6
     foreground, 21.8.4     append rows, 3.5.9.6
     grid lines, 19.1.4     extras, 3.5.8
     hide, 19.1.30          plot function, 3.5.8.1
     hyperlink, 15.2.13     identify ligand binding pocket, 3.5.5.5
     insert, 19.1.25     oda, 3.5.5.4
     join, 3.5.9.4     superimpose, 3.5.7
     label, 15.2.12     table, 3.5.9
     landscape, 19.1.16          Learn, 3.5.9.1
     mark, 15.2.12          clustering, 3.5.9.3
     merge, 3.5.9.4, 15.2.20, 16.17          merge, 3.5.9.4
     mouse, 19.1.35          predict, 3.5.9.2
     name, 19.1.13torsion, 4.8.6, 21.4.16
     new, 19.1.1     angles, 4.8, 4.8.6
     options, 19.1.12transition.blend, 21.3.32
     orientation, 19.1.16transitions, 5, 21.3.31
     portrait, 19.1.16translate, 3.1.2, 4, 4.8, 15.2.28
     print, 15.2.9, 19.1.4, 19.1.17translation, 3.1.3, 4.8.3, 8.2.3, 19.3.13
     read, 19.1.2transparent, 3.6.5.7
     rename, 19.1.13     background, 4.11.3
     right click, 19.1.12     ribbon, 21.3.3
     row, 19.1.25tree, 8.5.4, 19.6.1, 19.6.2, 19.6.3
     rows, 3.5.9.6     branch swapping, 8.5.4
     save, 15.2.7, 19.1.3, 19.1.4, 19.1.19     distance, 16.15.3
     scale, 19.1.16     edit, 16.15.4
     scroll, 19.1.4     reorder, 16.15.3
     sdf, 15.2.7trouble shooting, 21.9.1
     select, 19.1.21trouble-shooting, 21.9.2
     setup, 19.1.16troubleshooting, 21.9
     sort, 15.2.3, 16.18, 19.1.32truncating a mesh object, 21.3.14
     standard, 19.1     crash qlock, 21.9.3
tut analyze alternative orientations, 22.8.3updates, 1
          occupancy, 22.8.2use activeicm, 6.4
          symmetry, 22.8.1user, 1, 15.12.4
     bind pocket, 22.6user-defined groups, 15.3.3
     hydrogen bond, 22.6.3uundisplay-all, 3.5.3.1
     ligand pocket, 22.6.1van der waal, 4.4.15
     multiple receptor, 22.19variable, 3.5.1.15.7, 21.3.8
     pocket conservation, 22.6.2verbose, 16.10
tut2, 22.4vicinity, 16.10
tut2a, 22.4.1video, 7, 7.1
tut2b, 22.4.2     intro, 7.1
tut3, 22.7view, 3.5.3.19, 15.2.26, 21.3.23, 21.7.2
tut3a, 22.7.1     center, 3.5.3.20
tut3b, 22.7.2     color background, 3.5.3.18
tut3bb, 22.7.3     dock results, 17.1.11
tut3c, 22.7.4     macroshape, 3.5.3.22
tut3e, 22.8.4     menu, 3.5.3
tut3f, 22.7.5     mesh clip, 4.9.1
tut4b, 22.9.1     selection level, 3.5.3.3
tut4c, 22.10.1          mode, 3.5.3.4
tut4d, 22.10.2     tools, 3.5.3
tut5, 22.16     tools2, 4.6
tut5a, 22.16.1     tree, 19.6.3
tut5b, 22.16.2     undisplay all, 3.5.3.1
tut5c, 22.17.1     stach, 3.5.15.10, 14.10
tut5e, 22.17.2virtual, 17.4, 17.4.1, 17.4.2, 22.16, 22.17.1
tutorial 2D pharmacophore, 22.10.4     screening examples, 22.17
     3D pharmacophore, 22.10.3virus, 3.5.4.3, 11.3
     chemical search, 22.10vls, 17.2, 17.4, 17.4.5, 21.5.8, 21.5.9, 22.17.2
     edit chemical, 22.9.2     getting started, 17.4.2
     graphical selections, 22.2     histogram, 17.4.11
     molecular documents, 22.3          scatter plot, 17.4.10
     sequence alignment, 22.5     introduction, 17.4.1
               link, 22.5.3     preferences, 17.4.4
               load pdb, 22.5.1     results, 17.4.8
                    sequence, 22.5.2     run, 17.4.5
               sequence conservation, 22.5.4     scatterplot, 17.4.12
tutorials, 22     results, 17.4.8
tween, 7.3.4volume, 15.3.5
two, 15.2.21, 21.6.11wavefront, 3.6.5, 3.6.5.9
unclip, 3.6.5.8, 4.9.1weak, 21.4.20
undisplay, 3.1.7, 4.1.1, 21.3.9, 21.3.33web, 22.3
     origin, 4.4.12     browser, 3.5.1.11
undo, 3.5.1.15, 3.5.2.9, 15.3.12weight, 16.1, 21.6.12, 21.6.15
     redo structure, 15.3.12weighted, 19.6
uniprot, 3.3.1what to dock, 17.1.2
unique, 15.2.26, 16.19width, 19.1.20
unit, 3.5.4.3, 11.3window, 3.1.17
units, 21.5.1windows, 3.1.18, 15.12.1
unix, 21.8.2wire, 3.5.1.15.5, 3.6.1, 4.1.3, 4.1.4, 21.3.4, 21.3.22
working with pdb, 3.6.4.6 
          the molecular editor, 22.9 
workspace, 3.1.7, 3.4.4, 16.9.2, 22.2.2 
     panel, 3.1.7 
     selection, 3.2.6 
     navigation, 3.2.7 
write, 3.1.19, 4.11.1, 19.3.16, 21.6.4, 21.7.1 
     image, 3.5.1.14 
     image, 3.5.1.14 
     object, 3.1.13 
     picture, 3.5.1.14 
     project, 3.1.14, 3.5.1.7 
     table, 19.1.3 
writing a pdb file, 21.4.3 
     ray, 3.5.4 
xi, 4.4.5, 21.3.17 
xstick, 4.1.5, 21.3.22 
xyz, 21.3.9 
zoom, 3.1.2, 3.1.3, 4, 4.8, 4.8.4, 15.2.28, 19.3.13 

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