Index

2D, 5.5.9, 16.2.21, 16.2.26, 17.4, 17.6.2, 17.6.4Display, 23.3.25
     to 3D, 17.6, 17.6.3Distance, 18.4.9.5
     depiction, 17.6.2Dock Directory, 3.4.1.15.2
3D, 5.5.9, 16.2.21, 16.2.26, 16.2.29, 17.6.2, 22.1.11Docking, 23.3.25
     chemical, 17.6.1Editor, 3.4.1.15.2
     ligand editor.add substituent, 22.6.13Error in saving configuation settings: You are not a license administrator, 23.10.1
               atomic energy circles, 22.6.7FILTER.Z, 3.4.1.15.2
               begin edit, 22.6.11     gz, 3.4.1.15.2
               center ligand, 22.6.10     uue, 3.4.1.15.2
               display, 22.6.4Filter.zip, 3.4.1.15.2
               dock, 22.6.20Formula, 23.7.12, 23.7.15
               dock-tether, 22.6.21Frequently Asked Questions, 23
               edit 2D, 22.6.15GAMESS, 3.4.16.11, 15.11
               fragment linkers, 22.6.23GIF, 3.4.1.14, 8
               hydrogen atoms, 22.6.8GRAPHIC.store Display, 3.4.1.15.3
                    bond, 22.6.6     NtoC Rainbow, 3.4.1.15.4
               ligand setup, 22.6.1     alignment Rainbow, 3.4.1.15.4
               minimization, 22.6.19     atomLabelShift, 3.4.1.15.7
               multiple substituent, 22.6.14     ballStickRatio, 3.4.1.15.1
               preferences, 22.6.3     center Follows Clipping, 3.4.1.15.3
               purple box, 22.6.18     clash Style, 3.4.1.15.3
               receptor setup, 22.6.2     clashWidth, 3.4.1.15.3
               save spreadsheet, 22.6.17     clip Grobs, 3.4.1.15.3
               screen substituents, 22.6.22          Skin, 3.4.1.15.3
               surface, 22.6.5          Static, 3.4.1.15.3
               undo redo, 22.6.12     discrete Rainbow, 3.4.1.15.4
               unsatisfied hydrogen bonds, 22.6.9     displayLineLabels, 3.4.1.15.7
     object, 5.2.6     displayMapBox, 3.4.1.15.3
     predict, 14     distance Label Drag, 3.4.1.15.1
          helices strands, 14.1     dnaBallRadius, 3.4.1.15.9
          local flexibility, 14.3     dnaRibbonRatio, 3.4.1.15.9
          protein health, 14.2     dnaRibbonWidth, 3.4.1.15.9
          tools identify ligand binding pocket, 14.5     dnaRibbonWorm, 3.4.1.15.9
               oda, 14.4     dnaStickRadius, 3.4.1.15.9
4D, 22.9.1     dnaWormRadius, 3.4.1.15.9
64, 23.1.2     font Scale, 3.4.1.15.7
APF, 17.18.5     fontColor, 3.4.1.15.7
     template, 17.18.4     fontLineSpacing, 3.4.1.15.7
ActiveICM, 3.4.1.11     grobLineWidth, 3.4.1.15.3
Area, 23.3.25     hbond Ball Period, 3.4.1.15.1
Atom Single Style, 3.4.1.15.3               Style, 3.4.1.15.1
Bad Groups, 23.7.12, 23.7.15     hbondAngleSharpness, 3.4.1.15.1
Blast, 23.3.24     hbondMinStrength, 3.4.1.15.1
BlastDB Directory, 3.4.1.15.2     hbondStyle, 3.4.1.15.1
     alphas, 5.5.3     hbondWidth, 3.4.1.15.1
COLLADA, 3.4.1.6     hetatmZoom, 3.4.1.15.1
CPK, 3.5.1, 5.1.1     hydrogenDisplay, 3.4.1.15.1
CisTransAmide Angle, 18.4.9.5     light, 3.4.1.15.3
Clash Threshold, 3.4.1.15.10     lightPosition, 3.4.1.15.3
DNA, 3.4.1.1.4, 9, 9.2.3     mapLineWidth, 3.4.1.15.3

     occupancyDisplay, 3.4.1.15.3     graphics crash, 23.10.2
     quality, 3.4.1.15.3IMAGE.bondLength2D, 3.4.1.15.6
     rainbow Bar Style, 3.4.1.15.4     color, 3.4.1.15.6
     resLabelDrag, 3.4.1.15.7     compress, 3.4.1.15.6
     resize Keep Scale, 3.4.1.15.3     gammaCorrection, 3.4.1.15.6
     ribbonRatio, 3.4.1.15.9     generateAlpha, 3.4.1.15.6
     ribbonWidth, 3.4.1.15.9     lineWidth, 3.4.1.15.6
     ribbonWorm, 3.4.1.15.9     lineWidth2D, 3.4.1.15.6
     rocking, 3.4.1.15.4     orientation, 3.4.1.15.6
          Range, 3.4.1.15.4     paper Size, 3.4.1.15.6
          Speed, 3.4.1.15.4     previewResolution, 3.4.1.15.6
     selectionStyle, 3.4.1.15.3     previewer, 3.4.1.15.6
     site Label Drag, 3.4.1.15.7     print, 3.4.1.15.6
               Shift, 3.4.1.15.7     printerDPI, 3.4.1.15.6
     siteArrow, 3.4.1.15.7     scale, 3.4.1.15.6
     stereoMode, 3.4.1.15.3     stereoAngle, 3.4.1.15.6
     stickRadius, 3.4.1.15.1     stereoBase, 3.4.1.15.6
     surfaceDotDensity, 3.4.1.15.3     stereoText, 3.4.1.15.6
     surfaceDotSize, 3.4.1.15.3ISIS, 23.7.8
     surfaceProbeRadius, 3.4.1.15.3IUPAC, 16.8
     transparency, 3.4.1.15.3Icm Prompt, 3.4.1.15.10
     wire Width, 3.4.1.15.1Inx Directory, 3.4.1.15.2
     wormRadius, 3.4.1.15.9JPEG, 3.4.1.14
     xstick Backbone Ratio, 3.4.1.15.1KMZ, 3.4.1.6
          Hydrogen Ratio, 3.4.1.15.1Log Directory, 3.4.1.15.2
          Style, 3.4.1.15.1LogP, 20.6
          Vw Ratio, 3.4.1.15.1LogS, 20.6
GROB.arrowRadius, 3.4.1.15.3MOL, 16, 16.1.1, 16.2.1, 16.2.21, 16.2.22, 16.2.23, 16.2.24, 18.4.3, 20.2
     atomSphereRadius, 3.4.1.15.3MOL2, 16.1.1, 18.4.3
     contourSigmaIncrement, 3.4.1.15.3MOLT, 21.1
     relArrow Size, 3.4.1.15.3MOVIE.frame Grab Mode, 3.4.1.15.4
     relArrowHead, 3.4.1.15.3Map Atom Margin, 3.4.1.15.10
GUI, 1     Sigma Level, 3.4.1.15.10
     auto Save, 3.4.1.15.4Markush, 17.17.6
               Interval, 3.4.1.15.4     create, 17.17.2
     autoSave, 23.3.32Max_Fused_Rings, 17.1
     autoSaveInterval, 23.3.32Mnconf, 3.4.1.15.10
     max Sequence Length, 3.4.1.15.4MolIPSA, 23.7.12, 23.7.15
     table Row Mark Colors, 3.4.1.15.4MolLogP, 23.7.12, 23.7.15
     workspace Folder Style, 3.4.1.15.4MolLogS, 23.7.12, 23.7.15
     workspaceTabStyle, 3.4.1.15.4MolPSA, 17.1
HBA, 23.7.12, 23.7.15MolVol, 17.1
HBD, 23.7.12, 23.7.15Molcart, 16.9.3
Hbond to selection, 18.4.9.5MoldHf, 17.1, 23.7.12, 23.7.15
How To Guide, 2Movie.fade Nof Frames, 3.4.1.15.4
Html, 4.1.8     quality, 3.4.1.15.4
Hydrogen.bond, 3.4.1.15.5          Auto, 3.4.1.15.4
ICM, 1NCBI, 23.3.24
     Browser How To, 2.1NMR, 4.1.1
          Pro How To, 2.2Nof_Atoms, 17.1

Nof_HBA, 17.1     Reference, 20.1.31
Nof_HBD, 17.1QSAR, 20.6, 20.6.1
Nof_Rings, 17.1     build model, 22.5.13
Nof_RotBonds, 17.1     predict, 22.5.14
Non-overlap, 18.4.9.5R, 16.12, 17.17.5
Nvidia GL failutre, 23.10.2     and S, 23.6.22
ODA, 23.3.25R-group, 16.11
Optimal, 23.3.25RMSD, 11.2
Output Directory, 3.4.1.15.2Ramachandran Plot, 10.9
PBS, 18.4.6Real Format, 3.4.1.15.10
PCA, 20.6.1, 20.6.3Receptor Setup, 18.1.5
     analysis, 17.13     Label Shift, 3.4.1.15.7
PDB, 3.4.5.3, 4.1.4, 4.1.8, 4.2, 9.1, 12.3, 16.4          Style, 3.4.1.15.7
     Directory, 3.4.1.15.2RotB, 23.7.12, 23.7.15
          Style, 3.4.1.15.2SAR, 20.6
     link, 20.1.31     table, 17.17.6
     Search, 3.4.2.12, 3.4.2.13, 3.4.2.14, 3.4.2.15, 3.4.2.16SCORE, 23.6.7, 23.6.18
          Field, 3.4.2.13SDF, 16, 16.1.1, 16.2.21, 16.2.22, 16.2.23, 16.2.24, 18.4.3, 20.2
          Homology, 3.4.2.15SEQUENCE.site Colors, 3.4.1.15.4
          Identity, 3.4.2.14SITE.label Style, 3.4.1.15.7
          Sequence, 3.4.2.16     labelOffset, 3.4.1.15.7
     convert, 4.2, 22.3.2     wrap Comment, 3.4.1.15.7
     query, 4.1.1.1SLIDE.ignore Background Color, 3.4.1.15.4
     search, 4.1.1, 4.1.1.1, 4.1.2, 22.3.1          Fog, 3.4.1.15.4
     sensitive search, 4.1.2SMILES, 16.3.11, 16.6.2
     similarity, 4.1.2Select Min Grad, 3.4.1.15.10
PFAM, 3.4.1.6Show Res Code In Selection, 3.4.1.15.7
PLOT.Yratio, 3.4.1.15.8Smiles, 23.7.12, 23.7.15, 23.7.17
     color, 3.4.1.15.8Swissprot, 3.4.1.6
     date, 3.4.1.15.8     Dat, 3.4.1.15.2
     draw Tics, 3.4.1.15.8     link, 20.1.31
     font, 3.4.1.15.8Temp Directory, 3.4.1.15.2
     fontSize, 3.4.1.15.8UNIX, 18.4.6
     labelFont, 3.4.1.15.8Uniprot, 20.1.31
     lineWidth, 3.4.1.15.8VLS, 18.4, 18.4.1, 18.4.2, 18.4.6, 18.4.9.2
     logo, 3.4.1.15.8     preferences, 18.4.4
     markSize, 3.4.1.15.8Var Label Style, 3.4.1.15.7
     orientation, 3.4.1.15.8Volume, 23.7.12, 23.7.15
     paper Size, 3.4.1.15.8     Change, 18.4.9.5
     previewer, 3.4.1.15.8Water Radius, 3.4.1.15.10
     rainbowStyle, 3.4.1.15.8Wire Style, 3.4.1.15.1
     seriesLabels, 3.4.1.15.8X-ray, 4.1.1, 18.1.1
PLS, 20.6.1XPDB Directory, 3.4.1.15.2
PNG, 3.1.19, 3.4.1.14, 8Xstick, 3.5.1, 5.1.1
Pharmacophore RMSD, 18.4.9.5a-bright, 3.5.2
Projects Directory, 3.4.1.15.2acceptor, 16.3.5
Prosite Dat, 3.4.1.15.2acid, 3.4.1.1.4
Protein, 23.3.25active, 7, 23.4.3
     Viewer, 3.4.1.15.2activeICM, 7.1
PubMed, 4.1.9activeicm, 7, 7.4, 7.6, 7.6.1, 23.4

     background images, 7.7     save, 9.5.2
     control, 7.5     search, 9.5.9
activityy, 20.6     selection, 9.5.10, 9.5.11, 9.5.12
add image album, 5.12.4     sequence offset, 9.5.7
adding fragment, 16.3.4     shade, 9.5.6
          in editor, 16.3.4     table, 9.5.7
administration, 16.13.4     view, 9.5.7
advanced alignment selectioection, 9.5.12alignments, 3.3, 9.4, 22.2
album, 5.12.4alpha, 3.5.2
alias, 16.3.3     channel, 3.4.1.15.6
align, 3.1.15, 3.3.5, 9.4.1, 17.4ambient, 3.5.2
     color 2D scaffold, 17.4amidinium, 17.5
     dna protein, 9.4.3amino, 3.4.1.1.4
     multiple sequences, 9.4.4analysis, 3.4.4, 9.2
     two sequences, 9.4.2angle, 3.4.7.7, 3.4.7.8, 5.5.5, 5.6, 5.9.6, 10.7, 10.8, 23.3.17, 23.5.16
     DNA to protein, 9.2.7, 9.4.3angstrom, 23.5.7
     multiple, 9.4.4animate, 3.4.3.15, 5.7.6
     sequence, 9.4, 9.4.5     view, 5.7.6
     two sequences, 9.2.5, 9.4.2animation, 6.1, 6.1.1, 6.1.2, 6.1.3, 6.1.4
alignment, 3.3.6, 22.3.3, 22.3.5, 23.5.12     store, 6.1.4
     comment, 9.5.3animations, 6
     editing, 9.5.1annotate, 17.3
     editor, 9.5     by substructure, 17.3
     example, 9.2.14antialias, 3.4.1.14, 3.4.3.10
     font size, 23.3.1     lines, 3.4.3.17
     format, 9.5.8     lines, 3.4.3.17
     gaps, 9.5.8apf, 23.7.18
     introduction, 9.4.1     super, 17.18.4
     reorder, 9.2.12     alignment, 17.18.5
     search, 9.5.9apf3Dqsa, 23.7.18
     selection, 9.5.10append.rows, 3.4.10.7
     view options, 9.5.7applying prediction models, 20.6.2
     box, 9.5.6area, 3.4.6.4, 3.4.7.3, 10.3, 14.4, 18.6, 18.6.1, 18.6.2
     color, 9.5.5, 9.5.6aromatic, 16.2.26
     comment, 9.5.3arrange, 3.1.18
     consensus, 9.5.5, 9.5.12     window, 3.1.18
     cut, 9.2.11arrow, 3.4.1.1.8
     delete, 9.5.2     graph, 23.3.8
     display title, 9.5.7as_graph, 23.3.8
     editor, 9.5asparagine, 3.4.16.2, 15.2
     extract, 9.2.10assign, 5.1.4
     gaps, 9.5.8     2D coordinates, 17.6.2
     horizontal scroll, 9.5.7     helices, 3.4.6.1, 14.1
     linked, 22.4.3     strands, 3.4.6.1, 14.1
     multiple, 9.2.8atom, 3.4.1.15.5, 16.2.26, 22.1.6, 22.1.7, 23.3.4, 23.3.5, 23.3.8, 23.3.15, 23.3.16, 23.5.10
     options, 9.5.7     charge, 23.5.21
     print, 9.5.2atomLabelStyle, 3.4.1.15.7
     rename, 9.5.7attachment, 16.3.2, 16.9.1
     reorder, 9.2.12     point, 17.17.3
     ruler, 9.5.7author, 4.1.1.4

autofit, 18.5break, 3.1.10
autosave, 23.3.32browse, 16.2.29, 18.1.12
ave, 20.7     mode, 16.2.29
avi, 8, 8.1     molt, 21.2
axes, 20.4.11     stack, 3.4.16.10, 15.10
axis, 20.4.7bugs, 23.10
     options, 20.4.6build, 6.1.1
     grid, 20.4.6     homology model, 13.3
     range, 20.4.6     hydrogens, 3.4.16.5, 15.5
     title, 20.4.6buried molSurface, 18.4.9.5
b-factor, 3.4.6.3, 14.3, 18.1.1, 22.3.9buttons, 7.6
backbone, 23.3.12bye, 3.4.1.18
background, 5.3.2, 5.3.3cache, 7.6.1
     color shortcut, 23.3.2calculate, 17.1, 23.6.2
     images activeicm, 7.7     properties, 17.1
     image, 5.3.3     startup, 23.9.2
backup, 3.4.2.11carbon, 23.3.4, 23.3.5
bad, 17.1carboxylic acid, 17.5
     groups, 16.3.5cartesian, 17.9
ball, 3.4.1.15.5cavities, 10
     and stick, 3.5.1, 5.1.1     closed, 3.4.7.4, 10.4
bank, 4.1.1ccp4, 23.3.26, 23.3.27
basic alignment selection, 9.5.11cell, 3.4.5.2, 12.2
basicsel, 3.2.3center, 3.1.2, 3.4.3.20, 5.9, 5.9.5, 20.1.31, 23.5.22
batch, 18.1.10, 18.4.6, 18.6.8     and representative members, 20.7.1
beep, 23.3.34chain.breaks, 23.3.33
begin docking simulation, 18.1.8chains, 3.4.7.1
best, 16.2.32chair, 23.6.21
binding, 23.3.13, 23.6.2, 23.6.11chair-boat, 23.6.3
     pocket, 22.3.3change selection, 3.2.5
     properties, 5.2.1     speed range, 6.1.2
bioinfo align dna protein, 9.2.7changing font in alignment editor, 9.5
          multiple, 9.2.8charge, 3.4.3.21, 4.2.1, 4.2.2, 5.5.2, 16.3.2, 16.5.1, 16.5.2, 16.5.3, 16.9.1, 18.4.9.5, 23.5.1
          two sequences, 9.2.5     groups, 23.6.23
     links, 9.2.9chem convert, 23.7.10
     menu, 3.4.4     save, 16.6
     secondary structure, 9.2.2          editor, 16.6.2
     translation, 9.2.3          image, 16.6.4
biological, 3.4.5.3, 12.3          table, 16.6.1
biomolecule, 3.4.5, 3.4.5.3, 12.3, 22.3.7, 22.3.11          workspace, 16.6.3
bit, 23.1.2     super, 17.18
blast, 9.3     view, 16.2.26
boat, 23.6.21chemical, 16, 16.2.25, 16.2.26, 16.2.28, 16.2.29, 16.2.32, 16.2.33, 16.3.6, 16.12, 16.13.3, 17.6.2, 17.10, 17.17.3, 17.17.7, 17.18, 20.7, 23.7.9, 23.7.10, 23.7.12, 23.7.13, 23.7.14, 23.7.15
bond, 4.4, 13.9, 16.3.6, 22.3.6, 23.5.1, 23.7.12, 23.7.15     clustering, 17.12
     covalent, 23.5.2     dictionary, 16.3.3
     type, 4.2.1, 4.2.2, 16.5.1, 16.5.2, 16.5.3     draw load, 16.1
bonding, 5.1.9     editor, 16.3, 16.3.4
     preferences, 3.4.1.15.1          not starting, 23.10.4
box, 3.4.1.1.9, 3.4.1.15.7, 5.5.16, 23.6.10     find replace, 16.11
bpmc, 22.4.4     fragments, 16.2.31

     groups, 16.3.3, 16.3.4     smiles, 17.6.3
     right click, 16.3.2     duplicates, 17.16
     search, 16.9     remove.redundant, 17.16
          filter, 16.9.2chemlib.so, 23.1.2
          text, 16.9.4chi, 5.5.5, 23.3.17
     smiles, 16.1.2chiral, 17.11
     spreadsheet, 23.7.19chirality, 17.11
          compare, 16.2.19chminformaitcs tutorials, 22.5
     spreadsheets, 16.2chrome, 23.4
     structure, 16clash, 3.4.1.15.5, 5.5.15
     superimpose.apf, 22.5.17classes, 16.2.26
          rigid flexible, 22.5.16clear display and planes, 3.4.3.2
     table, 23.7.17     selection, 3.2.4
          display, 16.2.1     planes, 3.4.3.2
     tables, 20.2click, 3.1.16, 5.8, 5.9
     2D, 16.5clip, 5.2.9, 5.10.1, 23.3.10
     3D, 16.5clipboard, 5.12.2, 20.7.2
     append, 16.3.7clipping, 23.3.18
     clustering, 17.12, 17.12.1     planes, 3.1.3, 5
     convert, 3.4.16.1, 4.2.1, 4.2.2, 15.1, 16.5, 16.5.1, 16.5.2, 16.5.3, 23.5.1     tool, 5.10
     display.fit, 23.7.19     tools, 5.10
     draw, 16.3.1, 22.5.1closed cavities, 3.4.6.5, 3.4.7.4, 14.5
     duplicates, 16.2.18cluster, 18.4.6, 20.7
     edit, 16.3.8, 22.5.2     representative.center, 17.12.2
     editor, 16.6, 16.6.1, 16.6.2, 16.6.3, 16.6.4clustering, 20.6.4
     load, 16.1, 16.1.1collada, 3.5.5, 5.2.4
     merge, 17.15color, 3.4.6.2, 5.3, 5.3.1, 5.5.2, 5.5.3, 14.2, 16.2.33, 17.4, 20.1.34, 20.7.3, 22.3.3, 23.3.4, 23.3.5, 23.3.15, 23.3.19
     name, 16.8     alignment, 9.5.5
     new, 16.3.1     background, 5.3.2
     properties, 16.2.17     by, 5.3
     query, 16.3.2, 16.9.1, 16.9.3     chemical, 16.2.33
     read, 16.1, 16.1.1     display mesh, 5.2.8
     redo, 16.3.12     faq, 23.3.19
     save, 16.3.7, 16.6, 16.6.1, 16.6.2, 16.6.3, 16.6.4     table, 16.2.24
     search, 16.3.2, 16.9, 16.9.1, 16.9.3, 22.5.4, 22.5.5     2D sketch, 16.10.5
     similarity, 16.3.2, 16.9, 16.9.1, 16.9.3, 22.5.4, 22.5.5     background, 3.4.3.18, 5.3.2
     smiles, 16.1.2     distance, 5.5.11
     spreadsheet, 16.2, 16.6, 16.6.1, 16.6.2, 16.6.3, 16.6.4     mesh, 5.2.8
     structure, 16.1.1, 16.3.7, 16.3.8     table, 16.2.24
     substructure, 22.5.5coloring, 5.3.1
     superimpose, 17.18.1, 17.18.2, 17.18.3column, 20, 20.1.20, 20.1.30, 20.1.31, 20.4, 20.4.1, 23.7.12
     superposition, 17.18.4, 17.18.5     row width, 20.1.20
     table, 16.2, 20.2, 22.5.1, 22.5.2     statistics, 20.1.24
     undo, 16.3.12     color, 20.1.8
cheminformatics, 16.2, 23.7     hide, 16.2.6
chemistry, 17.10, 23.7     show, 16.2.6
     convert, 17.6combinatorial chemistry, 17.17
          2dto3d, 17.6.1     library, 17.17.4
     menu, 17combine, 3.4.10.5
     pca, 17.13     display style, 3.4.1.15.9

     line, 23.3.31          structure, 16.3.10
commands, 3.4.1.1.5, 23.9.1     row, 20.1.27
compare, 16.2.27, 17.14, 17.15     selection to table, 20.1.28
     table, 16.2.19     chemical, 16.2.14
     tables, 17.14cpk, 5.1.6, 23.3.20
compatible, 3.4.1.9crash, 3.4.2.11
compound, 17.10, 20.2creat, 6.6.1
compounds, 23.7.3create, 20.1.1
compress, 3.4.1.15.6     modify markush, 17.17.1
conditions, 16.9.2cross, 23.3.9
     gen, 17.9     section, 5.10
conformation, 17.9, 18.2.2crystal, 3.4.5.2, 12.2
conformations, 23.8.2crystallographic analysis, 12
conformers, 17.9          biomolecule, 12.3
connect, 5.2.7, 5.9, 5.9.7          contour map, 12.6
     object, 5.9.7          convert2grid, 12.7
connectivity, 16.3.2, 16.9.1          crystallographic cell, 12.2
consensus, 3.4.7.1          load eds, 12.4
conservation, 22.3.3          maps cell, 12.5
construct, 3.4.1.1, 3.4.1.1.1, 6.1.1          symmetry packing, 12.1
     DNA, 3.4.1.1.3          tools, 22.3.7
     RNA, 3.4.1.1.3     cell, 3.4.5.2
     chemical, 3.4.1.1.2     cell, 3.4.5
     compound, 3.4.1.1.2     neigbor, 3.4.5.1, 12.1
     molecule, 3.4.1.1     neighbors, 3.4.5
     nucleic, 3.4.1.1.4crystallography, 3.4.5.4, 3.4.5.6, 3.4.5.7, 12.4, 12.6, 12.7, 23.3.26, 23.3.27
     object, 3.4.1.1csv, 20.1.2, 20.1.3, 20.1.19
     protein, 3.4.1.1.4current, 23.3.21
     sequence, 3.4.1.1.4     slide, 7.5
contact, 3.4.7.3, 10, 10.3custom, 5.9, 16.2.1, 17.18
     areas, 3.4.7.3     actions, 20.1.31
contour, 3.4.5.6, 3.4.5.7, 12.6, 12.7     fragments, 17.3
     map, 3.4.5.6     label, 5.5.9
convert, 4.2, 17.6.1, 17.6.5, 23.7.10     rotation, 5.9.2
     2D to 3D.conformer generator, 22.5.11cut, 20.1.26
                    from table, 22.5.10     vertical alignment block, 9.2.11
                    molecule editor, 22.5.9damaged skin, 23.10.3
     chemical, 16.2.21dash, 23.3.11
          2D 3D, 16.5data, 4.1.1
     local database, 3.4.1.5database, 9.3, 16.13, 17.17.3, 18.1.2, 18.4.3, 18.4.5, 21.1
     pdb chem, 16.5.1     file format, 18.4.3
     smiles to 2D, 23.7.17     seach and alignment, 9.3
     local.database, 3.4.1.5databases, 23.7.3
     smiles, 17.6, 17.6.3, 17.6.4decompose.library, 17.17.6
convert2grid, 3.4.5.7decomposition, 17.17.3, 17.17.5
converting pdb, 4.2default, 3.1.17
copy, 16.2.22, 16.3.13, 16.10.2, 20.1.26delete, 3.2.4, 3.4.2.1, 6.6.7, 23.5.9
     cell, 20.1.27     column row, 20.1.29
     chemical, 16.2.22     label, 5.5.10
     paste row, 20.1.26     all, 3.4.2.2

     column, 20.1.29     molecule, 16.2.21
     distance.label, 5.6.4     origin, 5.5.12
     label, 5.5.10     potential, 3.4.3.21
     row, 20.1.29     representations, 3.5.1, 5.1.1
     selection, 3.4.2.1     restraints, 5.5.14
     tether, 3.4.16.5, 15.5     ribbon, 5.1.4
deleteall, 3.4.2.2     skin, 5.1.5
density, 3.4.5.4, 3.4.5.6, 3.4.5.7, 12.4, 12.6, 12.7, 23.3.26, 23.3.27     status, 23.3.31
depth, 5.2.11     surface, 5.1.7, 5.2.1
deselect, 23.3.7     surfaces, 3.5.5
deviation, 23.5.7     table, 16.2.1
dialog, 6.6.5     tethers, 5.5.13
diffuse, 3.5.2     wire, 5.1.2
dihedral, 3.4.7.8, 5.5.5, 10.8, 23.3.17     xstick, 5.1.3
     angle, 10distance, 3.4.7.6, 5.5.11, 5.6, 10, 10.6, 17.14, 23.3.11, 23.5.8, 23.5.10
dimensional, 23.7.11     faq, 23.5.10
directories preferences, 3.4.1.15.2     label, 3.4.1.15.7
directory, 3.4.1.15distances, 3.5.3
disappearing labels, 23.10.3disulfide, 13.9
display, 3.1.7, 3.1.18, 3.4.1.15, 4.4, 5.5.15, 5.11, 16.2.25, 17.11, 22.1.5, 22.3.4, 22.3.6, 23.3.4, 23.3.5, 23.3.8, 23.3.9, 23.3.10, 23.3.16, 23.3.20, 23.3.29, 23.3.31, 23.5.10, 23.5.11, 23.5.20, 23.7.9diverse set, 20.6.4
     chemical, 16.2.25dock, 18, 18.1, 18.1.2, 18.5, 22.8.1, 22.8.2, 22.9.1, 23.6.3, 23.6.4, 23.6.5, 23.6.6, 23.6.8, 23.6.9, 23.6.11, 23.6.12, 23.6.13, 23.6.14, 23.6.15, 23.6.16, 23.6.17, 23.6.22
     delete distances, 5.6.4     command, 23.6.17
     dihedral, 5.6.3     macrocylce, 23.6.21
     distance restraints, 5.5.14docking, 3.4.6.4, 14.4, 18, 18.1.3, 18.1.15, 18.2, 18.2.1, 18.2.2, 18.4, 18.4.1, 18.4.2, 18.4.5, 18.6, 18.6.1, 18.6.2, 18.6.3, 18.6.4, 18.6.5, 18.6.7, 18.6.8, 18.6.9, 22.7, 22.7.1, 22.7.2, 22.8.3, 22.9, 22.9.2, 23.6, 23.6.1, 23.6.10, 23.6.18, 23.6.19
     distance2, 5.6.1     explicit group, 22.9.2
          angles, 5.6               docking explicit, 22.9.2.5
     formal charge, 5.1.10                    project, 22.9.2.3
     gradient, 5.5.17               receptor setup, 22.9.2.1
     hbonds, 18.4.9.5               rotate hydroxyls, 22.9.2.2
     hydrogen, 5.1.8               run docking, 22.9.2.4
     mesh, 5.2.2     start, 18.1.3
     meshes, 5.2.5     template, 18.3
     planar angle, 5.6.2     adjust, 18.1.6
     structure, 3.1.8     background, 23.6.20
     tab, 3.5.1, 23.3.15     batch, 18.1.10
     tether, 5.5.13     binding, 18.1.6
     toggle, 5.5.16     conformations, 23.6.21
     CPK, 5.1.6     flexible.rings, 23.6.21
     angle, 5.6.2     hitlist, 18.1.14
     chemical, 16.2.1     interactive, 18.1.9
     dihedral.angle, 5.6.3     maps, 18.1.7
     distace, 5.5.11     preparation, 18.1.3
     distance, 5.5.14, 5.6.1     procedure, 18.1.8
     electrostatic, 3.4.3.21     project name, 18.1.4
     energy.gradient, 5.5.17     rank, 18.1.14
     hydrogen, 5.1.8     receptor setup, 18.1.5
          polar, 5.1.8     results, 18.1.11, 18.1.12, 18.1.13, 18.1.14
     macroshape, 5.2.3     sampling, 23.6.21
     meshes, 5.2.2     score, 18.1.14
          and display.macroshape, 3.5.5     stack, 18.1.13

document, 3.4.1.1.6, 6.6.4, 6.6.5elegant sketch, 5.7.4
     navigation, 6.6.6element, 16.3.6
documents, 5.12.4embed browser, 7.3
dollar, 23.9.3     powerpoint03, 7.1
donator, 16.3.5     powerpoint07, 7.2
     envelope, 3.5.1, 5.1.1     activeicm, 7.5
     surface, 3.4.1.15.5          script, 7.5
dots, 3.1.10     browser, 7, 7.3
dotted lines, 3.1.10, 23.3.33     firefox, 7, 7.3
double, 16.3.6     internet.explorer, 7, 7.3
download, 23.7.3     microsoft, 7
drag, 3.1.15, 3.3.6, 3.4.1.15.7, 5.5.3, 6.6.4, 9.4.5, 23.5.5     powerpoint, 7, 7.1, 7.2
     and drop sequences, 9.4.5enantiomer, 23.6.22
     residue label, 3.4.3.16energy, 3.4.6.2, 5.5.15, 14.2, 18.1.13, 23.6.1, 23.6.2, 23.8.2
draganddrop, 3.1.15     terms, 3.4.16.12, 15.12
draw, 16.3.13, 17.17.7, 23.7.7enumerate.reaction, 17.17.8
     chemical, 16.3.1enumeration, 17.17.3
drop, 3.1.15, 3.3.6, 6.6.4, 9.4.5, 23.5.5eps, 16.6.4
drug, 17.1, 23.7.12, 23.7.14epsilon, 23.5.15
druglikeness, 16.3.5errno, 23.1.2
dsPocket, 3.1.12error, 23.1.2, 23.3.34
easy rotate, 3.4.3.12escaping, 3.1.3
edit, 23.7.8exact, 17.14
     alignment, 9.5.1excel, 16.7
     chemical, 16.3.8exclude fragment, 16.9.2
          moledit, 16.2.23exit, 3.4.1.18
     ligand, 19.5explicit, 16.2.26, 18.2.1
          editor preferences, 19.2     flex, 18.2.1
          tools, 3.4.2.17     groups, 22.9.2
     menu, 3.4.2export, 3.4.7.9, 10.10
     molecular document, 6.6.1     excel, 16.7
     molecule, 16.3extract, 3.3.4, 9.1, 22.3.5, 23.5.12, 23.7.13
     molt, 21.3     icb, 3.4.1.4
     movie, 8.2.7     sub alignment, 9.2.10
     selection, 3.4.2.5     2D chemical sketch, 16.4
     slide, 6.4.1     icb, 3.4.1.4
     table row, 20.1.22     phrarmacophore, 16.10.4
     molecule, 16.2.23faq, 23, 23.2, 23.3, 23.3.12, 23.5, 23.6, 23.8, 23.9, 23.9.2
     movie, 8.2.7     ISISdraw, 23.7.8
     structure, 16.2.23     activeicm, 23.4
editor, 22.3.5, 23.5.12          path, 23.4.3
editpdbsearch, 3.4.2.12     apf model, 23.7.18
eds, 3.4.5.4, 3.4.5.6, 3.4.5.7, 12.4, 12.6, 12.7     atom charge, 23.5.21
electron, 3.4.5.4, 3.4.5.6, 3.4.5.7, 12.4, 12.6, 12.7, 23.3.26, 23.3.27          display, 23.3.16
     denisty map, 3.4.5.5, 12.5     autosave, 23.3.32
     densitry map.contour, 3.4.5     backbone, 23.3.12
          map, 3.4.1.6, 3.4.5, 18.5     background color, 23.3.2
electrostatic potential, 3.4.3.21          job, 23.6.20
     surface, 5.2     beep, 23.3.34
electrostatics, 5.2.1, 18.6.7     binding energy, 23.6.2

     breaks, 23.3.33     movie planes, 23.3.18
     change torsion, 23.5.16     newscript, 23.9.1
     chem table display, 23.7.9     nmr, 23.5.18
     chemical monitor, 23.7.15     nvidia error, 23.1.1
          query2, 23.7.5     origin, 23.3.9
     cheminformatics, 23.7     pmf score, 23.6.7
     clipping plane, 23.3.10     pockets, 23.3.13
     closest, 23.5.22     preserve coordinates, 23.7.11
     color carbon, 23.3.4     quad buffer, 23.2.3
          skin, 23.3.15     receptor selection, 23.6.15
     command line display, 23.3.31     reload dock, 23.6.5
     convert chemical from pdb, 23.5.1     remove salt, 23.7.20
     covalent bond, 23.5.2          select, 23.3.6
     delete, 23.5.9     renumber, 23.5.4
     deselect, 23.3.7     residue number selection, 23.3.35
     dihedral, 23.3.17     ringflex dock, 23.6.3
     dock charge groups, 23.6.23     rmsd, 23.5.7
          probe, 23.6.14     rmsdtips, 23.5.8
          racemic, 23.6.22     rocking active ppt, 23.4.1
          repeat, 23.6.6          speed, 23.4.2
          working directory, 23.6.24     rotate chemical, 23.7.19
     docking, 23.6     scanScoreExternal, 23.6.18
     docktime, 23.6.12     scanScoreExternal2, 23.6.19
     dollar, 23.9.3     score, 23.6.9
     druglikeness, 23.7.14     script, 23.9
     energy, 23.6.1     simulations, 23.8
     error admin, 23.10.1     smiles, 23.7.17
     extract ligand, 23.7.13     solvent accessible surface table, 23.5.19
     flexible dock, 23.6.16     ss, 23.5.17
          ring docking, 23.6.21     structure, 23.5
     font size, 23.3.1     superimpose, 23.5.6
     foreground table, 23.9.4     thoroughness, 23.6.13
     gl failure, 23.10.2     transparent ribbon, 23.3.3
     gui, 23.3     truncate mesh, 23.3.14
     guided dock, 23.6.4     view stack, 23.8.2
     hardware, 23.2     weak hydrogen bonds, 23.5.20
     hitlist, 23.6.8     write pdb, 23.5.3
     iSee, 23.3.29faqcontour, 23.3.27
     icmPocketFinder, 23.6.11faqhbondstrength, 23.3.28
     insert column, 23.7.12faqmaps, 23.3.26
     installation, 23.1faqoda, 23.3.25
     interactions, 23.3.11faqstereo, 23.10.5
     ligandbox, 23.6.10fasta, 3.3, 3.3.2
     merge, 23.5.5field, 4.1.1.4
     molcart 64bit, 23.1.2file, 3.4.1.2, 4.1.4
          query, 23.7.6     close, 3.4.1.12
          sdf, 23.7.4     compatible, 3.4.1.9
          text search, 23.7.16     export, 3.4.1.11
     molecule c, 23.3.5     load, 3.4.1.6
     moledit, 23.7.7     menu, 3.4.1

     quick image, 3.4.1.13          tutorial, 22.1
     icb, 3.1.14               2D3D labels, 22.1.4
     recent, 3.4.1.16               annotation, 22.1.2
     bak, 3.4.2.11               color representation, 22.1.1
filter, 21.2, 23.3.4               labels, 22.1.3
     selection, 3.2.6     user interface, 23.3
          tut, 22.1.9     card, 23.1.1
find, 3.4.7.1     controls, 5
     chemical, 16.2.30     defects, 23.10.3
     related chains, 3.4.7.1     effects, 5.7
finding dihedral angle, 3.4.7.8     preferences, 3.4.1.15.3
     planar angle, 3.4.7.7     tips, 3.1.3
fingerprint, 23.7.5, 23.7.6     shadow, 3.4.3.13, 5.7.2
firefox, 23.4grid, 16.2.1, 16.2.4, 17.18, 22.9.1, 23.7.9
fit, 16.2.32, 18.5, 23.6.16grob, 3.4.1.15.5, 3.4.5.4, 3.4.5.6, 3.4.5.7, 5.2, 12.4, 12.6, 12.7
fitting, 18.5, 20.4.12group, 17.17.5, 19.7
flex super, 17.18.3groups, 16.12, 17.1, 17.2
flexibility, 3.4.6.3, 14.3, 22.9guanidinium, 17.5
flexible, 17.18, 18.2, 18.2.1, 18.2.2, 22.9.1, 23.6.16gui, 3.4.1.15.4
     rings, 23.6.3     menus, 3.4
fog, 3.4.3.5, 5, 5.7.1     preferences, 3.4.1.15.4
font, 3.4.1.15, 3.4.1.15.7, 5.5.2, 5.5.3, 16.2.26, 20.1.31, 20.7.3     tabs, 3.5
     preferences, 3.4.1.15.7guided docking, 23.6.4
     size, 9.5, 23.3.1h-bond, 4.4, 22.3.6, 23.3.11
form, 16.2.4hardware, 23.2
     view, 20.1.5     stereo, 3.4.3.7
formal, 23.5.21hbond, 23.3.28
     charge, 5.1.10, 17.5     strength, 23.3.28
format, 20.1.2, 20.1.31header, 4.1.8, 20.4.5
formula, 16.3.5, 17.1health, 3.4.6.2, 14.2, 22.4.5
fragment, 16.2.33, 17.17.5helices strands, 3.4.6.1
fragments, 16.12helix, 23.3.19
frame, 9.2.3hetero, 16.2.26
frequency, 16.2.33hidden block format, 9.5.8
front, 5.2.9, 5.10.1          width, 9.5.8
full scene antialias, 3.4.3.10hide, 20.1.30
     screen, 3.4.3.8high, 3.4.1.14
function, 20.1.23, 20.1.24     quality, 3.4.3.11
functional.groups, 17.3his, 23.5.15
general preferences, 3.4.1.15.5histidine, 3.4.16.2, 15.2, 23.5.15
generalselecttools, 3.2.2     tautomer, 23.5.15
generator, 3.4.5.3, 12.3, 17.9histogram, 18.4.9.2, 18.4.9.3, 20.4, 20.4.1, 20.4.5, 20.4.7, 20.4.9, 20.4.10, 20.4.11, 20.4.12, 20.4.13, 20.4.14, 20.4.15, 20.4.17, 22.1.12, 22.1.13
getting started, 3     bins, 20.4.3
glasses, 23.2.2, 23.10.5     options, 20.4.2
glutamine proline, 3.4.16.2, 15.2     bin.size, 20.4.2
google, 3.4.1.6     bins, 20.4.3
     objects, 5.2.4     color, 20.4.2
     3D, 3.5.5, 5.2.4     source, 20.4.2
graphical, 1, 23.3.4     style, 20.4.2
     display, 4.2.1, 4.2.2, 16.5.2, 16.5.3     title, 20.4.2

homology, 3.4.7.1, 13, 13.1, 13.2, 13.4.1, 13.6, 13.7, 22.4, 22.4.1     histogram, 22.1.13
     loops, 13.5     mark row, 16.2.12
     model introduction, 13.1     markush, 17.17.4
          start, 13.2          structure, 17.17.2
     modeling, 22.4.2     merge tables, 16.2.20
     3D editor, 22.6     plot, 22.1.14
               add substituent, 22.6.13     plots, 22.1.12
               begin edit, 22.6.11     properties, 16.2.17
               center ligand, 22.6.10     qsar, 22.5.12
               default, 22.6.4          build model, 22.5.13
               dock, 22.6.20          predict, 22.5.14
                    tether, 22.6.21     reactions, 17.17.8
               edit 2d, 22.6.15     reorder, 17.12.3
               energy circles, 22.6.7     sdf, 16.2.7
                    hydrogen, 22.6.8     show hide, 16.2.6
               fragment linkers, 22.6.23     smiles, 16.3.11
               hydrogen bond, 22.6.6     sort column, 16.2.3
               minimization, 22.6.19     standardize, 16.2.16
               multiple substituent, 22.6.14     table hyperlinks, 16.2.13
               preferences, 22.6.3          print, 16.2.9
               purple box, 22.6.18          activeicm, 2.3
               save spreadsheet, 22.6.17               create molecular documents, 2.3.3
               screen substituents, 22.6.22                    slides, 2.3.2
               setup ligand, 22.6.1               getting started, 2.3.1
                    receptor, 22.6.2               ppt, 2.3.4
               surface, 22.6.5               web, 2.3.5
               undo redo, 22.6.12          chemical clusering, 17.12.1
               unsatisfied hydrogen bonds, 22.6.9          display, 3.1
     add columns, 16.2.2          icm browser convert display pocket, 2.1.4
     change view, 16.2.4                    distances angles, 2.1.9
     chemical 2D 3D, 22.5.8                    get started, 2.1.1
                    conformer generator, 22.5.11                    graphical display, 2.1.2
                    from table, 22.5.10                         effects, 2.1.5
                    molecule editor, 22.5.9                    images, 2.1.7
          superimpose, 22.5.15                    labels annotation, 2.1.6
               apf, 22.5.17                    pro crystallographic tools, 2.2.6
               rigid flexible, 22.5.16                         get started, 2.2.1
     cluster center, 17.12.2                         graphics, 2.2.2
     color 2D by ph4, 16.10.5                         plots, 2.2.8
     copy 2D, 16.2.14                         sequence analysis, 2.2.7
          paste, 16.2.5                         structure analysis, 2.2.3
     decompose, 17.17.6                         superimpose, 2.2.5
     duplicate chemicals, 16.2.18                         surfaces, 2.2.4
     edit table, 16.2.15                    selections, 2.1.3
          tree, 17.12.4                    superimpose, 2.1.8
     excel, 16.2.8hrydrogen.bond, 23.3.28
     extract 2D, 16.4html, 3.4.1.1.6, 3.4.1.11, 6.6.1, 6.6.6, 23.4
          3D ph4, 16.10.4html-doc font size, 23.3.1
     filter, 16.2.10hybridization, 16.3.2, 16.9.1
     find replace, 16.2.11hydrogen, 4.4, 5.1.9, 16.3.2, 16.9.1, 22.3.6, 23.3.11, 23.7.12, 23.7.15

     bond, 16.3.5, 23.5.20     modeling, 13.4, 13.4.1
hydrogens, 16.2.26     modeling, 13.4
     remove, 16.2.16interface, 1
hyperlink, 6.6.1, 6.6.2, 20.1.31internet explorer, 23.4
iSee, 3.1.14, 3.4.1.1.6, 3.4.1.4, 3.4.1.11, 5.12.4, 22.1.11, 23.3.29, 23.3.30, 23.4.3interrupt, 6.1.3
icb, 23.3.29, 23.4.3     animation, 6.1.3
icm, 23.4.3introduction, 1
     chemist howto chemical search, 2.4.3invert selection, 20.1.21
               cluster, 2.4.5invisible residue label, 23.10.3
               combi library, 2.4.7isee, 6.6.5
               ph4, 2.4.4isis, 16.3.13
               plots, 2.4.8isotope, 16.3.2, 16.9.1
               sketch, 2.4.1iupac, 16.8
               spreadsheets, 2.4.2job, 23.6.20
               stereoisomers tautomers, 2.4.6jobs, 18.4.6
          pro 3D ligand editor, 2.5.1join, 17.15
               chem3D, 2.5.2jpg, 5.12, 5.12.1
               chemsuper, 2.5.3     means, 20.7
               qsar, 2.5.4key chemical, 16.3.6
               tutorials, 2.5keyboard mouse, 5.8
          tutorials, 2.4keystokes in chem-edit, 16.3.6
     hanging, 23.10.4kinase build model, 22.4.2.3
     script, 20.1.31     model loop, 22.4.2.4
icm-crash, 23.10.4kinasemod, 22.4.2
icmFastAlignment, 9.3     search, 22.4.2.1
icmPocketFinder, 3.4.6.5, 14.5, 23.3.13, 23.6.11     sequence alignment, 22.4.2.2
image, 3.1.19, 3.4.1.15, 3.4.1.15.5, 5.12.1, 5.12.2, 5.12.3, 5.12.4, 6.6.3, 16.6, 16.6.4, 20.4.16kmz, 3.5.5, 5.2.4
     advanced, 5.12.3label, 3.4.1.15.7, 20.7.3, 23.3.16
     clipboard, 5.12.2     annotation, 5.5.7
     preferences, 3.4.1.15.6     atoms, 5.5.2
     multiple, 3.4.1.6     color, 5.5.8
     quality, 3.4.3.11     move, 5.5.4
     quick, 3.4.1.13     residues, 5.5.3
images, 5.12     sites, 5.5.6
in-a-window, 23.2.3     variables, 5.5.5
index, 23.7.16     2D, 3.5.3
induced, 23.6.16     3D, 3.5.3, 5.5.1
     fit, 18.2, 18.2.1, 22.9, 22.9.1     annotation, 5.5.7
insert, 6.6.4     atom, 5.5.1
     column, 20.1.23     atoms, 5.5.2
     image, 6.6.3     color, 5.5.8
     row, 20.1.25     custom, 5.5.9
     script, 6.6.4     delete, 5.5.1, 5.5.10
install, 1, 16.13.1, 23.1.2, 23.1.3     distance, 5.5.11
installation, 23.1     drag, 3.4.3.16
interactio, 23.6.2     move, 3.4.3.16, 5.5.4
interaction, 3.4.7.3, 10.3, 23.3.11     residue, 5.5.1
interactive, 18.1.9, 22.1.11     residues, 5.5.3
     loop, 13.4.3     site, 5.5.1
     make, 13.4.1     sites, 5.5.6

     variables, 5.5.5, 23.3.17linux, 16.13.1
labeling, 5.5.1load, 3.3, 3.3.2, 3.4.1.2, 3.4.1.16, 3.4.5.4, 3.4.5.6, 3.4.5.7, 4.1.4, 9.1, 12.4, 12.6, 12.7
labels, 5.5, 16.2.26     eds, 3.4.5.4
     distances, 5.5.11     example alignment, 9.2.14
     tab, 3.5.3     nmr model, 4.1.5
landscape, 3.4.1.15.6     pdb, 4.1.4
lasso, 22.1.6, 22.1.7          hyperlinks, 4.1.7
layer, 5.11     sequence, 9.1
layers, 5.11          extract pdb, 9.1.3
learn, 17.7, 17.8, 20.6, 20.6.1, 23.7.18          from file, 9.1.4
learning, 20.6          paste, 9.1.2
     theory, 20.6.3          swissprot, 9.1.1
least.squares, 20.4.12     libraries, 3.4.16.6, 15.6
library, 17.17.3     pdb, 4.1.3
     reaction, 17.17.8     sequence, 3.3.1
license, 23.1.3local, 23.3.23, 23.3.24
ligand, 18.1.2, 18.2, 18.6.5, 18.6.6, 22.3.4, 23.5.5, 23.5.11, 23.6.2, 23.6.10, 23.7.13     databases, 21
     best replace, 19.7     flexibility, 3.4.6.3
     code, 4.1.1.3     database.browse, 21.2
     editor, 19          edit, 21.3
          preferences, 3.4.2.18          query, 21.4
     linker, 19.6          row, 21.3
     pocket, 23.5.11localpdb, 23.3.23
     tether, 19.8localseq, 23.3.24
     convert, 3.4.16.1, 15.1lock, 5.2.9, 5.10.1, 16.2.29
     editor, 19, 19.1, 19.6log, 20.4.7
          binding.re-dock ligand, 19.4logP, 16.3.5, 17.1
          display, 19.3logS, 16.3.5, 17.1
          edit, 19.5logarithmic, 20.4.7
          energy, 19.3logout, 3.4.1.18
          hydrogen.bond, 19.3loop, 13.6, 23.3.19
          pocket, 19.3     model, 13.6
          preferences, 19.2     modeling, 13.4.3
          restraint, 19.8     model, 3.4.16.8, 15.8
          surface, 19.3     sample, 3.4.16.8, 15.8
          tether, 19.8mac, 16.13.1
     optimization, 22.8.3macros, 7.6
     pocket, 3.1.12macroshape, 3.4.3.22, 5.2, 5.2.3
     receptor.contact, 3.4.7.3, 10.3make, 3.4.1.1.1, 3.4.1.1.7, 6.1.1, 20.1.1
     surface, 22.6.5     animation, 6.1.1
light, 3.5.2     complex, 18.4.9.5
     tab, 3.5.2     flat, 23.7.19
lighting, 5.4     images, 5.12
likeness, 17.1, 23.7.14     molecular document, 6.6
line, 3.4.1.15.5, 20.7.3, 23.3.11     molt, 21.1
lineWidth, 3.4.1.15.3     movie, 8.2
link, 9.2.9, 22.3.3     receptor maps, 18.1.7
     structure to alignment, 22.2     selection, 3.2
linker, 19.6     DNA, 3.4.1.1.3
links, 3.2.15     RNA, 3.4.1.1.3

     chemical, 3.4.1.1.2     loop, 13.5
     compound, 3.4.1.1.2modelers view, 13.4.2
     disulfide, 13.9, 23.5.17     view, 13.4.2
     molecule, 3.4.1.1modeling, 3.4.16.3, 15.3
     object, 3.4.1.1modeller view, 13.4
     sequence, 3.4.1.1.4mol, 16.6, 16.6.1, 16.6.2, 16.6.3, 16.6.4, 22.8.2
making molecular slides, 6.2mol2, 16.6, 16.6.1, 16.6.2, 16.6.3, 16.6.4
     html, 6.6molcart, 16.13, 16.13.1, 16.13.2, 16.13.3, 16.13.4, 21, 23.1.2, 23.7, 23.7.3, 23.7.4, 23.7.5, 23.7.6, 23.7.16
     color, 20.4.10     administration, 16.13.4
map, 3.4.1.15.7, 3.4.5.4, 3.4.5.6, 3.4.5.7, 12.4, 12.6, 12.7     connect, 23.7.2
     cel, 3.4.5.5, 12.5     download dbs, 23.7.3
maps, 18.6.7, 22.9.1, 23.3.26, 23.3.27, 23.6.10     hostid, 23.7.1
     cell, 3.4.5.5     installation, 16.13.1
mark, 20.1.34     license, 23.1.3
     row, 20.1.34     search, 16.13.3
     shape, 20.4.9     start, 16.13.2
     size, 20.4.9     connect, 23.7.2
markush, 17.17.1, 17.17.5, 22.8.3     hostid, 23.7.1
     docking, 22.8.3     license, 23.7.1
     library, 17.17.4molclart, 23.1.3
mass, 23.5.22molecular, 16.2.28, 16.2.29, 16.2.32, 16.2.33, 17.9, 23.7.12, 23.7.15
materials, 3.5.5     animations slides, 6
max, 20.7          transitions, 6.1
maxColorPotential, 3.4.1.15.10     document, 3.4.1.1.6
mean, 23.5.7     documents, 22.1.11
menu, 6.6.5     editor, 23.7.7
     chemistry, 3.4.14          copy, 16.3.10
     docking, 3.4.15          cut, 16.3.10
     homology, 3.4.13          paste, 16.3.10
     molmechanics, 3.4.16          redo, 16.3.12
     tools chemical search, 3.4.11          selections, 16.3.9
          molecular editor, 3.4.12          undo, 16.3.12
     windows, 3.4.17     graphics, 5
merge, 17.15, 23.5.5          molecule representation, 5.1
     two sets, 17.15     mechanics, 15
mesh, 3.4.5.4, 3.4.5.6, 3.4.5.7, 4.3, 5.2, 5.2.7, 5.2.9, 5.2.10, 5.2.11, 5.10.1, 12.4, 12.6, 12.7          convert, 15.1
     clip, 5.2.9          edit structure, 15.5
     options, 5.2.6          gamess, 15.11
     save, 5.2.10          generate normal mode stack, 15.9
     options, 5.2.6          his asn, 15.2
meshes surfaces grobs, 5.2          impose conformation, 15.4
     tab, 3.5.5          minimize, 15.7
min, 20.7          mmff, 15.6
minimize.cartesian, 3.4.16.7, 15.7          regularization, 15.3
     global, 3.4.16.7, 15.7          sample loop, 15.8
     local, 3.4.16.7, 15.7          terms, 15.12
mmff, 3.4.16.6, 15.6, 23.3.16, 23.7.10          view stack, 15.10
     type, 5.5.2     modeling, 13
mnSolutions, 3.4.1.15.10     table, 17.6.2
model, 13, 13.1, 13.2, 13.3, 13.6, 13.7, 22.4, 22.4.1     weight, 16.3.5

     editor, 16.3     scene, 8.2.2
molecules, 3.4.7.1     still, 8.2.3
moledit, 16.3.4     tween, 8.2.4
molmech icmconv, 3.4.16.1mpeg, 8, 8.1
molmechaincs gamess, 3.4.16.11mpg, 8
molmechanics, 23.8.2multi apf super, 17.18.5
     edit structure, 3.4.16.5multiple, 18.2.2, 22.9.1
     generate normal mode stack, 3.4.16.9     rec, 18.2.2
     his asn, 3.4.16.2     receptor, 22.9
     impose conformation, 3.4.16.4     protein, 23.3.5
     minimize, 3.4.16.7mutant, 23.5.13, 23.5.14
     mmff, 3.4.16.6mutate, 23.5.15
     regularization, 3.4.16.3     residue, 23.5.13
     sample loop, 3.4.16.8          N C, 23.5.14
     terms, 3.4.16.12     residue, 22.4.4
     view stack, 3.4.16.10mutation, 23.5.13, 23.5.14
     minimize, 3.4.16.7, 15.7navigate workspace, 3.2.8
     mmff, 3.4.16.6, 15.6nearest, 23.5.22
molt, 21, 21.4neighbors, 22.1.8
monitor, 23.7.15new, 3.3, 3.3.3, 3.4.1.1.1, 9.1
monochrome, 16.2.26     compound, 3.4.1.1.2
monte carlo, 22.4.4     dna, 3.4.1.1.3
montecarlo, 23.8.1     peptide, 3.4.1.1.1
mouse, 3.1.2, 5.8, 5.9     protein, 3.4.1.1.4
mov, 8, 8.1     table, 20.1.1
move, 3.1.15, 3.1.17, 3.4.3.19, 5.2.7, 5.9, 5.9.7, 23.5.5     chemical, 3.4.1.1.2
     resize mesh, 5.2.7     compound, 3.4.1.1.2
     slide, 6.4.2     dna, 3.4.1.1.3
     structure, 5.9     protein, 3.4.1.1.4
     tools, 5     rna, 3.4.1.1.3
     rotate, 5.8     script, 3.4.1.1.5
     slab, 5.8     table, 3.4.1.1.7, 20.1.1
     translate, 5.8nmr, 23.5.18
     z-rotation, 5.8     model, 4.1.5
     zoom, 5.8normal modes, 3.4.16.9, 15.9
movie, 3.5.6, 8.1, 8.2, 23.3.18, 23.8.1notations, 1
     directory, 8.2.1numbers, 16.2.26
     montecarlo, 23.8.1nvidia, 23.1.1
     scene, 8.2.2object, 3.1.15, 3.4.1.8.1, 3.4.1.8.2, 22.3, 23.3.8
     tab, 3.5.6objects, 4.2
     directory, 8.2.1     in table, 20.3
     edit, 8.2.7     in.table, 20.3
     export, 8.2.8occlusion, 5.2.11
     making, 8     shading, 5.2.11
     open, 8occupancy, 22.3.9
     powerpoint, 8.1     display, 4.1.6
     preview, 8.2.8oda, 3.4.6.4, 14.4, 18.6, 18.6.1, 18.6.2
     resolution, 8.2.1older version, 3.4.1.9
     rock, 8.2.6omega, 5.5.5, 23.3.17
     rotate, 8.2.5open, 3.4.1.2, 20.1.2

     movie, 8phylogenetic, 9.5.4
     password, 3.4.1.3phylogeny, 9.5.4
optimal, 3.4.6.4, 14.4, 18.6, 18.6.1, 18.6.2pick, 22.1.6, 22.1.7
optimize, 3.4.16.2, 15.2, 22.4.4picking, 5
origin, 5.5.12, 23.3.9     atoms, 3.1.3
other selection, 3.2.14     residues, 3.1.3
outside, 23.6.10picture, 3.1.19, 3.4.1.13, 6.6.3
overlay, 23.3.5, 23.5.6     tips, 3.1.19
package.activeicm, 7.5planar, 3.4.7.7, 5.5.5, 10.7, 23.3.17
packing, 3.4.5.1, 12.1     angle, 10
parallelization, 18.4.7     angle, 5.6.2
password, 16.13.4plane, 5.2.9, 5.10, 5.10.1, 5.11, 23.3.10, 23.3.18, 23.3.20
paste, 16.3.13, 20.1.26     faq, 23.3.20
pbs, 18.4.6plot, 3.4.1.15, 3.4.1.15.8, 18.4.9.2, 20.4, 20.4.1, 20.4.4, 20.4.5, 20.4.7, 20.4.9, 20.4.10, 20.4.11, 20.4.12, 20.4.13, 20.4.14, 20.4.15, 20.4.16, 20.4.17, 22.1.12, 22.1.14
pca, 20.5     axis, 20.4.7
pdb, 3.3.4, 3.4.1.6, 4.1.1, 4.1.1.3, 16.5.1, 22.3, 23.3.23, 23.3.24, 23.5.4     color, 20.4.10
     chem gl, 16.5.3     function, 3.4.9, 3.4.9.1
          iw, 16.5.2     grid, 20.4.11
     file, 23.5.3     header, 20.4.5
     html, 4.1.8     inline, 20.4.17
     preparation, 22.3.10     logarithmic, 20.4.8
     search, 4.1     mark, 20.4.9
          hyperlinks, 4.1.7     preferences, 3.4.1.15.8
     sensitive query, 4.1.2     regression, 20.4.12
     convert, 3.4.16.1, 15.1     selection, 20.4.14
     recent, 3.4.1.17     zoom translate, 20.4.13
     search, 3.1.1, 3.5.4, 4.1.3     axis, 20.4.11
     table, 4.1.3     display, 20.4.11
pdbsearchfield, 3.4.2.13     grid, 20.4.11
pdbsearchhomology, 3.4.2.15     inline, 20.4.17
pdbsearchidentity, 3.4.2.14     logarithmic, 20.4.8
pdbsearchresults, 4.1.3pls, 17.7, 17.8, 20.6
pdbsearcsequence, 3.4.2.16pmf, 23.6.7
peptides, 3.4.1.1.1png, 3.4.1.13, 5.12, 5.12.1, 6.6.3, 16.6, 16.6.4
perspective, 3.4.3.9, 5.7.5pocket, 3.1.12, 3.4.6.5, 4.3, 14.5, 18.1, 22.3.4, 23.3.13, 23.5.11, 23.6.11
ph4, 16.10     conservation, 23.5.12
     draw 2d, 16.10.1     display, 19.3
          3d, 16.10.2     peptide, 3.1.12
     search, 16.10.3     properties, 3.1.12
pharmacophore, 16.2.33, 16.10.5     surface, 22.6.5
     2D, 22.5.7portait, 3.4.1.15.6
     3D, 22.5.6post screen, 18.4.9
     clone, 16.10.2postscript, 3.4.1.15.6
     draw2D, 16.10.1potential mean force, 18.4.4
     draw3D, 16.10.2powerpoint, 22.1.11, 23.4
     edit, 16.10.1, 16.10.2ppbatch, 18.6.8
     move, 16.10.2ppepitope, 18.6.6
     new, 16.10.2ppmaps, 18.6.7
     search, 16.10, 16.10.3, 22.5.6, 22.5.7pprefine, 18.6.10
phi, 5.5.5, 23.3.17ppresults, 18.6.9

ppsetligand, 18.6.5          superimpose 3D, 11.3
ppsetproject, 18.6.3               grid, 11.5
ppsetreceptor, 18.6.4               multiple proteins, 11.4
ppt, 7.4, 7.6, 23.4.3protein-protein, 3.4.6.4, 14.4, 18.6, 18.6.1, 18.6.2, 18.6.3, 18.6.4, 18.6.5, 18.6.7, 18.6.8, 18.6.9
predict, 9.2.2, 17.7, 17.8, 20.6, 20.6.2, 23.7.14, 23.7.18     docking refinement, 18.6.10
predicting bioassays, 20.6.2protein-proteindocking, 18.6.6
     compound properties, 20.6.2     convert, 3.4.16.1, 15.1
preferences, 3.4.1.15, 23.3.23, 23.3.24protonated, 23.5.15
presentatio, 6.6.5protprot, 18.6
presentation, 7, 7.4psa, 16.3.5
presentations, 6psi, 5.5.5, 23.3.17
preserve, 23.7.11pubmed, 4.1.9
press-and-hold to rotate, 16.3.4purple box, 3.4.3.23
preview export movie, 8.2.8qs ddali, 3.3.6
primary aliphatic amines, 17.5     hydrogen bond, 4.4
principal component analysis, 20.5     pdb chem gl, 4.2.2
     components, 20.6.3               iw, 4.2.1
print, 20.4.15, 20.7.2     quick pocket, 4.3
     plot, 20.4.15     selection, 22.1.6
printer.resolution, 3.4.1.15.6          ws, 22.1.7
probe, 23.6.14          ali, 3.3
problem, 23.10.5          fasta, 3.3.2
problems, 23.10          load, 3.3.1
     with selection, 23.10.3          new, 3.3.3
project, 3.4.1.4, 18.6.3          pdb, 3.3.4
     name, 18.1.4qsar, 17.7, 17.8
     close, 3.4.1.12     learn predict, 17.7
     rename, 3.4.1.8     predict, 17.8
properties, 5.5.2, 17.1, 23.7.12quad.buffer, 23.2.3
property, 16.3.5, 23.7.12, 23.7.13, 23.7.14, 23.7.15quality, 3.4.1.14, 3.4.1.15.5
     expression, 18.4.9.5query, 13.3, 23.7.5, 23.7.6, 23.7.16
     monitor, 16.3.5     molt, 21.4
propogate, 22.1.10     pdb, 4.1.1.1
protect, 6.6.7          field, 4.1.1.4
protein, 9, 22.4.5, 23.5.5          ligand code, 4.1.1.3
     health, 3.4.6.2, 14.2          sequence, 4.1.1.2
     structure, 4     processing, 16.9.3
          analysis, 10     setup, 16.9.1
               closed cavities, 10.4quick, 3.1.19
               contact areas, 10.3     start chain breaks, 3.1.10
               distance, 10.6          move structure, 3.1.2
               find related chains, 10.1          read pdb, 3.1.1
               finding dihedral angle, 10.8          representation, 3.1.9
                    planar angle, 10.7          selection, 3.1.4
               rama export, 10.10               level, 3.1.5
               ramachandran plot, 10.9          sequence alignment, 3.3.5
               rmsd, 10.2          what is selected, 3.1.6
               surface area, 10.5     dispalay.distance, 5.6.1
     superposition, 11     start color, 3.1.11
          select superposition, 11.1quit, 3.4.1.18

racemic, 16.2.26, 17.6.5, 23.6.22     alternative orientaiton, 22.3.10
radius, 22.1.8     content, 9.2.1
rainbow, 3.4.1.15.5, 5.5.16, 16.2.33     number selection, 23.3.35
rama export, 3.4.7.9     propogate, 22.1.10
ramachandran plot, 3.4.7.9, 10, 10.10     content, 3.4.4, 9.2, 9.2.1
range, 6.1.2     mutate, 23.5.13, 23.5.14
ratio.selection, 3.4.1.15.5residues, 4.3, 23.3.13
     dock ligand, 19.4resize, 5.2.7, 5.12.3
reactions, 16.12, 17.17.7resolution, 4.1.1.4
read, 3.4.1.2, 3.4.1.8.1, 3.4.1.16, 4.1.1, 4.1.4, 9.1restore, 3.4.2.11, 5.2.9, 5.10.1
     chemical, 16.1.1     recent backup, 3.4.2.11
     table, 20.1.2results, 18.6.9
     pdb, 3.1.1, 4.1.3     stack, 18.1.13
     sequence, 3.3.1review and adjust binding site, 18.1.6
     table, 20rgroup, 17.17.3
reagent, 17.17.7ribbon, 3.1.10, 3.4.1.15.9, 3.5.1, 5.1.1, 5.1.4, 23.3.22, 23.3.33
rear, 5.2.9, 5.10.1     as a mesh object, 23.3.3
recent files, 3.4.1.16     faq, 23.3.22
     pdb codes, 3.4.1.17     preferences, 3.4.1.15.9
receptor, 18.2.2, 18.6.4, 18.6.6, 22.9.1, 23.6.2, 23.6.15, 23.6.16     style, 3.4.1.15.9
     from pdb, 18.1.1     breaks, 5.1.4
     flexibility, 22.9.2     cylinders, 5.1.4
     surface, 22.6.5     smooth, 5.1.4
recover, 3.4.2.11     worm, 5.1.4
rectangle, 22.1.6, 22.1.7ribbonColorStyle, 3.4.1.15.9
redo, 3.4.2.10, 16.3.12right, 3.1.16
refine, 13.7, 13.8     click, 3.1.16
     side chain, 13.8rigid, 17.18
region, 18.6.6     super, 17.18.2
regresion, 20.4.12          table, 17.18.1
regression, 20.6.1, 20.6.3ring, 16.3.2, 16.9.1
regul, 13.7rings, 16.2.26, 17.9, 17.18
regularization, 3.4.16.3, 13.7, 15.3rmsd, 3.4.7.2, 10, 10.2, 22.4.6, 23.5.7, 23.5.8
related, 3.4.7.1rock, 3.4.3.15, 5.7.6, 6, 6.1, 6.1.1, 8.2.6
relationship, 20.6     speed, 6.1.2
release, 1root, 23.5.7
reload, 3.4.1.8.1, 3.4.1.8.2, 18.1.15, 23.6.5     mean square deviation, 3.4.7.2, 10.2
     dock results, 18.1.15rotate, 3.1.2, 3.4.3.15, 5, 5.7.6, 5.9, 5.9.1, 5.9.2, 6, 6.1, 6.1.1, 8.2.5, 16.2.32, 23.7.19
reloading object not running, 3.4.1.8.2     chemical, 16.2.32
reloadingobjectrunning, 3.4.1.8.1     when pasting, 16.3.4
remove, 3.1.10, 23.3.6, 23.3.7, 23.3.9     easy, 3.4.3.12
     salt, 23.7.20     speed, 6.1.2
     explixit.hydrogens, 17.2rotating fragment in editor, 16.3.4
     salt, 17.2rotation, 3.1.3, 5.9.1
rename project, 3.4.1.8row, 20, 20.1.20, 20.1.26, 20.1.34
renumber, 23.5.4     flag, 20.1.11
replace chemical, 16.2.30     mark, 20.1.11
replacement, 19.7     hide, 16.2.6
representation, 3.4.3.19     show, 16.2.6
residue, 3.4.1.15.7, 23.3.8, 23.5.15, 23.5.22ruler, 5.5.16

safari, 23.4          graphic, 3.2.12
salts, 16.2.16     object, 3.2.9
sample, 17.18     superposition, 3.4.8.1
save, 5.2.10, 5.12.1, 6.1.4, 20.4.16, 20.7.2, 23.3.32     tree, 20.7.1
     chemical, 16.3.7     atom, 3.1.4, 3.1.5, 3.1.6
     image, 5.12.1     graphical, 3.1.4, 3.1.5, 3.1.6
          plot, 20.4.16     object, 3.1.4, 3.1.5, 3.1.6
     object, 3.1.13     purple.box, 3.4.3.23
     print delete alignment, 9.5.2     residue, 3.1.4, 3.1.5, 3.1.6
     project icb, 3.1.14     workspace, 3.1.4, 3.1.5, 3.1.6
     slide, 6.4selectall, 3.4.2.3
     table, 20.1.19selecting.neighbors, 3.2.12
     tree, 20.7.2selection, 20.4.14, 20.7.1, 20.7.3, 22.1.5, 22.1.6, 22.1.7, 23.3.4, 23.3.6, 23.3.7, 23.3.8, 23.3.12, 23.3.31, 23.5.9, 23.5.10, 23.5.22, 23.6.15
     image, 3.1.19, 3.4.1.14     clear, 3.4.2.7
     object, 3.1.13     neighbors, 3.4.2.8
     password, 3.4.1.10     toolbar, 3.2.1
     picture, 3.4.1.14     alignment, 3.2.14
     project, 3.1.14, 3.4.1.7, 3.4.1.8, 3.4.1.9     all, 3.4.2.3
     table.view, 20.1.6     alter, 3.2.5
saving, 3.4.1.7     amino, 3.2.10
     project, 3.4.1.7     atom, 3.2.1, 3.4.2.5
scaffold, 17.4     basic, 3.2.3
scale, 3.4.1.15.5     change, 3.2.5
scan, 18.1.12     clear, 3.4.2.7
     hits, 18.1.12     column, 20.1.21
scatter, 18.4.9.2     filter, 3.2.6, 3.4.2.5, 22.1.9
scatterplot, 18.4.9.4     graphical, 3.2.1, 3.2.12
score, 18.4.8, 23.6.8, 23.6.9, 23.6.19     invert, 3.4.2.6, 20.1.21
     threshold, 18.4.4     lasso, 3.2.1
screen, 22.7, 22.8.1     level, 3.4.3.3
screening, 18.4, 18.4.1, 18.4.2, 22.9     mode, 3.4.3.4
screenshot, 8     near atoms, 3.4.2.8
     movie, 8.1     neighbors, 3.2.11, 3.2.13, 3.4.2.5, 3.4.2.8
script, 3.4.1.1.5, 6.6.4, 6.6.5, 23.5.19, 23.9, 23.9.1, 23.9.2, 23.9.3     object, 3.2.9
sdf, 16.2.33, 16.6, 16.6.1, 16.6.2, 16.6.3, 16.6.4, 16.13, 17.6.1, 21.1, 22.8.2, 23.7.3, 23.7.4     other, 3.2.14
search, 4.1.1.3, 16.13, 16.13.3, 21.2, 23.7.16     pick, 3.2.1
     filter, 16.9.2     properties, 3.4.2.5
     in workspace, 3.4.2.4     range, 20.1.21
     pdb, 4.1.1.2, 4.1.1.4     residue, 3.4.2.5, 22.1.10
     in.workspace, 3.4.2.4     row, 20.1.21
secondary aliphatic amines, 17.5     sphere, 3.2.11
     structure, 3.4.6.1, 14.1, 23.3.19     spherical, 3.4.2.8, 22.1.8
     sctructure, 9.2.2     superposition, 3.4.8.1, 11.1
     structure, 3.4.4, 5.1.4, 9.2     table, 3.2.14, 20.1.21
select, 20, 20.1.34, 23.5.22          elements, 20.1.21
     a tree branch, 20.7.1     toolbar, 3.2.1
     amino acid, 3.2.10     tools, 3.2.2, 3.2.3, 3.2.5, 3.2.6
     chemical, 16.3.9     whole, 3.2.9
     duplicates, 17.16     workspace, 3.2.7, 3.2.13
     neighbors, 3.2.11selectioninvert, 3.4.2.6

     links, 9.2.9simulations, 23.8
selectneighbors workspace, 3.2.13single, 16.3.6
sequence, 3.3.1, 3.3.2, 3.3.3, 3.3.4, 3.3.6, 3.4.4, 4.1.1.2, 9, 9.1, 9.2, 9.2.8, 13.3, 22.2, 22.3, 22.3.3, 22.3.5, 23.5.12sketch accents, 5.7.3
     analysis, 9.2     accents, 3.4.3.14, 5.7.3
     reordering, 9.5.4skin, 3.5.1, 5.1.1, 5.1.5, 23.3.15
     structure, 9.2.6slab, 5.2.9, 5.10.1
     type, 9.2.4slice, 5.10
     DNA, 9.2.4slide, 6.1.4, 6.3.1, 6.6.1, 23.3.30
     alignment, 3.3.5, 9.2.5, 9.4.5     effects, 6.5
     nucleotide, 9.2.4     navigation, 6.3.2
     protein, 9.2.4     show, 6.3
     search, 9.3     blend, 6.5
     structure.alignment, 9.2.6     edit, 6.4.1
sequences, 3.3, 4.1.1, 9, 23.3.24     effect, 6.5
     unique, 9.2.13     smooth, 6.5
     extract, 9.2.13     transition, 6.5
     unique, 9.2.13slides, 6, 6.2, 6.3, 23.3.29
set, 16.2.29, 23.5.21smiles, 16.1.1, 16.3.5, 17.1, 17.6, 17.6.3, 17.6.4
     formal charges, 17.5solvent.accessible.area, 23.5.19
     bond type, 3.4.16.5, 15.5sort hitlist, 18.4.9.1
     charges, 3.4.16.6, 15.6     table, 3.4.10.4
     chirality, 3.4.16.5, 15.5sorting, 18.4.9.1
     disulfide, 13.9, 23.5.17     compounds, 20.6.4
          bond, 3.4.16.5, 15.5spec, 3.5.2
     formal charge, 3.4.16.5, 15.5specifications, 23.2.1
     tether, 3.4.16.5, 15.5     faq, 23.2.1
     types, 3.4.16.6, 15.6speed, 6.1.2
setAPFparams, 23.7.18sphere, 3.4.1.1.10, 22.3.4, 23.5.11
setup, 18.6.5, 23.6.14spherical, 22.3.5, 23.5.9, 23.5.12
     ligand receptor, 19.1     selection, 22.1.8
shade and box, 9.5.6split, 17.17.5
shading, 5.2.11spreadsheet, 17.6.2
shadow, 5.7.2square, 23.5.7
sheet, 23.3.19squence.amino acid, 9.2.4
shell preferences, 3.4.1.15.10stack, 18.1.11, 18.6.9, 23.8.2
shift, 5.5.3standard table, 20.1
shine, 3.4.1.15.5, 3.5.2standardize, 17.2
shineStyle, 3.4.1.15.3     table, 17.2
show, 6.3.1, 20.1.30start, 16.13.2
     hide column, 20.1.30     dock, 18.1
side, 16.2.27startup, 23.9.2
     by side, 16.2.27static, 23.5.8
               stereo, 3.4.3.6stereo, 3.4.1.15.6, 16.2.26, 23.2.2, 23.2.3, 23.10.5
     chains, 13.8     hardware, 3.4.3.7
side-chain sampling, 18.6.10     side-by-side, 3.4.3.6
side-chains, 18.2.1stereohard faq, 23.2.2
sigmaLevel, 3.4.5.6, 3.4.5.7, 12.6, 12.7stereoisomer, 17.6.5
similar, 3.4.7.1stereoisomers, 17.11
similarity, 17.14stick, 3.4.1.15.5
simulation, 23.8.2still, 8.2.3

store, 3.4.3.19, 6.1.4, 23.3.21     find, 20.1.7
     current view, 3.4.3.19          replace, 16.2.30
               faq, 23.3.21     font, 20.1.9
strain, 3.4.6.2, 14.2          size, 23.3.1
strip, 23.5.9     grid, 20.1.5
structure, 3.4.5.3, 12.3, 20.6, 22.3, 22.3.3, 23.5     histogram, 20.4.1
     ensemble, 3.4.16.9, 15.9     insert, 20.1.23
     representation, 5.1.1     layout, 20.1.5
     smiles, 17.6.4     mark, 20.1.11
     display, 3.1.8          row, 20.1.11
     undisplay, 3.1.8     mouse, 20.1.35
structures, 4.1.1, 16, 16.1     navigation, 20.1.4
style, 3.4.1.15.5     new, 3.4.1.1.7
substructure, 16.11, 16.13.3, 17.3, 23.7.5, 23.7.6          column, 20.1.23
     alerts, 17.3     plot, 20.4
suface, 23.5.19     print, 20.1.17
sulfur, 13.9     rename, 20.1.13
superimpose, 3.4.8, 11.2, 22.3.3, 22.4.6, 23.3.5, 23.5.6, 23.5.7, 23.5.8     rightclick, 20.1.12
     3D, 3.4.8.2     save, 20.1.3
     grid, 3.4.8.4          selection, 20.1.3
     multiple proteins, 3.4.8.3     search, 20.1.7
     3D, 3.4.8.2, 11.3     select, 20.1.21
     Calpha, 3.4.8.2, 11.3     setup, 20.1.16
     arrange.grid, 3.4.8.4, 11.5     sort, 20.1.32
     backbone, 3.4.8.2, 11.3     split fragments, 16.2.31
     flexible, 17.18.3     view, 20.1.5
     heavy atoms, 3.4.8.2, 11.3          save, 20.1.6
     multiple, 3.4.8.3, 11.4     zoom translate, 16.2.28
     rigid, 17.18.1, 17.18.2     action, 20.1.35
     substructure, 17.18.1, 17.18.2, 17.18.3     alignment, 20.1.10
superposition, 17.18     append, 20.1.33
surface, 3.4.1.15.5, 3.5.1, 5.1.1, 5.1.7, 5.2, 23.3.15     clone, 20.1.14
     area, 3.4.7.5, 10     color, 20.1.8
     area, 3.4.7.5, 10.5     column, 16.2.2, 20.1.23, 20.1.24, 20.1.30
surfaces, 5.2.1     columns, 16.2.6
surrounding, 4.3, 22.3.4, 23.5.11     compare, 16.2.19
swissprot, 3.3.1, 9.1     copy, 16.2.5
symmetry, 3.4.5.1, 3.4.5.3, 12.1, 12.3, 22.3.7, 22.3.8     cursor, 20.1.35
     packing, 3.4.5.1     delete, 20.1.12, 20.1.15
tab, 20.1.2, 20.1.19     display, 23.9.4
     pdb, 3.5.4     double.click, 20.1.35
table, 16.2.21, 16.2.22, 16.2.26, 16.2.28, 16.2.29, 16.2.32, 16.2.33, 17.6.2, 17.9, 17.18.1, 20, 20.1.26, 20.1.31, 20.1.34, 20.4, 20.4.1, 20.4.4, 20.4.5, 20.4.7, 20.4.9, 20.4.10, 20.4.11, 20.4.12, 20.4.13, 20.4.14, 20.4.15, 20.7, 23.5.19, 23.7.9, 23.7.10, 23.7.12, 23.7.13     edit, 16.2.15
     alignment, 20.1.10     excel, 16.2.8, 20.1.18
     clone, 20.1.14     export, 16.7
     color, 20.1.8     filter, 16.2.10, 20.1.33
     column format, 20.1.31     find-replace, 16.2.11
     copy, 20.1.27, 20.1.28          to screen, 20.1.4
     delete, 20.1.15     font, 20.1.9
     edit, 20.1.22     foreground, 23.9.4
     filter, 20.1.33     grid lines, 20.1.4

     hyperlink, 16.2.13          plot function, 3.4.9.1
     insert, 20.1.25     identify ligand binding pocket, 3.4.6.5
     join, 3.4.10.5     oda, 3.4.6.4
     label, 16.2.12     superimpose, 3.4.8
     landscape, 20.1.16     table, 3.4.10
     mark, 16.2.12          Learn, 3.4.10.1
     merge, 3.4.10.5, 16.2.20, 17.15          clustering, 3.4.10.3
     mouse, 20.1.35          merge, 3.4.10.5
     name, 20.1.13          predict, 3.4.10.2
     new, 20.1.1torsion, 5.9.6, 23.5.16
     options, 20.1.12     angles, 5.9, 5.9.6
     orientation, 20.1.16transition.blend, 23.3.30
     portrait, 20.1.16transitions, 6, 23.3.29
     print, 16.2.9, 20.1.4, 20.1.17translate, 3.1.2, 5, 5.9, 16.2.28
     read, 20.1.2translation, 3.1.3, 5.9.3, 9.2.3, 20.4.13
     rename, 20.1.13transparent, 5.2.8
     right click, 20.1.12     background, 5.12.3
     row, 20.1.25     ribbon, 23.3.3
     rows, 3.4.10.7tree, 9.5.4, 20.7.1, 20.7.2, 20.7.3
     save, 16.2.7, 20.1.3, 20.1.4, 20.1.19     branch swapping, 9.5.4
     scale, 20.1.16     distance, 17.12.3
     scroll, 20.1.4     edit, 17.12.4
     sdf, 16.2.7     reorder, 17.12.3
     select, 20.1.21trouble shooting, 23.10.2
     setup, 20.1.16trouble-shooting, 23.10.3
     sort, 3.4.10.4, 16.2.3, 20.1.32troubleshooting, 23.10
     standard, 20.1truncating a mesh object, 23.3.14
     view, 16.2.4, 16.2.27     crash qlock, 23.10.4
     width, 20.1.4tsv, 20.1.19
tables, 17.14, 20tut analyze alternative orientations, 22.3.10
tautomer, 17.10, 23.5.15          occupancy, 22.3.9
tautomers, 17.10          symmetry, 22.3.8
temperature, 3.4.6.3, 14.3     bind pocket, 22.3.3
template, 13.3, 17.18     hydrogen bond, 22.3.6
     docking, 23.6.4     ligand pocket, 22.3.4
terminal, 16.2.26     multiple receptor, 22.9.1
     font size, 23.3.1     pocket conservation, 22.3.5
text, 3.4.1.15.7, 6.6, 6.6.1, 6.6.6, 16.2.26, 16.13.3, 23.7.16tut2, 22.3
     search, 16.9.4tut2a, 22.3.1
texture, 3.5.5tut2b, 22.3.2
thoroughness, 17.9, 17.18, 23.6.13tut3, 22.4
three, 16.2.21, 23.7.11tut3a, 22.4.1
threshold, 3.4.1.15.5tut3b, 22.4.3
tier, 3.1.17tut3bb, 22.4.4
time, 23.6.12tut3c, 22.4.5
     racemic, 17.6tut3e, 22.3.11
tools 3D, 3.4.6tut3f, 22.4.6
     analysis, 3.4.7tut4b, 22.5.1
     append rows, 3.4.10.7tut4c, 22.5.4
     extras, 3.4.9tut4d, 22.5.5

tut5a, 22.7.1     shadow, 3.4.3.13
tut5b, 22.7.2     sketch accents, 3.4.3.14
tut5c, 22.8.1     slide show, 6.3.1
tut5e, 22.8.2     tools, 3.4.3
tutorial 2D pharmacophore, 22.5.7     tree, 20.7.3
     3D pharmacophore, 22.5.6     undisplay all, 3.4.3.1
     chemical search, 22.5.3     stach, 3.4.16.10, 15.10
     edit chemical, 22.5.2virtual, 18.4, 18.4.1, 18.4.2, 22.7, 22.8.1
     graphical selections, 22.1.5     screening examples, 22.8
     molecular documents, 22.1.11virus, 3.4.5.3, 12.3
     sequence alignment, 22.2vls, 18.2, 18.4, 18.4.5, 18.4.9.5, 22.8.2, 23.6.8, 23.6.9
               link, 22.2.3     analysis, 18.4.9.5
               load pdb, 22.2.1     getting started, 18.4.2
                    sequence, 22.2.2     histogram, 18.4.9.3
               sequence conservation, 22.2.4          scatter plot, 18.4.9.2
tutorials, 22     introduction, 18.4.1
tween, 8.2.4     preferences, 18.4.4
two, 16.2.21, 23.7.11     results, 18.4.8
unclip, 5.2.9, 5.10.1     run, 18.4.5
undisplay, 3.1.7, 5.1.8, 23.3.9, 23.3.31     scatterplot, 18.4.9.4
     origin, 5.5.12     results, 18.4.8
undo, 3.4.1.15, 3.4.2.9, 16.3.12volume, 16.3.5
     redo structure, 16.3.12wavefront, 3.5.5, 5.2.10
uniprot, 3.3.1weak, 23.5.20
unique, 16.2.26, 17.16web, 22.1.11
unit, 3.4.5.3, 12.3     browser, 3.4.1.11
units, 23.6.1weight, 17.1, 23.7.12, 23.7.15
unix, 23.9.2weighted, 20.7
updates, 1what to dock, 18.1.2
use activeicm, 7.4width, 20.1.20
user, 1, 16.13.4window, 3.1.17
user-defined groups, 16.3.3windows, 3.1.18, 16.13.1
uundisplay-all, 3.4.3.1wire, 3.4.1.15.5, 3.5.1, 5.1.1, 5.1.2, 23.3.4, 23.3.20
van der waal, 5.5.15wireBondSeparation, 3.4.1.15.1
variable, 3.4.1.15.7, 23.3.8working directory, 23.6.24
verbose, 17.9workspace, 3.1.7, 4.2.1, 16.5.2, 22.1.7
vicinity, 17.9     panel, 3.1.7
video, 8     selection, 3.2.7
view, 3.4.3.19, 6.3.1, 16.2.26, 23.3.21, 23.8.2     navigation, 3.2.8
     animate view, 3.4.3.15write, 3.1.19, 5.12.1, 20.4.16, 23.7.4, 23.8.1
     center, 3.4.3.20     image, 3.4.1.14
     color background, 3.4.3.18     image, 3.4.1.14
     dock results, 18.1.11     object, 3.1.13
     fog, 3.4.3.5     picture, 3.4.1.14
     macroshape, 3.4.3.22     project, 3.1.14, 3.4.1.7
     menu, 3.4.3     table, 20.1.3
     mesh clip, 5.10.1writing a pdb file, 23.5.3
     perspective, 3.4.3.9     ray, 3.4.5
     selection level, 3.4.3.3xi, 5.5.5, 23.3.17
          mode, 3.4.3.4xstick, 5.1.3, 23.3.20

zoom, 3.1.2, 3.1.3, 5, 5.9, 5.9.4, 16.2.28, 20.4.13