Jun 18 2013 Feedback.
Contents
 
Introduction
How To Guides & Videos
Getting Started
Protein Structure
Molecular Graphics
Slides and Documents
ActiveICM
Movie Making
Sequences & Alignments
Protein Structure Analysis
Protein Superposition
Crystallographic Analysis
Homology & Modeling
3D Predict
Molecular Mechanics
Cheminformatics
Chemistry Menu
Docking
3D Ligand Editor
Tables
Local Databases
KNIME
Tutorials
FAQs
 
Index

Index

2D, 5.5.10, 16.2.21, 16.2.26, 17.4, 17.6.2, 17.6.4     center Follows Clipping, 3.4.1.15.3
     to 3D, 17.6, 17.6.3     clash Style, 3.4.1.15.3
     depiction, 17.6.2     clashWidth, 3.4.1.15.3
3D, 5.5.10, 16.2.21, 16.2.26, 16.2.29, 17.6.2, 23.1.5     clip Grobs, 3.4.1.15.3
     chemical, 17.6.1          Skin, 3.4.1.15.3
     interactive ligand editor, 3.5.5          Static, 3.4.1.15.3
     ligand editor, 19.7     discrete Rainbow, 3.4.1.15.4
     object, 5.2.6     displayLineLabels, 3.4.1.15.7
     predict, 14     displayMapBox, 3.4.1.15.3
          helices strands, 14.1     distance Label Drag, 3.4.1.15.1
          local flexibility, 14.3     dnaBallRadius, 3.4.1.15.9
          protein health, 14.2     dnaRibbonRatio, 3.4.1.15.9
          tools identify ligand binding pocket, 14.5     dnaRibbonWidth, 3.4.1.15.9
               oda, 14.4     dnaRibbonWorm, 3.4.1.15.9
4D, 18.2.2, 23.9.1     dnaStickRadius, 3.4.1.15.9
     dock, 19.13     dnaWormRadius, 3.4.1.15.9
64, 24.1.2     font Scale, 3.4.1.15.7
APF, 17.20.3     fontColor, 3.4.1.15.7
     template, 17.20     fontLineSpacing, 3.4.1.15.7
ActiveICM, 3.4.1.11     grobLineWidth, 3.4.1.15.3
Area, 24.3.25     hbond Ball Period, 3.4.1.15.1
Atom Single Style, 3.4.1.15.3               Style, 3.4.1.15.1
Bad Groups, 24.7.12, 24.7.15     hbondAngleSharpness, 3.4.1.15.1
Blast, 24.3.24     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, 18.5.10.6     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
Display, 24.3.25     occupancy Radius Ratio, 3.4.1.15.3
Distance, 18.5.10.6     occupancyDisplay, 3.4.1.15.3
Dock Directory, 3.4.1.15.2     quality, 3.4.1.15.3
Docking, 24.3.25     rainbow Bar Style, 3.4.1.15.4
Editor, 3.4.1.15.2     resLabelDrag, 3.4.1.15.7
Error in saving configuation settings: You are not a license administrator, 24.10.2     resize Keep Scale, 3.4.1.15.3
FILTER.Z, 3.4.1.15.2     ribbonRatio, 3.4.1.15.9
     gz, 3.4.1.15.2     ribbonWidth, 3.4.1.15.9
     uue, 3.4.1.15.2     ribbonWorm, 3.4.1.15.9
Filter.zip, 3.4.1.15.2     rocking, 3.4.1.15.4
Formula, 24.7.12, 24.7.15          Range, 3.4.1.15.4
Frequently Asked Questions, 24          Speed, 3.4.1.15.4
GAMESS, 3.4.16.11, 15.13     selectionStyle, 3.4.1.15.3
GIF, 3.4.1.14, 8     site Label Drag, 3.4.1.15.7
GRAPHIC.store Display, 3.4.1.15.3               Shift, 3.4.1.15.7
     NtoC Rainbow, 3.4.1.15.4     siteArrow, 3.4.1.15.7
     alignment Rainbow, 3.4.1.15.4     stereoMode, 3.4.1.15.3
     atomLabelShift, 3.4.1.15.7     stickRadius, 3.4.1.15.1
     ballStickRatio, 3.4.1.15.1     surfaceDotDensity, 3.4.1.15.3
     surfaceProbeRadius, 3.4.1.15.3ISIS, 24.7.8
     transparency, 3.4.1.15.3IUPAC, 16.8
     wire Width, 3.4.1.15.1Icm Prompt, 3.4.1.15.10
     wormRadius, 3.4.1.15.9Internal Coordinates Table, 15.10
     xstick Backbone Ratio, 3.4.1.15.1     Directory, 3.4.1.15.2
          Hydrogen Ratio, 3.4.1.15.1JPEG, 3.4.1.14
          Style, 3.4.1.15.1KMZ, 3.4.1.6
          Vw Ratio, 3.4.1.15.1Log Directory, 3.4.1.15.2
GROB.arrowRadius, 3.4.1.15.3LogP, 20.6
     atomSphereRadius, 3.4.1.15.3LogS, 20.6
     contourSigmaIncrement, 3.4.1.15.3MOL, 16, 16.1.1, 16.2.1, 16.2.21, 16.2.22, 16.2.23, 16.2.24, 18.5.3, 20.2
     relArrow Size, 3.4.1.15.3MOL2, 16.1.1, 18.5.3
     relArrowHead, 3.4.1.15.3MOLT, 21.1
GUI, 1MOVIE.frame Grab Mode, 3.4.1.15.4
     auto Save, 3.4.1.15.4Map Atom Margin, 3.4.1.15.10
               Interval, 3.4.1.15.4     Sigma Level, 3.4.1.15.10
     autoSave, 24.3.32Markush, 23.5.21
     autoSaveInterval, 24.3.32     create, 23.5.19
     max Sequence Length, 3.4.1.15.4Max_Fused_Rings, 17.1
     table Row Mark Colors, 3.4.1.15.4Mnconf, 3.4.1.15.10
     workspace Folder Style, 3.4.1.15.4MolIPSA, 24.7.12, 24.7.15
     workspaceTabStyle, 3.4.1.15.4MolLogP, 24.7.12, 24.7.15
HBA, 24.7.12, 24.7.15MolLogS, 24.7.12, 24.7.15
HBD, 24.7.12, 24.7.15MolPSA, 17.1
Hbond to selection, 18.5.10.6MolVol, 17.1
Hbonds, 19.7Molcart, 16.9.3
How To Guide, 2MoldHf, 17.1, 24.7.12, 24.7.15
Html, 4.1.8Movie.fade Nof Frames, 3.4.1.15.4
Hydrogen.bond, 3.4.1.15.5     quality, 3.4.1.15.4
ICM, 1          Auto, 3.4.1.15.4
     Browser How To, 2.1NCBI, 24.3.24
          Pro How To, 2.2NMR, 4.1.1
     graphics crash, 24.10.3Nof_Atoms, 17.1
IMAGE.bondLength2D, 3.4.1.15.6Nof_Chirals, 17.1
     color, 3.4.1.15.6Nof_HBA, 17.1
     compress, 3.4.1.15.6Nof_HBD, 17.1
     gammaCorrection, 3.4.1.15.6Nof_Rings, 17.1
     generateAlpha, 3.4.1.15.6Nof_RotBonds, 17.1
     lineWidth, 3.4.1.15.6Non-overlap, 18.5.10.6
     lineWidth2D, 3.4.1.15.6Nvidia GL failutre, 24.10.3
     orientation, 3.4.1.15.6ODA, 24.3.25
     paper Size, 3.4.1.15.6Optimal, 24.3.25
     previewResolution, 3.4.1.15.6Output Directory, 3.4.1.15.2
     previewer, 3.4.1.15.6PBS, 18.5.7
     print, 3.4.1.15.6PCA, 20.6.1, 20.6.3
     printerDPI, 3.4.1.15.6     analysis, 17.14
     scale, 3.4.1.15.6PDB, 3.4.5.3, 4.1.4, 4.1.8, 4.2, 9.1, 12.3, 16.4, 19.16
     stereoAngle, 3.4.1.15.6     Directory, 3.4.1.15.2
     stereoBase, 3.4.1.15.6          Style, 3.4.1.15.2
     stereoText, 3.4.1.15.6     link, 20.1.31
          Field, 3.4.2.13SDF, 16, 16.1.1, 16.2.21, 16.2.22, 16.2.23, 16.2.24, 18.5.3, 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, 23.3.2     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, 23.3.1          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, 24.7.12, 24.7.15, 24.7.17
     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, 18.5.7
     labelFont, 3.4.1.15.8Uniprot, 20.1.31
     lineWidth, 3.4.1.15.8VLS, 18.5, 18.5.1, 18.5.2, 18.5.7, 18.5.10.2
     logo, 3.4.1.15.8     preferences, 18.5.4
     markSize, 3.4.1.15.8Var Label Style, 3.4.1.15.7
     orientation, 3.4.1.15.8Volume, 24.7.12, 24.7.15
     paper Size, 3.4.1.15.8     Change, 18.5.10.6
     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, 18.1.1.1
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, 18.5.10.6a-bright, 3.5.2
Projects Directory, 3.4.1.15.2acceptor, 16.3.5, 17.21.1
Prosite Dat, 3.4.1.15.2acid, 3.4.1.1.4
Protein, 24.3.25active, 7, 24.4.3
     Viewer, 3.4.1.15.2activeICM, 7.1
PubMed, 4.1.9activeicm, 7, 7.5, 7.7, 7.7.1, 24.4
     Reference, 20.1.31     advanced, 7.7
QSAR, 20.6, 20.6.1     background images, 7.8
     build model, 23.5.13     control, 7.6
     predict, 23.5.14activityy, 20.6
R, 16.12, 17.18.3add image album, 5.12.4
     and S, 24.6.22adding fragment, 16.3.4
R-group, 16.11          in editor, 16.3.4
RMSD, 11.2administration, 16.13.4
Ramachandran Plot, 10.9advanced alignment selectioection, 9.5.12
Real Format, 3.4.1.15.10album, 5.12.4
Receptor Setup, 18.1.4alias, 16.3.3
     Label Shift, 3.4.1.15.7align, 3.1.15, 3.3.5, 9.4.1, 17.4
          Style, 3.4.1.15.7     color 2D scaffold, 17.4
RotB, 24.7.12, 24.7.15     dna protein, 9.4.3
SAR, 20.6     multiple sequences, 9.4.4
     table, 23.5.21     two sequences, 9.4.2
SCORE, 24.6.7, 24.6.18     DNA to protein, 9.2.7, 9.4.3
     sequence, 9.4, 9.4.5animation, 6.1, 6.1.1, 6.1.2, 6.1.3, 6.1.4
     two sequences, 9.2.5, 9.4.2     store, 6.1.4
alignment, 3.3.6, 17.20.1, 17.20.2, 24.5.12animations, 6
     comment, 9.5.3annotate, 17.3
     editing, 9.5.1     by substructure, 17.3
     editor, 9.5antialias, 3.4.1.14, 3.4.3.10
     example, 9.2.14     lines, 3.4.3.17
     font size, 24.3.1     lines, 3.4.3.17
     format, 9.5.8apf, 11.6, 17.20.1, 17.20.2, 17.21, 18.5.10.7, 19.15, 23.5.18, 24.7.18
     gaps, 9.5.8     flexible template, 17.20.2
     introduction, 9.4.1     pairwise, 17.20.1
     reorder, 9.2.12     super, 17.20
     search, 9.5.9     tools, 17.21
     selection, 9.5.10          consensus ph4, 17.21.1
     view options, 9.5.7          pairwise score, 17.21.2
     box, 9.5.6          screen, 17.21.3
     color, 9.5.5, 9.5.6     alignment, 17.20.3
     comment, 9.5.3apf3Dqsa, 24.7.18
     consensus, 9.5.5, 9.5.12append.rows, 3.4.10.7
     cut, 9.2.11applying prediction models, 20.6.2
     delete, 9.5.2area, 3.4.6.4, 3.4.7.3, 10.3, 14.4, 18.7, 18.7.1, 18.7.2
     display title, 9.5.7aromatic, 16.2.26, 17.21.1
     editor, 9.5arrange, 3.1.18
     extract, 9.2.10     window, 3.1.18
     gaps, 9.5.8arrow, 3.4.1.1.8
     horizontal scroll, 9.5.7     graph, 24.3.8
     multiple, 9.2.8as_graph, 24.3.8
     options, 9.5.7asparagine, 3.4.16.2, 15.2
     print, 9.5.2assign, 5.1.4
     rename, 9.5.7     2D coordinates, 17.6.2
     reorder, 9.2.12     helices, 3.4.6.1, 14.1
     ruler, 9.5.7     strands, 3.4.6.1, 14.1
     save, 9.5.2atom, 3.4.1.15.5, 16.2.26, 24.3.4, 24.3.5, 24.3.8, 24.3.15, 24.3.16, 24.5.10
     search, 9.5.9     charge, 24.5.21
     selection, 9.5.10, 9.5.11, 9.5.12atomLabelStyle, 3.4.1.15.7
     sequence offset, 9.5.7atomic energy circles, 19.8
     shade, 9.5.6     property field, 17.20.1, 17.20.2
     table, 9.5.7               score, 17.21.2
     view, 9.5.7          fields, 11.6, 17.21, 17.21.1, 17.21.3, 23.5.18
alignments, 3.3, 9.4, 23.2attachment, 16.3.2, 16.9.1
alpha, 3.5.2     point, 17.18.2
     channel, 3.4.1.15.6author, 4.1.1.4
ambient, 3.5.2     play slide, 7.6
amidinium, 17.5autofit, 18.6
amino, 3.4.1.1.4autosave, 24.3.32
analysis, 3.4.4, 9.2ave, 20.7
angle, 3.4.7.7, 3.4.7.8, 5.5.5, 5.6, 5.9.6, 10.7, 10.8, 24.3.17, 24.5.16avi, 8
angstrom, 24.5.7axes, 20.4.11
animate, 3.4.3.15, 5.7.6axis, 20.4.7
     view, 5.7.6     options, 20.4.6
     range, 20.4.6     stack, 3.4.16.10, 15.12
     title, 20.4.6bugs, 24.10
b-factor, 3.4.6.3, 14.3, 18.1.1.1, 23.3.6build, 6.1.1
backbone, 24.3.12     homology model, 13.1.3
background, 5.3.2, 5.3.3     hydrogens, 3.4.16.5, 15.5
     color shortcut, 24.3.2buried molSurface, 18.5.10.6
     images activeicm, 7.8buttons, 7.7
     image, 5.3.3bye, 3.4.1.18
backup, 3.4.2.11cache, 7.7.1
bad, 17.1calculate, 17.1, 24.6.2
     groups, 16.3.5     properties, 17.1
ball, 3.4.1.15.5     startup, 24.9.2
     and stick, 3.5.1, 5.1.1carbon, 24.3.4, 24.3.5
bank, 4.1.1carboxylic acid, 17.5
basic alignment selection, 9.5.11cartesian, 17.9
basicsel, 3.2.3cavities, 10
batch, 18.1.10, 18.5.7, 18.7.8     closed, 3.4.7.4, 10.4
     file, 18.1.10.2ccp4, 24.3.26, 24.3.27
     index, 18.1.10.4cell, 3.4.5.2, 12.2
     loaded icm object, 18.1.10.1center, 3.1.2, 3.4.3.20, 5.9, 5.9.5, 20.1.31, 24.5.22
     mol mol2, 18.1.10.3     and representative members, 20.7.1
     molcart, 18.1.10.5chain.breaks, 24.3.33
     run, 18.1.11chains, 3.4.7.1
beep, 24.3.34chair, 24.6.21
begin docking simulation, 18.1.8chair-boat, 24.6.3
best, 16.2.32change selection, 3.2.5
binding, 24.3.13, 24.6.2, 24.6.11     speed range, 6.1.2
     properties, 5.2.1changing font in alignment editor, 9.5
bioinfo align dna protein, 9.2.7charge, 3.4.3.21, 4.3, 4.3.1, 4.3.2, 5.5.2, 16.3.2, 16.5.1, 16.5.2, 16.5.3, 16.9.1, 17.21.1, 18.5.10.6, 24.5.1
          multiple, 9.2.8     groups, 18.1.7, 24.6.23
          two sequences, 9.2.5chem convert, 24.7.10
     links, 9.2.9     save, 16.6
     menu, 3.4.4          editor, 16.6.2
     secondary structure, 9.2.2          image, 16.6.4
     translation, 9.2.3          table, 16.6.1
biological, 3.4.5.3, 12.3          workspace, 16.6.3
biomolecule, 3.4.5, 3.4.5.3, 12.3, 23.3.4, 23.3.8     super, 17.19
bit, 24.1.2     view, 16.2.26
blast, 9.3chemical, 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, 17.18.2, 17.18.4, 17.19, 17.20.1, 17.20.2, 20.7, 24.7.9, 24.7.10, 24.7.12, 24.7.13, 24.7.14, 24.7.15
boat, 24.6.21     clustering, 17.13
bond, 4.3, 4.5, 4.5.1, 4.5.2, 13.7, 16.3.6, 23.3.3, 24.5.1, 24.7.12, 24.7.15     dictionary, 16.3.3
     covalent, 24.5.2     draw load, 16.1
     type, 4.3.1, 4.3.2, 16.5.1, 16.5.2, 16.5.3     editor, 16.3, 16.3.4
bonding, 5.1.9          not starting, 24.10.5
     preferences, 3.4.1.15.1     find replace, 16.11
box, 3.4.1.1.9, 3.4.1.15.7, 5.5.17, 24.6.10     fragments, 16.2.31
break, 3.1.10     group, 16.3.3
browse, 16.2.29, 18.1.12.1     groups, 16.3.3, 16.3.4
     mode, 16.2.29     right click, 16.3.2
     molt, 21.2     search, 16.9
          text, 16.9.4     remove.redundant, 17.17
     smiles, 16.1.2chemlib.so, 24.1.2
     spreadsheet, 24.7.19chi, 5.5.5, 24.3.17
          compare, 16.2.19chiral, 17.11
     spreadsheets, 16.2chirality, 17.11
     structure, 16chrome, 24.4
     superimpose, 23.5.18cis trans proline, 23.4.3
          apf, 23.5.17clash, 3.4.1.15.5, 5.5.16
          rigid flexible, 23.5.16     volumes, 18.5.11
     table, 24.7.17classes, 16.2.26
          display, 16.2.1clear display and planes, 3.4.3.2
     tables, 20.2     selection, 3.2.4
     2D, 16.5     planes, 3.4.3.2
     3D, 16.5click, 3.1.16, 5.8, 5.9
     append, 16.3.7clip, 5.2.9, 5.10.1, 24.3.10
     clustering, 17.13, 17.13.1clipboard, 5.12.2, 20.7.2
     convert, 3.4.16.1, 4.3, 4.3.1, 4.3.2, 15.1, 16.5, 16.5.1, 16.5.2, 16.5.3, 24.5.1clipping, 24.3.18
     display.fit, 24.7.19     planes, 3.1.3, 5
     draw, 16.3.1, 23.5.1     tool, 5.10
     duplicates, 16.2.18     tools, 5.10
     edit, 16.3.8, 23.5.2closed cavities, 3.4.6.5, 3.4.7.4, 14.5
     editor, 16.6, 16.6.1, 16.6.2, 16.6.3, 16.6.4cluster, 18.5.7, 18.5.10.7, 20.7
     load, 16.1, 16.1.1     representative.center, 17.13.2
     merge, 17.16clustering, 20.6.4
     name, 16.8collada, 3.5.6, 5.2.4
     new, 16.3.1color, 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, 24.3.4, 24.3.5, 24.3.15, 24.3.19
     properties, 16.2.17     alignment, 9.5.5
     query, 16.3.2, 16.9.1, 16.9.3     background, 5.3.2
     read, 16.1, 16.1.1     by, 5.3
     redo, 16.3.12     chemical, 16.2.33
     save, 16.3.7, 16.6, 16.6.1, 16.6.2, 16.6.3, 16.6.4     display mesh, 5.2.8
     search, 16.3.2, 16.9, 16.9.1, 16.9.3, 23.5.4, 23.5.5     faq, 24.3.19
     similarity, 16.3.2, 16.9, 16.9.1, 16.9.3, 23.5.4, 23.5.5     table, 16.2.24
     smiles, 16.1.2     2D sketch, 16.10.5
     spreadsheet, 16.2, 16.6, 16.6.1, 16.6.2, 16.6.3, 16.6.4     background, 3.4.3.18, 5.3.2
     structure, 16.1.1, 16.3.7, 16.3.8     distance, 5.5.12
     substructure, 23.5.5     mesh, 5.2.8
     superimpose, 17.19.1, 17.19.2, 17.19.3     table, 16.2.24
     superposition, 17.20, 17.20.3coloring, 5.3.1
     table, 16.2, 20.2, 23.5.1, 23.5.2column, 20, 20.1.20, 20.1.30, 20.1.31, 20.4, 20.4.1, 24.7.12
     undo, 16.3.12     row width, 20.1.20
cheminformatics, 16.2, 24.7     statistics, 20.1.24
     tutorials, 23.5     color, 20.1.8
chemistry, 17.10, 24.7     hide, 16.2.6
     convert, 17.6     show, 16.2.6
          2dto3d, 17.6.1combinatorial chemistry, 17.18
     menu, 17     library, 23.5.20
     pca, 17.14combine, 3.4.10.5
     smiles, 17.6.3     display style, 3.4.1.15.9
     duplicates, 17.17command, 24.6.17
commands, 3.4.1.1.5, 24.9.1     paste row, 20.1.26
compare, 16.2.27, 17.15, 17.16          structure, 16.3.10
     table, 16.2.19     row, 20.1.27
     tables, 17.15     selection to table, 20.1.28
compatible, 3.4.1.9     chemical, 16.2.14
complex, 18.5.10.5covalent docking, 18.4, 19.14
compound, 17.10, 20.2cpk, 5.1.6, 24.3.20
compounds, 24.7.3crash, 3.4.2.11
compress, 3.4.1.15.6creat, 6.6.1
conditions, 16.9.2create, 20.1.1
     gen, 17.9     modify markush, 17.18.1
conformation, 17.9, 18.2.2cross, 24.3.9
conformational entropy, 17.12     section, 5.10
conformations, 24.8.2crystal, 3.4.5.2, 12.2
conformers, 17.9crystallographic analysis, 12
connect, 5.2.7, 5.9, 5.9.7          biomolecule, 12.3
     object, 5.9.7          contour map, 12.6
connectivity, 16.3.2, 16.9.1          convert2grid, 12.7
consensus, 3.4.7.1, 17.21          crystallographic cell, 12.2
     pharmacophore, 17.21.1          load eds, 12.4
construct, 3.4.1.1, 3.4.1.1.1, 6.1.1          maps cell, 12.5
     DNA, 3.4.1.1.3          symmetry packing, 12.1
     RNA, 3.4.1.1.3          tools, 23.3.4
     chemical, 3.4.1.1.2     cell, 3.4.5.2
     compound, 3.4.1.1.2     cell, 3.4.5
     molecule, 3.4.1.1     neigbor, 3.4.5.1, 12.1
     nucleic, 3.4.1.1.4     neighbors, 3.4.5
     object, 3.4.1.1crystallography, 3.4.5.4, 3.4.5.6, 3.4.5.7, 12.4, 12.6, 12.7, 24.3.26, 24.3.27
     protein, 3.4.1.1.4csv, 20.1.2, 20.1.3, 20.1.19
     sequence, 3.4.1.1.4current, 24.3.21
contact, 3.4.7.3, 10, 10.3     slide, 7.6
     areas, 3.4.7.3custom, 5.9, 16.2.1, 17.19
contour, 3.4.5.6, 3.4.5.7, 12.6, 12.7     actions, 20.1.31
     map, 3.4.5.6     fragments, 17.3
convert, 4.2, 17.6.1, 17.6.5, 24.7.10     label, 5.5.10
     2D to 3D.conformer generator, 23.5.11     rotation, 5.9.2
                    from table, 23.5.10cut, 20.1.26
                    molecule editor, 23.5.9     vertical alignment block, 9.2.11
     chemical, 16.2.21damaged skin, 24.10.4
          2D 3D, 16.5dash, 24.3.11
     local database, 3.4.1.5data, 4.1.1
     pdb chem, 16.5.1database, 9.3, 16.13, 17.18.2, 18.1.1.2, 18.5.3, 18.5.6, 21.1
     smiles to 2D, 24.7.17     file format, 18.5.3
     local.database, 3.4.1.5     seach and alignment, 9.3
     smiles, 17.6, 17.6.3, 17.6.4databases, 24.7.3
convert2grid, 3.4.5.7decompose.library, 23.5.21
converting pdb, 4.2decomposition, 17.18.2, 17.18.3
copy, 16.2.22, 16.3.13, 16.10.2, 20.1.26default, 3.1.17
     cell, 20.1.27delete, 3.2.4, 3.4.2.1, 6.6.7, 24.5.9
     chemical, 16.2.22     column row, 20.1.29
     all, 3.4.2.2          polar, 5.1.8
     angle.label, 5.6.4     macroshape, 5.2.3
     column, 20.1.29     meshes, 5.2.2
     distance.label, 5.6.4          and display.macroshape, 3.5.6
     label, 5.5.11     molecule, 16.2.21
     row, 20.1.29     origin, 5.5.13
     selection, 3.4.2.1     potential, 3.4.3.21
     tether, 3.4.16.5, 15.5     representations, 3.5.1, 5.1.1
deleteall, 3.4.2.2     restraints, 5.5.15
density, 3.4.5.4, 3.4.5.6, 3.4.5.7, 12.4, 12.6, 12.7, 24.3.26, 24.3.27     ribbon, 5.1.4
depth, 5.2.11     skin, 5.1.5
deselect, 24.3.7     status, 24.3.31
design loop, 13.4, 15.9     surface, 5.1.7, 5.2.1
deviation, 24.5.7     surfaces, 3.5.6
dialog, 6.6.5     table, 16.2.1
diffuse, 3.5.2     tethers, 5.5.14
dihedral, 3.4.7.8, 5.5.5, 10.8, 24.3.17     wire, 5.1.2
     angle, 10     xstick, 5.1.3
dimensional, 24.7.11distance, 3.4.7.6, 5.5.12, 5.6, 10, 10.6, 17.15, 24.3.11, 24.5.8, 24.5.10
directories preferences, 3.4.1.15.2     faq, 24.5.10
directory, 3.4.1.15     restraint, 19.12
disappearing labels, 24.10.4     label, 3.4.1.15.7
display, 3.1.7, 3.1.18, 3.4.1.15, 4.5, 4.5.1, 4.5.2, 5.5.16, 5.11, 16.2.25, 17.11, 18.1.7.3, 23.3.3, 24.3.4, 24.3.5, 24.3.8, 24.3.9, 24.3.10, 24.3.16, 24.3.20, 24.3.29, 24.3.31, 24.5.10, 24.5.11, 24.5.20, 24.7.9distances, 3.5.3
     chemical, 16.2.25disulfide, 13.7
     delete distances, 5.6.4diverse set, 20.6.4
     dihedral, 5.6.3dock, 18, 18.1, 18.1.1.2, 18.6, 23.8.1, 23.8.2, 23.9.1, 24.6.3, 24.6.4, 24.6.5, 24.6.6, 24.6.8, 24.6.9, 24.6.11, 24.6.12, 24.6.13, 24.6.14, 24.6.15, 24.6.16, 24.6.17, 24.6.22
     distance restraints, 5.5.15     apf, 19.15
     distance2, 5.6.1     chemical table, 18.1.14
          angles, 5.6     command, 24.6.17
     formal charge, 5.1.10     macrocylce, 24.6.21
     gradient, 5.5.18docking, 3.4.6.4, 14.4, 18, 18.1.2, 18.1.15, 18.2, 18.2.1, 18.2.2, 18.2.3, 18.5, 18.5.1, 18.5.2, 18.5.6, 18.7, 18.7.1, 18.7.2, 18.7.3, 18.7.4, 18.7.5, 18.7.7, 18.7.8, 18.7.9, 19.10, 23.7, 23.7.1, 23.7.2, 23.8.3, 23.9, 23.9.2, 24.6, 24.6.1, 24.6.10, 24.6.18, 24.6.19
     hbond, 18.5.10.5     batch index, 18.1.10.4
     hbonds, 18.5.10.6, 19.7     covalent, 18.4
     hydrogen, 5.1.8     explicit group, 23.9.2
     mesh, 5.2.2               docking explicit, 23.9.2.5
     meshes, 5.2.5                    project, 23.9.2.3
     planar angle, 5.6.2               receptor setup, 23.9.2.1
     structure, 3.1.8               rotate hydroxyls, 23.9.2.2
     tab, 3.5.1, 24.3.15               run docking, 23.9.2.4
     tether, 5.5.14     from table, 18.1.9.1, 18.1.9.2
     toggle, 5.5.17     introduction, 18.1.1
     CPK, 5.1.6     macrocycles, 18.1.7
     angle, 5.6.2     preferences, 18.1.7
     chemical, 16.2.1          database scan, 18.1.7.2
     dihedral.angle, 5.6.3          display, 18.1.7.3
     distace, 5.5.12          general, 18.1.7.1
     distance, 5.5.15, 5.6.1     project, 18.5.5
     electrostatic, 3.4.3.21          table, 18.5.5
     energy.gradient, 5.5.18     start, 18.1.2
     hydrogen, 5.1.8     template, 18.3
     background, 24.6.20     molt, 21.3
     batch, 18.1.10     selection, 3.4.2.5
     binding, 18.1.5     slide, 6.4.1
     conformations, 24.6.21     table row, 20.1.22
     flexible.rings, 24.6.21     molecule, 16.2.23
     hitlist, 18.1.13     structure, 16.2.23
     interactive, 18.1.9editor, 24.5.12
     maps, 18.1.6editpdbsearch, 3.4.2.12
     preparation, 18.1.2eds, 3.4.5.4, 3.4.5.6, 3.4.5.7, 12.4, 12.6, 12.7
     procedure, 18.1.8electron, 3.4.5.4, 3.4.5.6, 3.4.5.7, 12.4, 12.6, 12.7, 24.3.26, 24.3.27
     project name, 18.1.3     denisty map, 3.4.5.5, 12.5
     rank, 18.1.13     densitry map.contour, 3.4.5
     receptor setup, 18.1.4          map, 3.4.1.6, 3.4.5, 18.6
     results, 18.1.12, 18.1.12.1, 18.1.12.2, 18.1.13electrostatic potential, 3.4.3.21
     sampling, 24.6.21     surface, 5.2
     score, 18.1.13electrostatics, 5.2.1, 18.7.7
     stack, 18.1.12.2elegant sketch, 5.7.4
     template, 18.3element, 16.3.6
document, 3.4.1.1.6, 6.6.4, 6.6.5embed browser, 7.4
     navigation, 6.6.6     powerpoint03, 7.1
documents, 5.12.4     powerpoint07, 7.2
dollar, 24.9.3     powerpoint10, 7.3
donator, 16.3.5     activeicm, 7.6
     envelope, 3.5.1, 5.1.1          script, 7.6
     surface, 3.4.1.15.5     browser, 7, 7.4
dots, 3.1.10     firefox, 7, 7.4
dotted lines, 3.1.10, 24.3.33     internet.explorer, 7, 7.4
double, 16.3.6     microsoft, 7
download, 24.7.3     powerpoint, 7, 7.1, 7.2, 7.3
drag, 3.1.15, 3.3.6, 3.4.1.15.7, 5.5.3, 6.6.4, 9.4.5, 24.5.5enantiomer, 24.6.22
     and drop sequences, 9.4.5energy, 3.4.6.2, 5.5.16, 14.2, 17.12, 17.12.2, 18.1.12.2, 24.6.1, 24.6.2, 24.8.2
     residue label, 3.4.3.16     circles, 18.5.11
draganddrop, 3.1.15     terms, 3.4.16.12, 15.14
draw, 16.3.13, 17.18.4, 24.7.7ensemble, 18.2.2
     chemical, 16.3.1entropy, 17.12.1
drop, 3.1.15, 3.3.6, 6.6.4, 9.4.5, 24.5.5enumerate.reaction, 23.5.22
drug, 17.1, 24.7.12, 24.7.14enumeration, 17.18.2
druglikeness, 16.3.5eps, 16.6.4
dsPocket, 3.1.12epsilon, 24.5.15
easy rotate, 3.4.3.12errno, 24.1.2
edit, 4.5.1, 19.5, 24.7.8error, 24.1.2, 24.3.34
     alignment, 9.5.1escaping, 3.1.3
     chemical, 16.3.8exact, 17.15
          moledit, 16.2.23excel, 16.7
     ligand, 19.4exclude fragment, 16.9.2
          editor preferences, 19.2exit, 3.4.1.18
          tools, 3.4.2.17explicit, 16.2.26, 18.2.1
     menu, 3.4.2     flex, 18.2.1
     molecular document, 6.6.1     group, 18.2.3
     molecule, 16.3          docking, 18.2.3
export, 3.4.7.9, 10.10     extract ligand, 24.7.13
     dock project, 19.17     flexible dock, 24.6.16
     excel, 16.7          ring docking, 24.6.21
extract, 3.3.4, 9.1, 24.5.12, 24.7.13     font size, 24.3.1
     icb, 3.4.1.4     foreground table, 24.9.4
     sub alignment, 9.2.10     gl failure, 24.10.3
     2D chemical sketch, 16.4     gui, 24.3
     icb, 3.4.1.4     guided dock, 24.6.4
     pharmacophore, 16.10.4     hardware, 24.2
faq, 24, 24.2, 24.3, 24.3.12, 24.5, 24.6, 24.8, 24.9, 24.9.2     hitlist, 24.6.8
     ISISdraw, 24.7.8     iSee, 24.3.29
     activeicm, 24.4     icmPocketFinder, 24.6.11
          path, 24.4.3     insert column, 24.7.12
     apf model, 24.7.18     installation, 24.1
     atom charge, 24.5.21     interactions, 24.3.11
          display, 24.3.16     ligandbox, 24.6.10
     autosave, 24.3.32     merge, 24.5.5
     backbone, 24.3.12     molcart 64bit, 24.1.2
     background color, 24.3.2          query, 24.7.6
          job, 24.6.20          sdf, 24.7.4
     beep, 24.3.34          text search, 24.7.16
     binding energy, 24.6.2     molecule c, 24.3.5
     blend transition, 24.3.30     moledit, 24.7.7
     breaks, 24.3.33     movie planes, 24.3.18
     change torsion, 24.5.16     newscript, 24.9.1
     chem table display, 24.7.9     nmr, 24.5.18
     chemical monitor, 24.7.15     nvidia error, 24.1.1
          query2, 24.7.5     origin, 24.3.9
     cheminformatics, 24.7     plist, 24.10.1
     clipping plane, 24.3.10     pmf score, 24.6.7
     closest, 24.5.22     pockets, 24.3.13
     color carbon, 24.3.4     preserve coordinates, 24.7.11
          skin, 24.3.15     quad buffer, 24.2.3
     command line display, 24.3.31     receptor selection, 24.6.15
     convert chemical from pdb, 24.5.1     reload dock, 24.6.5
     covalent bond, 24.5.2     remove salt, 24.7.20
     delete, 24.5.9          select, 24.3.6
     deselect, 24.3.7     renumber, 24.5.4
     dihedral, 24.3.17     residue number selection, 24.3.35
     dock charge groups, 24.6.23     ringflex dock, 24.6.3
          probe, 24.6.14     rmsd, 24.5.7
          racemic, 24.6.22     rmsdtips, 24.5.8
          repeat, 24.6.6     rocking active ppt, 24.4.1
          working directory, 24.6.24          speed, 24.4.2
     docking, 24.6     rotate chemical, 24.7.19
     docktime, 24.6.12     scanScoreExternal, 24.6.18
     dollar, 24.9.3     scanScoreExternal2, 24.6.19
     druglikeness, 24.7.14     score, 24.6.9
     energy, 24.6.1     script, 24.9
     error admin, 24.10.2     simulations, 24.8
     solvent accessible surface table, 24.5.19     view, 20.1.5
     ss, 24.5.17formal, 4.3, 24.5.21
     structure, 24.5     charge, 5.1.10, 17.5
     superimpose, 24.5.6format, 20.1.2, 20.1.31
     thoroughness, 24.6.13formula, 16.3.5, 17.1
     transparent ribbon, 24.3.3fragment, 16.2.33, 17.18.3, 19.10
     truncate mesh, 24.3.14     linking, 19.10
     view stack, 24.8.2fragments, 16.12
     weak hydrogen bonds, 24.5.20frame, 9.2.3
     write pdb, 24.5.3frequency, 16.2.33
faqcontour, 24.3.27front, 5.2.9, 5.10.1
faqhbondstrength, 24.3.28full scene antialias, 3.4.3.10
faqmaps, 24.3.26     screen, 3.4.3.8
faqoda, 24.3.25function, 20.1.23, 20.1.24
faqstereo, 24.10.6functional.groups, 17.3
fasta, 3.3, 3.3.2gap, 13.4
field, 4.1.1.4general preferences, 3.4.1.15.5
file, 3.4.1.2, 4.1.4generalselecttools, 3.2.2
     close, 3.4.1.12generator, 3.4.5.3, 12.3, 17.9
     compatible, 3.4.1.9getting started, 3
     export, 3.4.1.11glasses, 24.2.2, 24.10.6
     load, 3.4.1.6glutamine proline, 3.4.16.2, 15.2
     menu, 3.4.1google, 3.4.1.6
     password, 3.4.1.10     objects, 5.2.4
     quick image, 3.4.1.13     3D, 3.5.6, 5.2.4
     icb, 3.1.14graphical, 1, 24.3.4
     recent, 3.4.1.16     display, 4.3.1, 4.3.2, 16.5.2, 16.5.3
     bak, 3.4.2.11          tutorial, 23.1
filter, 21.2, 24.3.4               2D3D labels, 23.1.4
     selection, 3.2.6               annotation, 23.1.2
filters, 18.5.5               color representation, 23.1.1
find, 3.4.7.1               labels, 23.1.3
     chemical, 16.2.30     user interface, 24.3
     related chains, 3.4.7.1     card, 24.1.1
finding dihedral angle, 3.4.7.8     controls, 5
     planar angle, 3.4.7.7     defects, 24.10.4
fingerprint, 24.7.5, 24.7.6     effects, 5.7
firefox, 24.4     preferences, 3.4.1.15.3
fit, 16.2.32, 18.6, 24.6.16     tips, 3.1.3
fitting, 18.6, 20.4.12     shadow, 3.4.3.13, 5.7.2
flex super, 17.19.3grid, 16.2.1, 16.2.4, 17.19, 23.9.1, 24.7.9
flexibility, 3.4.6.3, 14.3, 18.2.3, 23.9grob, 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
flexible, 17.19, 18.2, 18.2.1, 18.2.2, 23.9.1, 24.6.16group, 17.18.3, 19.6
     ring sampling level, 18.1.7groups, 16.12, 17.1, 17.2
     rings, 24.6.3guanidinium, 17.5
fog, 3.4.3.5, 5, 5.7.1gui, 3.4.1.15.4
font, 3.4.1.15, 3.4.1.15.7, 4.5.1, 5.5.2, 5.5.3, 16.2.26, 20.1.31, 20.7.3     menus, 3.4
     preferences, 3.4.1.15.7     preferences, 3.4.1.15.4
     size, 9.5, 24.3.1     tabs, 3.5
form, 16.2.4guided docking, 24.6.4
hardware, 24.2     duplicate chemicals, 16.2.18
     stereo, 3.4.3.7     edit table, 16.2.15
hbond, 24.3.28          tree, 17.13.4
     strength, 24.3.28     excel, 16.2.8
header, 4.1.8, 20.4.5     extract 2D, 16.4
health, 3.4.6.2, 14.2          3D ph4, 16.10.4
helices strands, 3.4.6.1     filter, 16.2.10
helix, 24.3.19     find replace, 16.2.11
hetero, 16.2.26     mark row, 16.2.12
hidden block format, 9.5.8     markush, 23.5.20
          width, 9.5.8          structure, 23.5.19
hide, 20.1.30     merge tables, 16.2.20
high, 3.4.1.14     properties, 16.2.17
     quality, 3.4.3.11     qsar, 23.5.12
his, 24.5.15          build model, 23.5.13
histidine, 3.4.16.2, 15.2, 24.5.15          predict, 23.5.14
     tautomer, 24.5.15     reactions, 23.5.22
histogram, 18.5.10.2, 18.5.10.3, 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     reorder, 17.13.3
     bins, 20.4.3     sdf, 16.2.7
     options, 20.4.2     show hide, 16.2.6
     bin.size, 20.4.2     smiles, 16.3.11
     bins, 20.4.3     sort column, 16.2.3
     color, 20.4.2     standardize, 16.2.16
     source, 20.4.2     table hyperlinks, 16.2.13
     style, 20.4.2          print, 16.2.9
     title, 20.4.2          activeicm, 2.3
hitlist, 18.1.12, 18.1.13, 18.5.9, 18.5.10.1, 18.5.10.3, 18.5.10.7, 24.6.8               create molecular documents, 2.3.3
     cluster apf, 18.5.10.7                    slides, 2.3.2
homology, 3.4.7.1, 13, 13.1, 13.1.1, 13.1.2, 13.2.1, 13.3, 13.5, 23.4, 23.4.1               getting started, 2.3.1
     loops, 13.1.4               ppt, 2.3.4
     model, 13.1               web, 2.3.5
          introduction, 13.1.1          chemical clusering, 17.13.1
          start, 13.1.2          display, 3.1
     modeling, 23.4.2          icm browser convert display pocket, 2.1.4
     3D editor, 23.6                    distances angles, 2.1.9
     add columns, 16.2.2                    get started, 2.1.1
     change view, 16.2.4                    graphical display, 2.1.2
     chemical 2D 3D, 23.5.8                         effects, 2.1.5
                    conformer generator, 23.5.11                    images, 2.1.7
                    from table, 23.5.10                    labels annotation, 2.1.6
                    molecule editor, 23.5.9                    pro crystallographic tools, 2.2.6
          superimpose, 23.5.15                         get started, 2.2.1
               apf, 23.5.17                         graphics, 2.2.2
                    pairwise, 23.5.18                         plots, 2.2.8
               rigid flexible, 23.5.16                         sequence analysis, 2.2.7
     cluster center, 17.13.2                         structure analysis, 2.2.3
     color 2D by ph4, 16.10.5                         superimpose, 2.2.5
     copy 2D, 16.2.14                         surfaces, 2.2.4
          paste, 16.2.5                    selections, 2.1.3
     decompose, 23.5.21                    superimpose, 2.1.8
html, 3.4.1.1.6, 3.4.1.11, 6.6.1, 6.6.6, 24.4     image, 6.6.3
html-doc font size, 24.3.1     row, 20.1.25
hybridization, 16.3.2, 16.9.1     script, 6.6.4
hydrogen, 4.5, 4.5.1, 4.5.2, 5.1.9, 16.3.2, 16.9.1, 23.3.3, 24.3.11, 24.7.12, 24.7.15install, 1, 16.13.1, 24.1.2, 24.1.3
     bond, 5.1.9, 18.5.10.5installation, 24.1
          donor, 17.21.1interactio, 24.6.2
          label edit, 4.5.1interaction, 3.4.7.3, 10.3, 24.3.11
               move, 4.5.2interactive, 18.1.9, 23.1.5
     bond, 16.3.5, 24.5.20     loaded ligand, 18.1.9.2
hydrogens, 16.2.26     loop, 13.2.3
     remove, 16.2.16     make, 13.2.1
hyperlink, 6.6.1, 6.6.2, 20.1.31     modeling, 13.2, 13.2.1
hyrophobic, 17.21.1          table ligand, 18.1.9.1
iSee, 3.1.14, 3.4.1.1.6, 3.4.1.4, 3.4.1.11, 5.12.4, 23.1.5, 24.3.29, 24.3.30, 24.4.3     modeling, 13.2
icb, 24.3.29, 24.4.3interface, 1
icm, 24.4.3internet explorer, 24.4
     chemist howto chemical search, 2.4.3interrupt, 6.1.3
               cluster, 2.4.5     animation, 6.1.3
               combi library, 2.4.7introduction, 1
               ph4, 2.4.4invert selection, 20.1.21
               plots, 2.4.8invisible residue label, 24.10.4
               sketch, 2.4.1isee, 6.6.5
               spreadsheets, 2.4.2isis, 16.3.13
               stereoisomers tautomers, 2.4.6isotope, 16.3.2, 16.9.1
          pro 3D ligand editor, 2.5.1iupac, 16.8
               chem3D, 2.5.2job, 24.6.20
               chemsuper, 2.5.3jobs, 18.5.7
               qsar, 2.5.4join, 17.16
               tutorials, 2.5jpg, 5.12, 5.12.1
          tutorials, 2.4     means, 20.7
     hanging, 24.10.5keep carboxyls neutral, 18.1.7
     script, 20.1.31     chemical, 16.3.6
icm-crash, 24.10.5keyboard mouse, 5.8
icmFastAlignment, 9.3keystokes in chem-edit, 16.3.6
icmPocketFinder, 3.4.6.5, 14.5, 24.3.13, 24.6.11kinase build model, 23.4.2.3
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, 20.4.16     model loop, 23.4.2.4
     advanced, 5.12.3kinasemod, 23.4.2
     clipboard, 5.12.2     search, 23.4.2.1
     preferences, 3.4.1.15.6     sequence alignment, 23.4.2.2
     multiple, 3.4.1.6kmz, 3.5.6, 5.2.4
     quality, 3.4.3.11knime, 22
     quick, 3.4.1.13label, 3.4.1.15.7, 20.7.3, 24.3.16
images, 5.12     annotation, 5.5.8
impose, 18.2.2     atoms, 5.5.2
in-a-window, 24.2.3     color, 5.5.9
index, 24.7.16     move, 5.5.4
induced, 24.6.16     residues, 5.5.3
     fit, 18.2, 18.2.1, 18.2.3, 23.9, 23.9.1     sites, 5.5.6
insert, 6.6.4     variables, 5.5.5
     column, 20.1.23     2D, 3.5.3
     annotation, 5.5.8          edit, 19.4
     atom, 5.5.1          energy, 19.3
     atoms, 5.5.2          hydrogen.bond, 19.3
     color, 5.5.9          pocket, 19.3
     custom, 5.5.10          preferences, 19.2
     delete, 5.5.1, 5.5.11          restraint, 19.11
     distance, 5.5.12          surface, 19.3
     drag, 3.4.3.16          tether, 19.11
     move, 3.4.3.16, 5.5.4     optimization, 23.8.3
     residue, 5.5.1     pocket, 3.1.12
     residues, 5.5.3     receptor.contact, 3.4.7.3, 10.3
     site, 5.5.1ligedit tab, 3.5.5
     sites, 5.5.6light, 3.5.2
     variable, 5.5.1     tab, 3.5.2
     variables, 5.5.5, 24.3.17lighting, 5.4
labeling, 5.5.1likeness, 17.1, 24.7.14
labels, 5.5, 16.2.26line, 3.4.1.15.5, 20.7.3, 24.3.11
     distances, 5.5.12lineWidth, 3.4.1.15.3
     tab, 3.5.3link, 9.2.9
landscape, 3.4.1.15.6     structure to alignment, 23.2
large font size, 24.10.1links, 3.2.15
layer, 5.11linux, 16.13.1
layers, 5.11load, 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
learn, 17.7, 17.8, 20.6, 20.6.1, 24.7.18     eds, 3.4.5.4
learning, 20.6     example alignment, 9.2.14
     theory, 20.6.3     nmr model, 4.1.5
least.squares, 20.4.12     pdb, 4.1.4
library, 17.18.2          hyperlinks, 4.1.7
     reaction, 23.5.22     sequence, 9.1
license, 24.1.3          extract pdb, 9.1.3
ligand, 17.12, 17.12.1, 17.12.2, 18.1.1.2, 18.2, 18.7.5, 18.7.6, 19.5, 19.10, 24.5.5, 24.5.11, 24.6.2, 24.6.10, 24.7.13          from file, 9.1.4
     based screen, 17.21.3          paste, 9.1.2
     best replace, 19.6          swissprot, 9.1.1
     code, 4.1.1.3     libraries, 3.4.16.6, 15.6
     editor, 19, 19.12, 19.14, 19.15     pdb, 4.1.3
          covalent docking, 19.14     sequence, 3.3.1
          distance restraint, 19.12local, 24.3.23, 24.3.24
          mrc, 19.13     databases, 21
          preferences, 3.4.2.18     flexibility, 3.4.6.3
     energetics, 17.12     database.browse, 21.2
          conformational entropy, 17.12.1          edit, 21.3
          strain, 17.12.2          query, 21.4
     pocket, 24.5.11          row, 21.3
          surface, 19.3.2localpdb, 24.3.23
     tether, 19.11localseq, 24.3.24
ligand-based screen, 23.5.18lock, 5.2.9, 5.10.1, 16.2.29
     convert, 3.4.16.1, 15.1log, 20.4.7
     editor, 19, 19.1logP, 16.3.5, 17.1
          binding.re-dock ligand, 19.9logS, 16.3.5, 17.1
          display, 19.3logarithmic, 20.4.7
loop, 13.3, 24.3.19     homology, 3.4.13
     design, 13.4     molmechanics, 3.4.16
     model, 13.3, 13.4, 23.4.3     tools chemical search, 3.4.11
          tutorial, 23.4.3          molecular editor, 3.4.12
     modeling, 13.2.3, 15.9     windows, 3.4.17
     model, 3.4.16.8, 15.8merge, 17.16, 24.5.5
     sample, 3.4.16.8, 15.8     two sets, 17.16
mac, 16.13.1, 24.10.1mesh, 3.4.5.4, 3.4.5.6, 3.4.5.7, 4.4, 5.2, 5.2.7, 5.2.9, 5.2.10, 5.2.11, 5.10.1, 12.4, 12.6, 12.7
macros, 7.7     clip, 5.2.9
macroshape, 3.4.3.22, 5.2, 5.2.3     options, 5.2.6
make, 3.4.1.1.1, 3.4.1.1.7, 6.1.1, 20.1.1     save, 5.2.10
     animation, 6.1.1     options, 5.2.6
     complex, 18.5.10.6meshes surfaces grobs, 5.2
     flat, 24.7.19     tab, 3.5.6
     images, 5.12min, 20.7
     molecular document, 6.6minimize.cartesian, 3.4.16.7, 15.7
     molt, 21.1     global, 3.4.16.7, 15.7
     receptor maps, 18.1.6     local, 3.4.16.7, 15.7
     selection, 3.2mmff, 3.4.16.6, 15.6, 24.3.16, 24.7.10
     DNA, 3.4.1.1.3     type, 5.5.2
     RNA, 3.4.1.1.3mnSolutions, 3.4.1.15.10
     bond, 24.5.2model, 13, 13.1, 13.1.1, 13.1.2, 13.1.3, 13.3, 13.5, 23.4, 23.4.1
     chemical, 3.4.1.1.2     loop, 13.1.4
     compound, 3.4.1.1.2modelers view, 13.2.2
     disulfide, 13.7, 24.5.17     view, 13.2.2
     molecule, 3.4.1.1modeling, 3.4.16.3, 15.3
     object, 3.4.1.1modeller view, 13.2
     sequence, 3.4.1.1.4modify group, 13.8
making molecular slides, 6.2mol, 16.6, 16.6.1, 16.6.2, 16.6.3, 16.6.4, 23.8.2
     html, 6.6mol2, 16.6, 16.6.1, 16.6.2, 16.6.3, 16.6.4
     color, 20.4.10molcart, 16.13, 16.13.1, 16.13.2, 16.13.3, 16.13.4, 21, 24.1.2, 24.7, 24.7.3, 24.7.4, 24.7.5, 24.7.6, 24.7.16
map, 3.4.1.15.7, 3.4.5.4, 3.4.5.6, 3.4.5.7, 12.4, 12.6, 12.7     administration, 16.13.4
     cel, 3.4.5.5, 12.5     connect, 24.7.2
maps, 18.7.7, 23.9.1, 24.3.26, 24.3.27, 24.6.10     download dbs, 24.7.3
     cell, 3.4.5.5     hostid, 24.7.1
mark, 20.1.34     installation, 16.13.1
     row, 20.1.34     license, 24.1.3
     shape, 20.4.9     search, 16.13.3
     size, 20.4.9     start, 16.13.2
markush, 17.18.1, 17.18.3, 23.8.3     connect, 24.7.2
     docking, 23.8.3     hostid, 24.7.1
     library, 23.5.20     license, 24.7.1
mass, 24.5.22molclart, 24.1.3
materials, 3.5.6molecular, 16.2.28, 16.2.29, 16.2.32, 16.2.33, 17.9, 24.7.12, 24.7.15
max, 20.7     animations slides, 6
maxColorPotential, 3.4.1.15.10          transitions, 6.1
mean, 24.5.7     document, 3.4.1.1.6
menu, 6.6.5     documents, 23.1.5
     chemistry, 3.4.14     editor, 24.7.7
     docking, 3.4.15          copy, 16.3.10
          paste, 16.3.10     resize mesh, 5.2.7
          redo, 16.3.12     slide, 6.4.2
          selections, 16.3.9     structure, 5.9
          undo, 16.3.12     tools, 5
     graphics, 5     rotate, 5.8
          molecule representation, 5.1     slab, 5.8
     mechanics, 15     translate, 5.8
          convert, 15.1     z-rotation, 5.8
          design loop, 15.9     zoom, 5.8
          edit structure, 15.5movie, 24.3.18, 24.8.1
          gamess, 15.13     montecarlo, 24.8.1
          generate normal mode stack, 15.11     making, 8
          his asn, 15.2     open, 8
          ic table, 15.10mpeg, 8
          impose conformation, 15.4mpg, 8
          minimize, 15.7multi apf super, 17.20.3
          mmff, 15.6multiple, 18.2.2, 23.9.1
          regularization, 15.3     rec, 18.2.2
          sample loop, 15.8     receptor, 23.9
          terms, 15.14          docking, 19.13
          view stack, 15.12     protein, 24.3.5
     modeling, 13mutant, 24.5.13, 24.5.14
     table, 17.6.2mutate, 24.5.15
     weight, 16.3.5     residue, 24.5.13
molecule, 24.3.8, 24.7.8          N C, 24.5.14
     editor, 16.3mutation, 13.8, 24.5.13, 24.5.14
molecules, 3.4.7.1navigate workspace, 3.2.8
moledit, 16.3.4nearest, 24.5.22
molmech icmconv, 3.4.16.1new, 3.3, 3.3.3, 3.4.1.1.1, 9.1
molmechaincs gamess, 3.4.16.11     compound, 3.4.1.1.2
molmechanics, 24.8.2     dna, 3.4.1.1.3
     edit structure, 3.4.16.5     peptide, 3.4.1.1.1
     generate normal mode stack, 3.4.16.9     protein, 3.4.1.1.4
     his asn, 3.4.16.2     table, 20.1.1
     impose conformation, 3.4.16.4     chemical, 3.4.1.1.2
     minimize, 3.4.16.7     compound, 3.4.1.1.2
     mmff, 3.4.16.6     dna, 3.4.1.1.3
     regularization, 3.4.16.3     protein, 3.4.1.1.4
     sample loop, 3.4.16.8     rna, 3.4.1.1.3
     terms, 3.4.16.12     script, 3.4.1.1.5
     view stack, 3.4.16.10     table, 3.4.1.1.7, 20.1.1
     minimize, 3.4.16.7, 15.7nmr, 24.5.18
     mmff, 3.4.16.6, 15.6     model, 4.1.5
molt, 21, 21.4normal modes, 3.4.16.9, 15.11
monitor, 24.7.15notations, 1
monochrome, 16.2.26numbers, 16.2.26
montecarlo, 24.8.1nvidia, 24.1.1
mouse, 3.1.2, 5.8, 5.9object, 3.1.15, 3.4.1.8.1, 3.4.1.8.2, 23.3, 24.3.8
mov, 8objects, 4.2
move, 3.1.15, 3.1.17, 3.4.3.19, 4.5.2, 5.2.7, 5.9, 5.9.7, 24.5.5     in table, 20.3
occlusion, 5.2.11pharmacophore, 16.2.33, 16.10.5
     shading, 5.2.11     2D, 23.5.7
occupancy, 23.3.6     3D, 23.5.6
     display, 4.1.6     clone, 16.10.2
oda, 3.4.6.4, 14.4, 18.7, 18.7.1, 18.7.2     draw2D, 16.10.1
older version, 3.4.1.9     draw3D, 16.10.2
omega, 5.5.5, 24.3.17     edit, 16.10.1, 16.10.2
open, 3.4.1.2, 20.1.2     move, 16.10.2
     with password, 3.4.1.3     new, 16.10.2
     movie, 8     search, 16.10, 16.10.3, 23.5.6, 23.5.7
     password, 3.4.1.3phi, 5.5.5, 24.3.17
optimal, 3.4.6.4, 14.4, 18.7, 18.7.1, 18.7.2phylogenetic, 9.5.4
optimize, 3.4.16.2, 15.2phylogeny, 9.5.4
origin, 5.5.13, 24.3.9picking, 5
other selection, 3.2.14     atoms, 3.1.3
outside, 24.6.10     residues, 3.1.3
overlay, 24.3.5, 24.5.6picture, 3.1.19, 3.4.1.13, 6.6.3
package.activeicm, 7.6     tips, 3.1.19
packing, 3.4.5.1, 12.1planar, 3.4.7.7, 5.5.5, 10.7, 24.3.17
pairwise, 17.20.1, 17.20.2     angle, 10
     apf score, 17.21     angle, 5.6.2
parallelization, 18.5.8plane, 5.2.9, 5.10, 5.10.1, 5.11, 24.3.10, 24.3.18, 24.3.20
password, 16.13.4     faq, 24.3.20
paste, 16.3.13, 20.1.26plot, 3.4.1.15, 3.4.1.15.8, 18.5.10.2, 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
pbs, 18.5.7     axis, 20.4.7
pca, 20.5     color, 20.4.10
pdb, 3.3.4, 3.4.1.6, 4.1.1, 4.1.1.3, 4.3, 16.5.1, 23.3, 24.3.23, 24.3.24, 24.5.4     function, 3.4.9, 3.4.9.1
     chem gl, 16.5.3     grid, 20.4.11
          iw, 16.5.2     header, 20.4.5
     file, 24.5.3     inline, 20.4.17
     html, 4.1.8     logarithmic, 20.4.8
     preparation, 23.3.7     mark, 20.4.9
     search, 4.1     preferences, 3.4.1.15.8
          hyperlinks, 4.1.7     regression, 20.4.12
     sensitive query, 4.1.2     selection, 20.4.14
     convert, 3.4.16.1, 15.1     zoom translate, 20.4.13
     recent, 3.4.1.17     axis, 20.4.11
     search, 3.1.1, 3.5.4, 4.1.3     display, 20.4.11
     table, 4.1.3     grid, 20.4.11
pdbsearchfield, 3.4.2.13     inline, 20.4.17
pdbsearchhomology, 3.4.2.15     logarithmic, 20.4.8
pdbsearchidentity, 3.4.2.14pls, 17.7, 17.8, 20.6
pdbsearchresults, 4.1.3pmf, 24.6.7
pdbsearcsequence, 3.4.2.16png, 3.4.1.13, 5.12, 5.12.1, 6.6.3, 16.6, 16.6.4
peptides, 3.4.1.1.1pocket, 3.1.12, 3.4.6.5, 4.4, 14.5, 18.1, 24.3.13, 24.5.11, 24.6.11
perspective, 3.4.3.9, 5.7.5     conservation, 24.5.12
ph4, 16.10     display, 19.3
     draw 2d, 16.10.1     surface, 18.5.11
          3d, 16.10.2     peptide, 3.1.12
     search, 16.10.3     properties, 3.1.12
post edit ligand, 19.5               distance, 10.6
     screen, 18.5.10               find related chains, 10.1
postscript, 3.4.1.15.6               finding dihedral angle, 10.8
potential mean force, 18.5.4                    planar angle, 10.7
powerpoint, 23.1.5, 24.4               rama export, 10.10
ppbatch, 18.7.8               ramachandran plot, 10.9
ppepitope, 18.7.6               rmsd, 10.2
ppmaps, 18.7.7               surface area, 10.5
pprefine, 18.7.10          tutorials, 23.3
ppresults, 18.7.9     superposition, 11
pproc, 18.7.2          select superposition, 11.1
ppsetligand, 18.7.5          sites by apf, 11.6
ppsetproject, 18.7.3          superimpose 3D, 11.3
ppsetreceptor, 18.7.4               grid, 11.5
ppt, 7.5, 7.7, 24.4.3               multiple proteins, 11.4
predict, 9.2.2, 17.7, 17.8, 20.6, 20.6.2, 24.7.14, 24.7.18protein-protein, 3.4.6.4, 14.4, 18.7, 18.7.1, 18.7.2, 18.7.3, 18.7.4, 18.7.5, 18.7.7, 18.7.8, 18.7.9
predicting bioassays, 20.6.2     docking refinement, 18.7.10
     compound properties, 20.6.2protein-proteindocking, 18.7.6
preferences, 3.4.1.15, 18.5.5, 24.3.23, 24.3.24     convert, 3.4.16.1, 15.1
presentatio, 6.6.5protonated, 24.5.15
presentation, 7, 7.5protprot, 18.7
presentations, 6psa, 16.3.5
preserve, 24.7.11psi, 5.5.5, 24.3.17
press-and-hold to rotate, 16.3.4pubmed, 4.1.9
primary aliphatic amines, 17.5purple box, 3.4.3.23
principal component analysis, 20.5qs convert chemical from pdb, 4.3
     components, 20.6.3     ddali, 3.3.6
print, 20.4.15, 20.7.2     hydrogen bond, 4.5
     plot, 20.4.15     pdb chem gl, 4.3.2
printer.resolution, 3.4.1.15.6               iw, 4.3.1
probe, 24.6.14     quick pocket, 4.4
problem, 24.10.6     seq ali, 3.3
problems, 24.10          fasta, 3.3.2
     with selection, 24.10.4          load, 3.3.1
project, 3.4.1.4, 18.7.3          new, 3.3.3
     name, 18.1.3          pdb, 3.3.4
     close, 3.4.1.12qsar, 17.7, 17.8
     rename, 3.4.1.8     learn predict, 17.7
properties, 5.5.2, 17.1, 24.7.12     predict, 17.8
property, 16.3.5, 24.7.12, 24.7.13, 24.7.14, 24.7.15quad.buffer, 24.2.3
     expression, 18.5.10.6quality, 3.4.1.14, 3.4.1.15.5
     monitor, 16.3.5query, 13.1.3, 24.7.5, 24.7.6, 24.7.16
protect, 6.6.7     molt, 21.4
protein, 9, 11.6, 24.5.5     pdb, 4.1.1.1
     chain, 13.4          field, 4.1.1.4
     health, 3.4.6.2, 14.2          ligand code, 4.1.1.3
     structure, 4          sequence, 4.1.1.2
          analysis, 10     processing, 16.9.3
               closed cavities, 10.4     setup, 16.9.1
               contact areas, 10.3quick, 3.1.19
          move structure, 3.1.2reloading object not running, 3.4.1.8.2
          read pdb, 3.1.1reloadingobjectrunning, 3.4.1.8.1
          representation, 3.1.9remove, 3.1.10, 24.3.6, 24.3.7, 24.3.9
          selection, 3.1.4     salt, 24.7.20
               level, 3.1.5     explixit.hydrogens, 17.2
          sequence alignment, 3.3.5     salt, 17.2
          what is selected, 3.1.6rename project, 3.4.1.8
     dispalay.distance, 5.6.1renumber, 24.5.4
     start color, 3.1.11replace chemical, 16.2.30
quit, 3.4.1.18replacement, 19.6
     group, 17.18.2representation, 3.4.3.19
racemic, 16.2.26, 17.6.5, 24.6.22residue, 3.4.1.15.7, 24.3.8, 24.5.15, 24.5.22
rainbow, 3.4.1.15.5, 5.5.17, 16.2.33     alternative orientaiton, 23.3.7
rama export, 3.4.7.9     content, 9.2.1
ramachandran plot, 3.4.7.9, 10, 10.10     number selection, 24.3.35
range, 6.1.2     content, 3.4.4, 9.2, 9.2.1
ratio.selection, 3.4.1.15.5     mutate, 24.5.13, 24.5.14
     dock ligand, 19.9residues, 4.4, 24.3.13
reactions, 16.12, 17.18.4resize, 5.2.7, 5.12.3
read, 3.4.1.2, 3.4.1.8.1, 3.4.1.16, 4.1.1, 4.1.4, 9.1resolution, 4.1.1.4
     chemical, 16.1.1restore, 3.4.2.11, 5.2.9, 5.10.1
     table, 20.1.2     default, 24.10.1
     pdb, 3.1.1, 4.1.3     recent backup, 3.4.2.11
     sequence, 3.3.1restrain two atoms, 19.12
     table, 20results, 18.7.9
reagent, 17.18.4     stack, 18.1.12.2
rear, 5.2.9, 5.10.1review and adjust binding site, 18.1.5
recent files, 3.4.1.16rgroup, 17.18.2
     pdb codes, 3.4.1.17ribbon, 3.1.10, 3.4.1.15.9, 3.5.1, 5.1.1, 5.1.4, 24.3.22, 24.3.33
receptor, 18.2.2, 18.7.4, 18.7.6, 23.9.1, 24.6.2, 24.6.15, 24.6.16     as a mesh object, 24.3.3
     flexibility, 19.13     faq, 24.3.22
     from pdb, 18.1.1.1     preferences, 3.4.1.15.9
     pocket, 19.3.1     style, 3.4.1.15.9
          surface, 19.3.1, 19.3.2     breaks, 5.1.4
     flexibility, 23.9.2     cylinders, 5.1.4
recover, 3.4.2.11     smooth, 5.1.4
redo, 3.4.2.10, 16.3.12     worm, 5.1.4
refine, 13.5, 13.6ribbonColorStyle, 3.4.1.15.9
     side chain, 13.6right, 3.1.16
region, 18.7.6     click, 3.1.16
regresion, 20.4.12rigid, 17.19
regression, 20.6.1, 20.6.3     super, 17.19.2
regul, 13.5          table, 17.19.1
regularization, 3.4.16.3, 13.5, 15.3ring, 16.3.2, 16.9.1
related, 3.4.7.1rings, 16.2.26, 17.9, 17.19
relationship, 20.6rmsd, 3.4.7.2, 10, 10.2, 24.5.7, 24.5.8
     covalent geometry, 18.1.7rock, 3.4.3.15, 5.7.6, 6, 6.1, 6.1.1
release, 1     speed, 6.1.2
reload, 3.4.1.8.1, 3.4.1.8.2, 18.1.15, 24.6.5root, 24.5.7
     dock results, 18.1.15     mean square deviation, 3.4.7.2, 10.2
     chemical, 16.2.32sdf, 16.2.33, 16.6, 16.6.1, 16.6.2, 16.6.3, 16.6.4, 16.13, 17.6.1, 21.1, 23.8.2, 24.7.3, 24.7.4
     when pasting, 16.3.4search, 4.1.1.3, 16.13, 16.13.3, 21.2, 24.7.16
     easy, 3.4.3.12     filter, 16.9.2
     speed, 6.1.2     in workspace, 3.4.2.4
rotating fragment in editor, 16.3.4     pdb, 4.1.1.2, 4.1.1.4
rotation, 3.1.3, 5.9.1     in.workspace, 3.4.2.4
row, 20, 20.1.20, 20.1.26, 20.1.34secondary aliphatic amines, 17.5
     flag, 20.1.11     structure, 3.4.6.1, 14.1, 24.3.19
     mark, 20.1.11     sctructure, 9.2.2
     hide, 16.2.6     structure, 3.4.4, 5.1.4, 9.2
     show, 16.2.6select, 20, 20.1.34, 24.5.22
ruler, 5.5.17     a tree branch, 20.7.1
rundock, 24.6.17     amino acid, 3.2.10
safari, 24.4     chemical, 16.3.9
salts, 16.2.16     duplicates, 17.17
sample, 17.19     neighbors, 3.2.11
     double bond cis trans, 18.1.7          graphic, 3.2.12
     racemic centers, 18.1.7     object, 3.2.9
save, 5.2.10, 5.12.1, 6.1.4, 20.4.16, 20.7.2, 24.3.32     superposition, 3.4.8.1
     chemical, 16.3.7     tree, 20.7.1
     docked ligand, 19.16     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
     ligand receptor complex, 19.16     purple.box, 3.4.3.23
     object, 3.1.13     residue, 3.1.4, 3.1.5, 3.1.6
     print delete alignment, 9.5.2     workspace, 3.1.4, 3.1.5, 3.1.6
     project icb, 3.1.14selectall, 3.4.2.3
     slide, 6.4selecting.neighbors, 3.2.12
     table, 20.1.19selection, 20.4.14, 20.7.1, 20.7.3, 24.3.4, 24.3.6, 24.3.7, 24.3.8, 24.3.12, 24.3.31, 24.5.9, 24.5.10, 24.5.22, 24.6.15
     tree, 20.7.2     clear, 3.4.2.7
     image, 3.1.19, 3.4.1.14     neighbors, 3.4.2.8
     object, 3.1.13     toolbar, 3.2.1
     password, 3.4.1.10     alignment, 3.2.14
     picture, 3.4.1.14     all, 3.4.2.3
     project, 3.1.14, 3.4.1.7, 3.4.1.8, 3.4.1.9     alter, 3.2.5
     table.view, 20.1.6     amino, 3.2.10
saving, 3.4.1.7     atom, 3.2.1, 3.4.2.5
     project, 3.4.1.7     basic, 3.2.3
scaffold, 17.4     change, 3.2.5
scale, 3.4.1.15.5     clear, 3.4.2.7
scan, 18.1.12.1     column, 20.1.21
     hits, 18.1.12.1     filter, 3.2.6, 3.4.2.5
scatter, 18.5.10.2     graphical, 3.2.1, 3.2.12
scatterplot, 18.5.10.4     invert, 3.4.2.6, 20.1.21
score, 18.5.9, 24.6.8, 24.6.9, 24.6.19     lasso, 3.2.1
     threshold, 18.5.4     level, 3.4.3.3
screen, 17.21, 23.7, 23.8.1     mode, 3.4.3.4
screening, 18.5, 18.5.1, 18.5.2, 23.9     near atoms, 3.4.2.8
screenshot, 8     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, 24.5.19, 24.9, 24.9.1, 24.9.2, 24.9.3     object, 3.2.9
     pick, 3.2.1shell preferences, 3.4.1.15.10
     properties, 3.4.2.5shift, 5.5.3
     range, 20.1.21shine, 3.4.1.15.5, 3.5.2
     residue, 3.4.2.5shineStyle, 3.4.1.15.3
     row, 20.1.21show, 6.3.1, 20.1.30
     sphere, 3.2.11     hide column, 20.1.30
     spherical, 3.4.2.8side, 16.2.27
     superposition, 3.4.8.1, 11.1     by side, 16.2.27
     table, 3.2.14, 20.1.21               stereo, 3.4.3.6
          elements, 20.1.21     chains, 13.6
     toolbar, 3.2.1side-chain sampling, 18.7.10
     tools, 3.2.2, 3.2.3, 3.2.5, 3.2.6side-chains, 18.2.1
     whole, 3.2.9sigmaLevel, 3.4.5.6, 3.4.5.7, 12.6, 12.7
     workspace, 3.2.7, 3.2.13similar, 3.4.7.1
selectioninvert, 3.4.2.6similarity, 17.15
selections, 3.2simulation, 24.8.2
     links, 9.2.9simulations, 24.8
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, 5.5.7, 9, 9.1, 9.2, 9.2.8, 13.1.3, 23.2, 23.3, 24.5.12sites, 5.5.7, 11.6
     analysis, 9.2size, 4.5.1
     reordering, 9.5.4sketch accents, 5.7.3
     structure, 9.2.6     accents, 3.4.3.14, 5.7.3
     type, 9.2.4skin, 3.5.1, 5.1.1, 5.1.5, 24.3.15
     DNA, 9.2.4slab, 5.2.9, 5.10.1
     alignment, 3.3.5, 9.2.5, 9.4.5slice, 5.10
     nucleotide, 9.2.4slide, 6.1.4, 6.3.1, 6.6.1, 24.3.30
     protein, 9.2.4     effects, 6.5
     search, 9.3     navigation, 6.3.2
     structure.alignment, 9.2.6     show, 6.3
sequences, 3.3, 4.1.1, 9, 24.3.24     blend, 6.5
     unique, 9.2.13     edit, 6.4.1
     extract, 9.2.13     effect, 6.5
     unique, 9.2.13     smooth, 6.5
set, 16.2.29, 24.5.21     transition, 6.5
     formal charges, 17.5slides, 6, 6.2, 6.3, 24.3.29
     bond type, 3.4.16.5, 15.5smiles, 16.1.1, 16.3.5, 17.1, 17.6, 17.6.3, 17.6.4
     charges, 3.4.16.6, 15.6solvent.accessible.area, 24.5.19
     chirality, 3.4.16.5, 15.5sort hitlist, 18.5.10.1
     disulfide, 13.7, 24.5.17     table, 3.4.10.4
          bond, 3.4.16.5, 15.5sorting, 18.5.10.1
     formal charge, 3.4.16.5, 15.5     compounds, 20.6.4
     tether, 3.4.16.5, 15.5spec, 3.5.2
     types, 3.4.16.6, 15.6specifications, 24.2.1
setAPFparams, 24.7.18     faq, 24.2.1
setup, 18.7.5, 24.6.14speed, 6.1.2
     ligand receptor, 19.1sphere, 3.4.1.1.10, 24.5.11
shade and box, 9.5.6spherical, 24.5.9, 24.5.12
shading, 5.2.11split, 17.18.3
shadow, 5.7.2spreadsheet, 17.6.2
sheet, 24.3.19square, 24.5.7
stack, 18.1.12, 18.7.9, 24.8.2     area, 3.4.7.5, 10.5
standard table, 20.1surfaces, 5.2.1
standardize, 17.2surrounding, 4.4, 24.5.11
     table, 17.2swissprot, 3.3.1, 9.1
start, 16.13.2symmetry, 3.4.5.1, 3.4.5.3, 12.1, 12.3, 23.3.4, 23.3.5
     dock, 18.1     packing, 3.4.5.1
startup, 24.9.2tab, 20.1.2, 20.1.19
static, 24.5.8     pdb, 3.5.4
stereo, 3.4.1.15.6, 16.2.26, 24.2.2, 24.2.3, 24.10.6table, 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, 17.19.1, 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, 24.5.19, 24.7.9, 24.7.10, 24.7.12, 24.7.13
     hardware, 3.4.3.7     alignment, 20.1.10
     side-by-side, 3.4.3.6     clone, 20.1.14
stereohard faq, 24.2.2     color, 20.1.8
stereoisomer, 17.6.5     column format, 20.1.31
stereoisomers, 17.11     copy, 20.1.27, 20.1.28
stick, 3.4.1.15.5     delete, 20.1.15
stop, 6.1.3     edit, 20.1.22
store, 3.4.3.19, 6.1.4, 24.3.21     filter, 20.1.33
     current view, 3.4.3.19     find, 20.1.7
               faq, 24.3.21          replace, 16.2.30
strain, 3.4.6.2, 14.2, 17.12, 17.12.2     font, 20.1.9
strip, 24.5.9          size, 24.3.1
structure, 3.4.5.3, 12.3, 20.6, 23.3, 24.5     grid, 20.1.5
     ensemble, 3.4.16.9, 15.11     histogram, 20.4.1
     representation, 5.1.1     insert, 20.1.23
     smiles, 17.6.4     layout, 20.1.5
     display, 3.1.8     mark, 20.1.11
     undisplay, 3.1.8          row, 20.1.11
structures, 4.1.1, 16, 16.1     mouse, 20.1.35
style, 3.4.1.15.5     navigation, 20.1.4
substructure, 16.11, 16.13.3, 17.3, 24.7.5, 24.7.6     new, 3.4.1.1.7
     alerts, 17.3          column, 20.1.23
suface, 24.5.19     plot, 20.4
sulfur, 13.7     print, 20.1.17
superimpose, 3.4.8, 11.2, 11.6, 24.3.5, 24.5.6, 24.5.7, 24.5.8     rename, 20.1.13
     3D, 3.4.8.2     rightclick, 20.1.12
     grid, 3.4.8.4     save, 20.1.3
     multiple proteins, 3.4.8.3          selection, 20.1.3
     protein apf, 3.4.8.5     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, 17.19.3     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, 17.19.1, 17.19.2     action, 20.1.35
     substructure, 17.19.1, 17.19.2, 17.19.3     alignment, 20.1.10
superposition, 17.19, 17.20.1, 17.20.2     append, 20.1.33
surface, 3.4.1.15.5, 3.5.1, 5.1.1, 5.1.7, 5.2, 24.3.15     clone, 20.1.14
     area, 3.4.7.5, 10     color, 20.1.8
     columns, 16.2.6template, 13.1.3, 17.19
     compare, 16.2.19     docking, 24.6.4
     copy, 16.2.5terminal, 16.2.26
     cursor, 20.1.35     font size, 24.3.1
     delete, 20.1.12, 20.1.15text, 3.4.1.15.7, 6.6, 6.6.1, 6.6.6, 16.2.26, 16.13.3, 24.7.16
     display, 24.9.4     search, 16.9.4
     double.click, 20.1.35texture, 3.5.6
     edit, 16.2.15thoroughness, 17.9, 17.19, 24.6.13
     excel, 16.2.8, 20.1.18three, 16.2.21, 24.7.11
     export, 16.7threshold, 3.4.1.15.5
     filter, 16.2.10, 20.1.33tier, 3.1.17
     find-replace, 16.2.11time, 24.6.12
          to screen, 20.1.4     racemic, 17.6
     font, 20.1.9tools 3D, 3.4.6
     foreground, 24.9.4     analysis, 3.4.7
     grid lines, 20.1.4     append rows, 3.4.10.7
     hide, 20.1.30     extras, 3.4.9
     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, 17.16          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, 24.5.16
     options, 20.1.12     angles, 5.9, 5.9.6
     orientation, 20.1.16transition.blend, 24.3.30
     portrait, 20.1.16transitions, 6, 24.3.29
     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, 24.3.3
     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, 17.13.3
     scroll, 20.1.4     edit, 17.13.4
     sdf, 16.2.7     reorder, 17.13.3
     select, 20.1.21trouble shooting, 24.10.3
     setup, 20.1.16trouble-shooting, 24.10.4
     sort, 3.4.10.4, 16.2.3, 20.1.32troubleshooting, 24.10
     standard, 20.1truncating a mesh object, 24.3.14
     view, 16.2.4, 16.2.27     crash qlock, 24.10.5
     width, 20.1.4tsv, 20.1.19
tables, 17.15, 20tut analyze alternative orientations, 23.3.7
tautomer, 17.10, 24.5.15          occupancy, 23.3.6
tautomers, 17.10          symmetry, 23.3.5
temperature, 3.4.6.3, 14.3     hydrogen bond, 23.3.3
tut2a, 23.3.1     dock results, 18.1.12
tut2b, 23.3.2     fog, 3.4.3.5
tut3, 23.4     macroshape, 3.4.3.22
tut3a, 23.4.1     menu, 3.4.3
tut3e, 23.3.8     mesh clip, 5.10.1
tut4b, 23.5.1     perspective, 3.4.3.9
tut4c, 23.5.4     selection level, 3.4.3.3
tut4d, 23.5.5          mode, 3.4.3.4
tut5, 23.7     shadow, 3.4.3.13
tut5a, 23.7.1     sketch accents, 3.4.3.14
tut5b, 23.7.2     slide show, 6.3.1
tut5c, 23.8.1     tools, 3.4.3
tut5e, 23.8.2     tree, 20.7.3
tutorial 2D pharmacophore, 23.5.7     undisplay all, 3.4.3.1
     3D pharmacophore, 23.5.6     stach, 3.4.16.10, 15.12
     chemical search, 23.5.3virtual, 18.5, 18.5.1, 18.5.2, 23.7, 23.8.1
     edit chemical, 23.5.2     screening examples, 23.8
     molecular documents, 23.1.5virus, 3.4.5.3, 12.3
     sequence alignment, 23.2vls, 18.2, 18.2.3, 18.5, 18.5.6, 18.5.10.6, 23.8.2, 24.6.8, 24.6.9
               link, 23.2.2     analysis, 18.5.10.6
               load sequence, 23.2.1          display, 18.5.10.5
               sequence conservation, 23.2.3     getting started, 18.5.2
tutorials, 23     histogram, 18.5.10.3
two, 16.2.21, 24.7.11          scatter plot, 18.5.10.2
unclip, 5.2.9, 5.10.1     introduction, 18.5.1
undisplay, 3.1.7, 5.1.8, 24.3.9, 24.3.31     preferences, 18.5.4
     origin, 5.5.13     results, 18.5.9
undo, 3.4.1.15, 3.4.2.9, 16.3.12     run, 18.5.6
     redo structure, 16.3.12     scatterplot, 18.5.10.4
uniprot, 3.3.1     visualization, 18.5.11
     sites, 5.5.7     results, 18.5.9
uniptrot, 5.5.7volume, 16.3.5
unique, 16.2.26, 17.17wavefront, 3.5.6, 5.2.10
unit, 3.4.5.3, 12.3weak, 24.5.20
units, 24.6.1web, 23.1.5
unix, 24.9.2     browser, 3.4.1.11
updates, 1weight, 17.1, 24.7.12, 24.7.15
use activeicm, 7.5weighted, 20.7
user, 1, 16.13.4what to dock, 18.1.1.2
user-defined groups, 16.3.3width, 20.1.20
uundisplay-all, 3.4.3.1window, 3.1.17
van der waal, 5.5.16windows, 3.1.18, 16.13.1
variable, 3.4.1.15.7, 24.3.8wire, 3.4.1.15.5, 3.5.1, 5.1.1, 5.1.2, 24.3.4, 24.3.20
verbose, 17.9wireBondSeparation, 3.4.1.15.1
vicinity, 17.9working directory, 24.6.24
video, 8workspace, 3.1.7, 4.3.1, 16.5.2
view, 3.4.3.19, 6.3.1, 16.2.26, 24.3.21, 24.8.2     panel, 3.1.7
     animate view, 3.4.3.15     selection, 3.2.7
     center, 3.4.3.20     navigation, 3.2.8
     color background, 3.4.3.18write, 3.1.19, 5.12.1, 20.4.16, 24.7.4, 24.8.1
     image, 3.4.1.14 
     object, 3.1.13 
     picture, 3.4.1.14 
     project, 3.1.14, 3.4.1.7 
     table, 20.1.3 
writing a pdb file, 24.5.3 
     ray, 3.4.5 
xi, 5.5.5, 24.3.17 
xstick, 5.1.3, 24.3.20 
xyz, 24.3.9 
zoom, 3.1.2, 3.1.3, 5, 5.9, 5.9.4, 16.2.28, 20.4.13 

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