Nov 22 2021 Feedback.
Contents
 
Introduction
Help Videos
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Sequences & Alignments
Protein Modeling
Cheminformatics
Learn and Predict
Docking
Virtual Screening
MolScreen
3D Ligand Editor
Tables and Plots
Local Databases
ICM-Scarab
KNIME
Tutorials
FAQs
 
Index

Index

2D, 6.8.8, 10.3.24, 10.3.28, 10.14, 10.17.2, 10.17.4DNA, 4.3, 8, 8.3.3
     Interaction Diagram, 15.3.7Decomposition, 10.33.3
     bioisostere, 10.9.1Display, 21.2.26
     from PDB, 10.1.1Distance, 13.1.9.6
     screening, 14Dock Directory, 4.7.2
     to 3D, 10.17, 10.17.3Docking, 21.2.26
     depiction, 10.17.2Drug Bank, 4.2.8
3D, 6.6, 6.8.8, 10.1.3, 10.3.24, 10.3.28, 10.3.31, 10.17.2, 20.2Editor, 4.7.2
     QSAR, 10.36.4, 11.4, 20.14Eintl, 12.1.1.7
     chemical, 10.4.16, 10.17.1Error in saving configuation settings: You are not a license administrator, 21.1.10
     interactive ligand editor, 3.7.5FILTER.Z, 4.7.2
     ligand editor, 15.3.4     gz, 4.7.2
     object, 6.3.9     uue, 4.7.2
     pharmacophore, 13.3, 15.3.11FTP.createFile, 4.7.11
     print, 6.7     keep File, 4.7.11
     printing, 6.7     proxy, 4.7.11
     screening, 14Filter.zip, 4.7.2
     stereo, 6.6Force Auto Bond Typing, 4.7.11
3DQsar, 11.4Formula, 21.8.7, 21.8.10
3Dqsar tutorial, 20.14Free Wilson, 10.33.2
     bioisostere, 10.9.2Frequently Asked Questions, 21
     predict, 5.6GAMESS, 9.20.16
          helices strands, 5.6.1GIF, 3.6.1.15, 6.16, 6.16.2
          local flexibility, 5.6.4GPCR Modeling Example, 20.5.1
          protein health, 5.6.3GRAPHIC.store Display, 4.7.3
          tools identify ligand binding pocket, 5.6.6     NtoC Rainbow, 4.7.4
               oda, 5.6.5     alignment Rainbow, 4.7.4
4D, 12.2.2, 20.12.1     atomLabelShift, 4.7.7
     dock, 15.16     ballStickRatio, 4.7.1
     docking, 4.2.2     center Follows Clipping, 4.7.3
64, 21.1.3     clash Style, 4.7.3
APF, 10.35.3, 10.36.4, 11.4, 14, 14.6, 20.14     clashWidth, 4.7.3
     template, 10.35     clip Grobs, 4.7.3
ActiveICM, 3.6.1.12          Skin, 4.7.3
Area, 21.2.26          Static, 4.7.3
Atom Single Style, 4.7.3     discrete Rainbow, 4.7.4
Atomic Property Fields, 11.4, 20.14     displayLineLabels, 4.7.7
Bad Groups, 21.8.7, 21.8.10     displayMapBox, 4.7.3
Baell, 10.4.9     distance Label Drag, 4.7.1
Beep, 4.7.11     dnaBallRadius, 4.7.9
Blast, 21.2.25     dnaRibbonRatio, 4.7.9
BlastDB Directory, 4.7.2     dnaRibbonWidth, 4.7.9
     alphas, 6.8.3     dnaRibbonWorm, 4.7.9
COLLADA, 3.6.1.7     dnaStickRadius, 4.7.9
CPK, 3.7.1     dnaWormRadius, 4.7.9
ChEMBL, 4.2.3, 10.1     font Scale, 4.7.7
Chemical Cluster, 20.6.3     fontColor, 4.7.7
     Search, 20.6.2     fontLineSpacing, 4.7.7
CisTransAmide Angle, 13.1.9.6     grobLineWidth, 4.7.3
Clash Threshold, 4.7.10     hbond Ball Period, 4.7.1

     hbondAngleSharpness, 4.7.1               Image, 4.7.11
     hbondMinStrength, 4.7.1     table Row Mark Colors, 4.7.4
     hbondStyle, 4.7.1     workspace Folder Style, 4.7.4
     hbondWidth, 4.7.1     workspaceTabStyle, 4.7.4
     hetatmZoom, 4.7.1HBA, 21.8.7, 21.8.10
     hydrogenDisplay, 4.7.1HBD, 21.8.7, 21.8.10
     light, 4.7.3HTTP.proxy, 4.7.11
     lightPosition, 4.7.3     support Cookies, 4.7.11
     mapLineWidth, 4.7.3     user Agent, 4.7.11
     occupancy Radius Ratio, 4.7.3Hbond to selection, 13.1.9.6
     occupancyDisplay, 4.7.3Hbonds, 15.3.4
     quality, 4.7.3How To Guide, 3
     rainbow Bar Style, 4.7.4Html, 4.2.1.6
     resLabelDrag, 4.7.7Http Read Style, 4.7.11
     resize Keep Scale, 4.7.3Hydrogen.bond, 4.7.5
     ribbonRatio, 4.7.9ICM Browser How To, 3.1
     ribbonWidth, 4.7.9          Pro How To, 3.2
     ribbonWorm, 4.7.9     graphics crash, 21.1.11
     rocking, 4.7.4     start, 1
          Range, 4.7.4IMAGE.bondLength2D, 4.7.6
          Speed, 4.7.4     color, 4.7.6
     selectionStyle, 4.7.3     compress, 4.7.6
     site Label Drag, 4.7.7     gammaCorrection, 4.7.6
               Shift, 4.7.7     generateAlpha, 4.7.6
     siteArrow, 4.7.7     lineWidth, 4.7.6
     stereoMode, 4.7.3     lineWidth2D, 4.7.6
     stickRadius, 4.7.1     orientation, 4.7.6
     surfaceDotDensity, 4.7.3     paper Size, 4.7.6
     surfaceDotSize, 4.7.3     previewResolution, 4.7.6
     surfaceProbeRadius, 4.7.3     previewer, 4.7.6
     transparency, 4.7.3     print, 4.7.6
     wire Width, 4.7.1     printerDPI, 4.7.6
     wormRadius, 4.7.9     scale, 4.7.6
     xstick Backbone Ratio, 4.7.1     stereoAngle, 4.7.6
          Hydrogen Ratio, 4.7.1     stereoBase, 4.7.6
          Style, 4.7.1     stereoText, 4.7.6
          Vw Ratio, 4.7.1INCHI, 10.17.3
GROB.arrowRadius, 4.7.3IQR, 16.4.6
     atomSphereRadius, 4.7.3ISIS, 21.8.3
     contourSigmaIncrement, 4.7.3Icm Prompt, 4.7.10
     relArrow Size, 4.7.3InChi, 10.3.20, 10.4.12, 10.17.3
     relArrowHead, 4.7.3     key, 10.3.20
GUI.auto Save, 4.7.4Interaction Diagram 2D, 15.3.7
               Interval, 4.7.4Internal Coordinates Table, 9.20.13
     autoSave, 21.2.33     Directory, 4.7.2
     autoSaveInterval, 21.2.33JPEG, 3.6.1.15
     enumberation Memory Limit, 4.7.11KMZ, 3.6.1.7
     max Nof Recent Files, 4.7.11Log Directory, 4.7.2
          Sequence Length, 4.7.4LogP, 11, 16.6
     splash Screen Delay, 4.7.11LogS, 11, 16.6

MOL2, 13.1.3          Sequence, 3.6.2.16
MOLT, 17.1     convert, 5.1.2
MOVIE.frame Grab Mode, 4.7.4PFAM, 3.6.1.7
MPO, 10.31PLOT.Yratio, 4.7.8
Mac, 21.1.15     color, 4.7.8
     Atom Margin, 4.7.10     date, 4.7.8
     Sigma Level, 4.7.10     draw Tics, 4.7.8
Markush, 20.6.9     font, 4.7.8
     create, 20.6.7     fontSize, 4.7.8
     File Size Mb, 4.7.11     labelFont, 4.7.8
Max_Fused_Rings, 10.11     lineWidth, 4.7.8
Mnconf, 4.7.10     logo, 4.7.8
Model, 11.4     markSize, 4.7.8
MolCart, 21.9     orientation, 4.7.8
MolIPSA, 21.8.7, 21.8.10     paper Size, 4.7.8
MolLogP, 21.8.7, 21.8.10     previewer, 4.7.8
MolLogS, 21.8.7, 21.8.10     rainbowStyle, 4.7.8
MolPSA, 10.11     seriesLabels, 4.7.8
MolScreen, 14PLS, 11.1
MolVol, 10.11PNG, 3.6.1.15, 4.1.14, 6.16, 6.16.2
Molcart, 10.5.3Pharmacophore RMSD, 13.1.9.6
MoldHf, 10.11, 21.8.7, 21.8.10Projects Directory, 4.7.2
Movie.fade Nof Frames, 4.7.4Prosite Dat, 4.7.2
     quality, 4.7.4Protein, 21.2.26
          Auto, 4.7.4     Viewer, 4.7.2
NCBI, 21.2.25Pub Chem, 4.2.9
NVIDIA, 21.1PubMed, 4.2.1.7
Nof_Atoms, 10.11     Reference, 16.1.40
Nof_Chirals, 10.11Pubchem, 4.2.9
Nof_HBA, 10.11QSAR, 11, 11.1, 16.6, 20.14
Nof_HBD, 10.11R, 10.8, 10.33.1
Nof_Rings, 10.11     and S, 21.5.21
Nof_RotBonds, 10.11R-Group, 10.33.3
Non-overlap, 13.1.9.6R-groups, 15.5.3
Nvidia GL failutre, 21.1.11REAL, 10.5.5
ODA, 21.2.26RMSD, 5.4.2
Optimal, 21.2.26RNA, 4.3
Output Directory, 4.7.2RTCNN, 12.1.1.3, 12.1.13.1
PAINS, 10.4.9, 10.11.3Ramachandran Plot, 5.5.9
     chemica, 10.4.9Real Format, 4.7.10
PCA, 11.1, 11.5, 20.6.4     Label Shift, 4.7.7
     analysis, 10.26          Style, 4.7.7
PDB, 4.2.1.6, 5.1.2, 5.3.3, 8.1, 10.1.1, 15.19RotB, 21.8.7, 21.8.10
     Directory, 4.7.2SALI, 10.33.5, 20.6.11
          Style, 4.7.2SAR, 11, 14.6, 16.4.25, 16.6
     link, 16.1.40     table, 10.33.3, 20.6.9
     Search, 3.6.2.12, 3.6.2.13, 3.6.2.14, 3.6.2.15, 3.6.2.16SCARE, 12.2.4
          Field, 3.6.2.13SCORE, 21.5.6, 21.5.17
          Homology, 3.6.2.15SDF, 10, 10.3.24, 10.3.25, 10.3.26, 10.3.27, 13.1.3, 16.2
          Identity, 3.6.2.14SEQUENCE.site Colors, 4.7.4

     labelOffset, 4.7.7administration, 10.10.5
     wrap Comment, 4.7.7advanced alignment selection, 8.7.14
SLIDE.ignore Background Color, 4.7.4alanine, 12.2.4
          Fog, 4.7.4album, 6.15.3
SMILES, 10.1.2, 10.2.4, 10.4.12alias, 10.4.5
Score, 12.1.1.3align, 4.1.11, 10.14
Select Min Grad, 4.7.10     color 2D scaffold, 10.14
Show Res Code In Selection, 4.7.7     dna protein, 8.6.4
Smiles, 21.8.7, 21.8.10, 21.8.11     multiple, 8.6.5
SureChEMBL, 4.2.4     sequence structure, 8.6.3
Swissprot, 3.6.1.7     two sequences, 8.6.2
     Dat, 4.7.2     DNA to protein, 8.6.4
     link, 16.1.40     sequence, 8.6, 8.6.6
Temp Directory, 4.7.2     two sequences, 8.3.5, 8.6.2
USER.email, 4.7.11alignment, 8.3.8, 8.6.1, 8.7.7, 8.7.7.1, 8.7.16, 8.8, 10.35.1, 10.35.2, 20.4.4, 21.4.12, 21.6, 21.6.2
     friends, 4.7.11     annotation tutorial, 20.4.4
     full Name, 4.7.11     box shade font, 8.7.7
     organization, 4.7.11     editing, 8.7.1
     phone, 4.7.11     editor, 8.7
Uniprot, 16.1.40     example, 8.3.14
VLS, 13.1, 13.1.1, 13.1.2, 13.1.9.2     font size, 21.2.1
     preferences, 13.1.4     format, 8.7.11
Van Drie, 10.33.5     gaps, 8.7.11
     Label Style, 4.7.7     image, 8.7.2
Volume, 21.8.7, 21.8.10     profile, 20.4.4
     Change, 13.1.9.6     reorder, 8.3.12
Water Radius, 4.7.10     search, 8.7.12
Wilson, 10.33.2     secondary, 20.4.4
Wire Style, 4.7.1          structure, 8.7.16, 21.6.2
XPDB Directory, 4.7.2     selection, 8.7.13
Xstick, 3.7.1     strength, 8.3.8
a-bright, 3.7.2          profile, 8.3.8
about model, 11.1.1     view options, 8.7.10
acceptor, 10.4.9, 10.36.1     color, 8.7.9
active, 7.7, 21.3.3     comment, 8.7.6
activeICM, 7.8     consensus, 8.7.9, 8.7.14
activeicm, 7.7, 7.12, 7.14, 7.14.1, 21.3     cut, 8.3.11
     advanced, 7.14     display title, 8.7.10
     background images, 7.15     editor, 8.7
     control, 7.13     extract, 8.3.10
activeicmjs, 7.16     gaps, 8.7.11
activity cliff, 10.33.5, 10.33.6, 20.6.11     horizontal scroll, 8.7.10
          tutorial, 20.6.11     image, 8.7.2
activityy, 11, 16.6     multiple, 8.3.7, 8.6.5
add database, 10.10.3     options, 8.7.10
     new data, 10.3.7     rename, 8.7.10
     to table, 15.5.7     reorder, 8.3.12
adding fragment, 10.4.8     ruler, 8.7.10
          in editor, 10.4.8     save, 8.7.2
adjust row height, 21.2.39     search, 8.7.12

     sequence offset, 8.7.10applying prediction models, 11.2
     table, 8.7.10area, 5.5.3, 5.6.5, 12.7, 12.7.2, 12.7.3, 20.3.5
     view, 8.7.10aromatic, 10.3.28, 10.36.1
alignments, 8.6, 20.4arrange, 4.1.13.1
allosteric, 5.6.6     window, 4.1.13.1
alpha, 3.7.2     graph, 21.2.8
     channel, 4.7.6as2_graph, 4.6.5
ambient, 3.7.2as_graph, 21.2.8
amidinium, 10.15asparagine, 9.20.2
amino acid, 4.3assign, 6.1.3
     acids, 10.4.6     2D coordinates, 10.17.2
anaglyph, 6.6, 21.1, 21.1.8     helices, 5.6.1
     stereo faq, 21.1.8     strands, 5.6.1
analysis, 3.6.4, 8.3atom, 4.7.5, 10.3.28, 21.2.4, 21.2.5, 21.2.8, 21.2.16, 21.2.17, 21.4.10
angle, 5.5.7, 5.5.8, 6.8.5, 6.9, 6.12.6, 21.2.18, 21.4.16     charge, 21.4.21
angstrom, 21.4.7atomLabelStyle, 4.7.7
animate, 3.6.3.15, 6.10.7atomic energy circles, 15.3.5
     view, 6.10.7     property field, 10.35.1, 10.35.2, 15.3.11
animation, 6.10.7.1, 6.10.7.2, 6.10.7.3, 6.10.7.4               score, 10.36.2
     store, 6.10.7.4          fields, 5.4.6, 10.36, 10.36.1, 10.36.3, 13, 20.8
animations, 7attachment, 10.4.3, 10.5.1
annotate, 4.6.21, 10.13     point, 10.32.4
     alignment, 8.7.6author, 4.2.1.3
     by substructure, 10.13     close tree, 10.25.5
     plot, 16.4.24     play slide, 7.13
annotation, 8.7.6autofit, 12.5
antialias, 3.6.1.15, 3.6.3.10autosave, 21.2.33
     lines, 3.6.3.17available properties, 10.11.1
     lines, 3.6.3.17ave, 16.7.1
apf, 5.4.6, 10.35.1, 10.35.2, 10.36, 11, 12.3, 13, 13.1.9.7, 13.3, 13.4, 15.3.11, 15.18, 20.8, 20.8.1, 20.8.2, 20.8.3, 20.8.4, 20.8.5, 21.8.12avi, 6.16, 6.16.2
     flexible template, 10.35.2axes, 16.4.15
     pairwise, 10.35.1axis, 16.4.11
     super, 10.35     options, 16.4.10
     template, 15.13     grid, 16.4.10
     tools, 10.36     range, 16.4.10
          3DQSAR, 10.36.4     title, 16.4.10
          consensus ph4, 10.36.1b-factor, 5.6.4, 20.3.10
          pairwise score, 10.36.2     coloring scale, 21.2.38
          screen, 10.36.3backbone, 6.1.10, 21.2.13
     tutorial, 20.8background, 6.4.2, 6.4.3
          cluster, 20.8.5     color shortcut, 21.2.2
          consensus, 20.8.2     images activeicm, 7.15
          score, 20.8.3     image, 6.4.3
          screen, 20.8.4backup, 3.6.2.11
          superposition, 20.8.1bad, 10.11
     alignment, 10.35.3     groups, 10.4.9
apf3Dqsa, 21.8.12ball, 4.7.5
append, 16.1.44     and stick, 3.7.1
     table, 16.1.44balloon, 16.4.26
     rows, 3.6.10.7bases, 10.4.6

batch, 12.1.10, 12.7.9     trace, 6.1.10
     file, 12.1.10.2ca-trace, 6.1.10
     index, 12.1.10.4cache, 7.14.1
     loaded icm object, 12.1.10.1calculate, 10.11, 21.5.2
     mol mol2, 12.1.10.3     properties, 10.11
     molcart, 12.1.10.5     sequence similarity, 8.7.15
     run, 12.1.11     startup, 21.10.2
bayesian classifier, 11carbon, 21.2.4, 21.2.5
bbb, 10.11.4carboxylic acid, 10.15
beep, 21.2.35cartesian, 10.20
begin docking simulation, 12.1.8cavities, 5.5
best, 10.3.34     closed, 5.5.4
bicyclics, 10.4.6ccp4, 21.2.27, 21.2.28
binding, 20.5.3, 21.2.14, 21.5.2, 21.5.10cell, 5.3.2
     properties, 6.3.1center, 3.6.3.20, 4.1.3, 6.12, 6.12.5, 15.3.13, 16.1.40, 21.4.22
bioinfo align multiple, 8.3.7     on ligand, 15.3.13
          two sequences, 8.3.5     and representative members, 16.7.2
     links, 8.3.9chain.breaks, 21.2.34
     menu, 3.6.4chair, 21.5.20
     secondary structure, 8.3.2change box size, 15.9.1
     translation, 8.3.3     height of all rows, 16.1.7
bioisoester, 10.9     ligand, 15.5.1
bioisostere, 10.9, 10.9.1, 10.9.2, 15.8     row height, 16.1.7
biological, 5.3.3     selection, 4.6.7
biomolecule, 3.6.5, 5.3.3, 20.3.8, 20.3.12     speed range, 6.10.7.2
bit, 21.1.3changing font in alignment editor, 8.7
blast, 4.2.5, 8.4charge, 3.6.3.21, 5.1.3, 5.1.3.1, 5.1.3.2, 6.8.2, 10.4.3, 10.5.1, 10.7.1, 10.7.2, 10.7.3, 10.36.1, 13.1.9.6, 21.4.1
     search, 4.2.5     groups, 12.1.6, 21.5.22
blood brain barrier, 10.11.4check box, 7.6.6
blue lines, 8.2     convert, 21.8.5
boat, 21.5.20     export excel, 10.2.3
bond, 5.1.3, 5.2.3, 5.2.3.1, 5.2.3.2, 9.9, 10.4.10, 21.4.1, 21.8.7, 21.8.10     save, 10.2
     covalent, 21.4.2          3D, 10.2.5
     type, 5.1.3.1, 5.1.3.2, 10.7.1, 10.7.2, 10.7.3          editor, 10.2.4
bonding, 6.1.8          image, 10.2.6
     preferences, 4.7.1          table, 10.2.2
box, 4.7.7, 6.8.15, 8.7.7, 8.7.7.1, 21.5.9     super, 10.34
     alignment, 20.4.4     view, 10.3.28
     size, 15.9.1chembl, 4.2.3, 4.2.4
browse, 10.3.31, 12.1.12.1, 18.4chemical, 10, 10.3.28, 10.3.30, 10.3.31, 10.3.34, 10.3.35, 10.4.10, 10.8, 10.10.4, 10.11.3, 10.17.2, 10.21, 10.32.4, 10.32.5, 10.34, 10.35.1, 10.35.2, 16.7.1, 20.6.4, 21.8.4, 21.8.5, 21.8.7, 21.8.8, 21.8.9, 21.8.10
     mode, 10.3.31     clustering, 10.25, 10.25.6
     molt, 17.2     descriptors, 21.8.15
     stack, 9.20.15     dictionary, 10.4.4, 10.4.5, 10.4.6
build, 6.10.7.1     draw, 20.6.1
     homology model, 9.1.2          spreadsheet tutorial, 20.6.1
     hydrogens, 9.20.5     edit buttons, 10.4.11
buried molSurface, 13.1.9.6     editor, 10.4, 10.4.8
buttons, 7.14          not starting, 21.1.13
bye, 3.6.1.19     fingerprint, 14
     alpha, 6.1.10     fingerprints, 21.8.15

     group, 10.4.5     duplicates, 10.30
     groups, 10.4.5, 10.4.8     remove.redundant, 10.30
     modifiers, 10.32.2chemlib.so, 21.1.3
     properties, 20.6.4chemspace append, 20.6.4.4
     right click, 10.4.3     build visualize, 20.6.4.1
     search, 10.5, 13.4     compare, 20.6.4.8
          filter, 10.5.2     delete row, 20.6.4.3
          text, 10.5.4     distinguish, 20.6.4.7
     sketch, 20.6.1     export, 20.6.4.5
     space, 10.27     project, 20.6.4.6
     spreadsheet, 4.2.3, 10.1.3, 10.3.1, 10.4.14, 20.6.1, 21.8.13     select, 20.6.4.2
          compare, 10.3.22chi, 6.8.5, 21.2.18
          template, 10.3.2chiral, 10.22, 12.1.1.4
     spreadsheets, 10.3chirality, 10.22, 12.1.1.4
     substituent, 10.9     considerations, 12.1.1.4
     substructure, 4.2.1.1chrome, 21.3
     table, 15.10, 21.8.11cis trans proline, 20.5.2
          display, 10.3.3clash, 4.7.5, 6.8.14
     tables, 16.2     volumes, 13.1.10
     toxicity, 10.11.3classes, 10.3.28
     2D, 10.7classification model, 14.5
     3D, 10.7clear display and planes, 3.6.3.2
     append, 10.4.13     selection, 4.6.6
     clustering, 10.25, 10.25.1     planes, 3.6.3.2
     convert, 5.1.3, 5.1.3.1, 5.1.3.2, 9.20.1, 10.7, 10.7.1, 10.7.2, 10.7.3, 21.4.1click, 4.1.12, 6.11, 6.12
     display.fit, 21.8.13clip, 6.3.10, 6.13.1, 21.2.11
     draw, 10.4.1clipboard, 6.15.3, 16.7.3
     duplicates, 10.3.21clipping, 21.2.19
     editor, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6     planes, 6
     load, 10.1     tool, 6.13
     merge, 10.29     tools, 6.13
     new, 10.4.1clone, 3.6.1.2
     properties, 10.3.19close, 6.3.3, 6.3.4, 15.21
     query, 10.4.3, 10.5.1, 10.5.3     downstream cluster, 10.25.5
     read, 10.1     project, 15.21
     save, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6, 10.4.13     cavities, 5.6.6
     search, 10.4.3, 10.5, 10.5.1, 10.5.3cloud, 13.1.7, 13.1.7.2
     similarity, 10.4.3, 10.5, 10.5.1, 10.5.3cluster, 13.1.7, 13.1.9.7, 16.7.1
     spreadsheet, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6, 10.3     representative.center, 10.25.2
     structure, 10.4.13clustering, 16.7, 20.6.3
     superimpose, 10.34.1, 10.34.2, 10.34.3cns, 10.31
     superposition, 10.35, 10.35.3collada, 3.7.6, 6.3.7
     table, 10.3, 16.2color, 5.6.3, 6.3.2, 6.3.3, 6.3.4, 6.3.9.4, 6.4, 6.4.1, 6.8.2, 6.8.3, 8.8, 10.3.35, 10.14, 16.1.45, 16.7.4, 21.2.4, 21.2.5, 21.2.16, 21.2.20
cheminformatics, 10, 10.3, 21.8     alignment, 8.7.9
     tutorials, 20.6     background, 6.4.2
chemistry, 10.21, 21.8     by, 6.4
     convert, 10.17          alignment, 8.8
          2dto3d, 10.17.1     chemical, 10.3.35
     pca, 10.26     faq, 21.2.20
     smiles, 10.17.3     key, 21.2.38

     surface by proximity, 6.3.3construct, 3.6.1.1, 6.10.7.1
               selection, 6.3.4     molecule, 3.6.1.1
     table, 10.3.27     object, 3.6.1.1
     2D sketch, 10.5.6.5contact, 5.5, 5.5.3, 20.3.5
     background, 3.6.3.18, 6.4.2     surface, 6.3.2
     distance, 6.8.10contacts, 6.3.3, 6.3.4, 10.6, 13.1.9.8, 15.3.12
     mesh, 6.3.9.3contour, 5.3.6, 5.3.7
     table, 10.3.27convert, 5.1.2, 10.17.1, 10.17.5, 21.8.5
coloring, 6.4.1     chemical, 10.3.24
coloumn, 16.1.25          2D 3D, 10.7
column, 16, 16.1.6, 16.1.22, 16.1.39, 16.1.40, 16.4, 16.4.1, 21.8.7          3D molecular editor, 10.4.16
     annotation, 16.1.41          from pdb, 5.1.3
     order, 16.1.29     local database, 3.6.1.6
     plot, 16.4.6     pdb, 20.3.2
     row width, 16.1.22          chem, 10.7.1
     statistics, 16.1.32     smiles to 2D, 21.8.11
     visibility order, 16.1.28     local.database, 3.6.1.6
     color, 16.1.10     smiles, 10.17, 10.17.3, 10.17.4
     hide, 10.3.8converting pdb, 5.1.2
     show, 10.3.8coordinates, 10.1.3
combinatorial chemistry, 10.32copy, 10.3.25, 10.4.11, 10.4.18, 10.5.6.2, 16.1.35
     library, 20.6.8     cell, 16.1.36
combine, 3.6.10.5     chemical, 10.3.25
     display style, 4.7.9     loop, 9.4
command, 21.5.16     paste row, 16.1.35
     line, 21.2.32     row, 16.1.36
commands, 21.10.1     rows, 16.1.44
compact tree, 10.25.5     selection to table, 16.1.37
compare, 10.3.29, 10.28, 10.29     chemical, 10.3.16
     table, 10.3.22covalent, 15.10.1
     tables, 10.28     bond, 5.6.2, 20.9.3
compatible, 3.6.1.10     docking, 12.4, 12.4.1, 15.17, 20.9.3
complex, 10.6, 13.1.9.5          tutorial, 20.9.3
compound, 4.2.1.3, 10.21, 16.2cpk, 6.1.5, 21.2.21
compounds, 21.9.3crash, 3.6.2.11
compress, 4.7.6creat, 7.6.1
compressed, 16.1.6create, 16.1.1
     table view, 16.1.6     markush, 10.32.3
conditions, 10.5.2     new objects, 4.3
     gen, 10.20cross, 21.2.10
configuration error, 21.1.19     section, 6.13
conformation, 10.20, 12.2.2cryptic, 5.6.6
conformational entropy, 10.24crystal, 5.3.2
conformations, 21.9.8crystallographic analysis, 5.3
conformers, 10.20          biomolecule, 5.3.3
connect, 6.3.9.1, 6.12, 6.12.7          contour map, 5.3.6
     object, 6.12.7          convert2grid, 5.3.7
connectivity, 10.4.3, 10.5.1          crystallographic cell, 5.3.2
consensus, 10.36, 20.8.2          load eds, 5.3.4
     pharmacophore, 10.36.1          maps cell, 5.3.5

          tools, 20.3.8dialog, 7.6.5
     cell, 3.6.5diffuse, 3.7.2
     neigbor, 5.3.1dihedral, 5.5.8, 6.8.5, 21.2.18
     neighbors, 3.6.5     angle, 5.5
crystallography, 5.3.4, 5.3.6, 5.3.7, 21.2.27, 21.2.28dimensional, 21.8.6
csv, 10.2.3, 16.1.2, 16.1.3, 16.1.21, 18.2directories preferences, 4.7.2
current, 21.2.22directory, 4.7
     slide, 7.13disappearing labels, 21.1.12
curves, 16.4.5dislay ligand receptor interaction, 10.6
custom, 6.12, 10.3.3, 10.34display, 4.1.4, 4.1.13.1, 4.7, 5.2.3, 5.2.3.1, 5.2.3.2, 6.8.14, 6.14, 10.22, 12.1.6.3, 21.2.4, 21.2.5, 21.2.8, 21.2.10, 21.2.11, 21.2.17, 21.2.21, 21.2.30, 21.2.32, 21.4.10, 21.4.11, 21.4.20, 21.8.4
     actions, 16.1.40     delete distances, 6.9.4
     fragments, 10.13     dihedral, 6.9.3
     label, 6.8.8     distance restraints, 6.8.13
     rotation, 6.12.2     distance2, 6.9.1
cut, 16.1.35          angles, 6.9
     vertical alignment block, 8.3.11     formal charge, 6.1.9
cyclic peptide, 9.19     gradient, 6.8.16
cys, 5.6.2     hbond, 13.1.9.5
cysteine reactivity, 5.6.2     hbonds, 13.1.9.6, 15.3.4
damaged skin, 21.1.12     hydrogen, 6.1.7
dash, 21.2.12          atoms ligand editor, 15.3.3
database, 8.4, 10.10, 10.32.4, 13.1.3, 13.1.6, 17.1, 18     mesh, 6.3.5
     file format, 13.1.3     meshes, 6.3.8
     seach and alignment, 8.4     options, 15.3
databases, 21.9.3     planar angle, 6.9.2
decompose.library, 20.6.9     tab, 3.7.1, 21.2.16
decomposition, 10.32.4, 10.33.1, 16.4.25     tether, 6.8.12
default, 4.1.13     toggle, 6.8.15
delete, 3.6.2.1, 4.6.6, 7.6.8, 21.4.9     CPK, 6.1.5
     alignment, 8.7.5     angle, 6.9.2
     all, 3.6.2.2     chemical, 10.3.3
     column row, 16.1.38     dihedral.angle, 6.9.3
     label, 6.8.9     distace, 6.8.10
     alignment, 8.7.5     distance, 6.8.13, 6.9.1
     all, 3.6.2.2     electrostatic, 3.6.3.21
     angle.label, 6.9.4     energy.gradient, 6.8.16
     column, 16.1.38     hydrogen, 6.1.7
     distance.label, 6.9.4          polar, 6.1.7
     label, 6.8.9     macroshape, 6.3.6
     row, 16.1.38     meshes, 6.3.5
     selection, 3.6.2.1          and display.macroshape, 3.7.6
     tether, 9.20.5     molecule, 10.3.24
dendrogram, 10.27.1     origin, 6.8.11
density, 5.3.4, 5.3.6, 5.3.7, 21.2.27, 21.2.28     potential, 3.6.3.21
depth, 6.3.12, 6.10.5     representations, 3.7.1
deselect, 21.2.7     restraints, 6.8.13
design loop, 9.3, 9.20.10     ribbon, 6.1.3
deviation, 21.4.7     skin, 6.1.4
dfa, 14.3.3     status, 21.2.32
dfz, 14.3.2     surface, 6.1.6, 6.3.1

     table, 10.3.3     rank, 12.1.13
     tethers, 6.8.12     results, 12.1.12, 12.1.12.1, 12.1.12.2, 12.1.13
     wire, 6.1.1     sampling, 21.5.20
     xstick, 6.1.2     score, 12.1.13
distance, 5.5, 5.5.6, 6.8.10, 6.9, 10.28, 21.2.12, 21.4.8, 21.4.10     stack, 12.1.12.2
     faq, 21.4.10     template, 12.3
     restraint, 12.1.7document, 7.6.4, 7.6.5
     label, 4.7.7     navigation, 7.6.7
distances, 3.7.3documents, 6.15.3
disulfide, 9.9, 9.16dollar, 21.10.3
     bonds, 9.16donator, 10.4.9
diverse set, 16.7     envelope, 3.7.1
dock, 12, 12.1, 12.5, 15.10, 15.10.1, 20.9.3, 20.11.1, 20.11.2, 20.12.1, 21.5.3, 21.5.4, 21.5.5, 21.5.7, 21.5.8, 21.5.10, 21.5.11, 21.5.12, 21.5.13, 21.5.14, 21.5.15, 21.5.16, 21.5.21     surface, 4.7.5
     apf, 15.18dotted line, 6.1.3
     chemical table, 12.1.15     lines, 21.2.34
     command, 21.5.16double, 10.4.10
     macrocylce, 21.5.20doublet, 10.4.7
     table, 15.10download, 21.1.1, 21.9.3
          covalent, 15.10.1dpc, 14.3.4
docked ligand strain, 12.1.1.7drag, 4.1.11, 4.7.7, 6.8.3, 7.6.4, 8.6.6, 21.4.5
docking, 5.6.5, 12, 12.1.1, 12.1.2, 12.1.3, 12.1.16, 12.2, 12.2.1, 12.2.2, 12.2.3, 12.7, 12.7.1, 12.7.2, 12.7.3, 12.7.4, 12.7.5, 12.7.6, 12.7.8, 12.7.9, 12.7.10, 13.1, 13.1.1, 13.1.2, 13.1.6, 13.2, 15.10, 15.10.1, 15.11, 20.9, 20.9.1, 20.9.2, 20.11.3, 20.12, 20.12.2, 21.5, 21.5.1, 21.5.9, 21.5.17, 21.5.18     and drop sequences, 8.6.6
     batch index, 12.1.10.4     residue label, 3.6.3.16
     covalent, 12.4draganddrop, 4.1.11
     display, 12.1.17draw, 10.4.18, 10.32.5, 21.8.2
     explicit group, 20.12.2     chemical, 10.4.1
     from table, 12.1.9.1, 12.1.9.2drop, 4.1.11, 7.6.4, 8.6.6, 21.4.5
     introduction, 12.1.1drug, 10.11, 21.8.7, 21.8.9
     macrocycles, 12.1.6     bank, 4.2, 4.2.8, 10.1
     maps, 12.1.4, 12.1.5     like, 10.11.4
     preferences, 12.1.6drugbank, 10.1
          database scan, 12.1.6.2druglikeness, 10.4.9
          display, 12.1.6.3dsPocket, 4.1.8
          general, 12.1.6.1dual alanine scanning, 12.2.4
     project, 13.1.5easy rotate, 3.6.3.12
          table, 13.1.5ecfp, 11.3
     results display, 12.1.17edit, 5.2.3.1, 15.5.8, 21.8.3
     setup, 21.5.13     2D, 15.5.1
     start, 12.1.3     add sequence, 10.4.17
     steps, 12.1.2     alignment, 8.7.1
     template, 12.3     chemical moledit, 10.3.26
     templates, 15.13     ligand, 15.5, 15.5.1
     tutorials, 20.9          2D, 15.5.1
     background, 21.5.19          editor preferences, 15.2
     batch, 12.1.10          multiple substituents, 15.5.2
     conformations, 21.5.20          tools, 3.6.2.17
     flexible.rings, 21.5.20     menu, 3.6.2
     hitlist, 12.1.13     molecular document, 7.6.1
     interactive, 12.1.9     molecule, 10.4
     preparation, 12.1.3     molt, 17.3
     procedure, 12.1.8     selection, 3.6.2.5

     table row, 16.1.24error, 21.1.3, 21.1.19, 21.2.35
     molecule, 10.3.26evaluate score strain, 15.4
     structure, 10.3.26exact, 10.28
editor, 21.4.12excel, 10.2.3
editpdbsearch, 3.6.2.12exclude fragment, 10.5.2
eds, 5.3.4, 5.3.6, 5.3.7     volume, 15.3.11
effect of mutation, 9.14, 9.15exit, 3.6.1.19
               on binding tutorial, 20.5.3explicit, 10.3.28, 12.2.1
                              example2, 20.5.3.1     flex, 12.2.1
                    stability tutorial, 20.5.4     group, 12.2.3
effort, 10.20, 10.34, 21.5.12          docking, 12.2.3
electron, 5.3.4, 5.3.6, 5.3.7, 21.2.27, 21.2.28     groups, 20.12.2
     denisty map, 5.3.5export, 5.5.10, 18.4
     densitry map.contour, 3.6.5     dock project, 15.20
          map, 3.6.1.7, 3.6.5, 5.3.4, 5.3.6, 12.5     pdb, 4.5
electrostatic coloring scale, 21.2.38extra windows, 6.2
     potential, 3.6.3.21extract, 4.4.2, 8.1, 10.1.3, 21.4.12, 21.8.8
     surface, 6.3     2D, 10.1.1
electrostatics, 6.3.1, 12.7.8     3d coordinates to spreadsheet, 10.1.3
elegant sketch, 6.10.4     icb, 3.6.1.5
element, 10.4.10     object icb, 4.4.2
eln, 18.7     sub alignment, 8.3.10
embed browser, 7.11     icb, 3.6.1.5
     powerpoint03, 7.8     pharmacophore, 10.5.6.4
     powerpoint07, 7.9faq, 21, 21.2, 21.2.13, 21.4, 21.5, 21.7, 21.10, 21.10.2
     powerpoint10, 7.10     ISISdraw, 21.8.3
     activeicm, 7.13     MolCart, 21.9
          script, 7.13     activeicm, 21.3
     browser, 7.7, 7.11          path, 21.3.3
     firefox, 7.7, 7.11     alignment secondary structure, 21.6.2
     internet.explorer, 7.7, 7.11     apf model, 21.8.12
     microsoft, 7.7     atom charge, 21.4.21
     powerpoint, 7.7, 7.8, 7.9, 7.10          display, 21.2.17
empty hostid, 21.1.18     autosave, 21.2.33
enamine, 10.5.5     backbone, 21.2.13
enantiomer, 21.5.21     background color, 21.2.2
enantiomers, 12.1.1.4          job, 21.5.19
energy, 5.6.3, 6.8.14, 10.24, 10.24.2, 12.1.12.2, 21.5.1, 21.5.2, 21.9.8     beep, 21.2.35
     circles, 13.1.10     binding energy, 21.5.2
     maps, 12.1.4, 12.1.5     blend transition, 21.2.31
     terms, 9.20.18     breaks, 21.2.34
ensemble, 12.2.2     change torsion, 21.4.16
entropy, 10.24.1     chem table display, 21.8.4
enumerate formal charge states, 10.16     chemical monitor, 21.8.10
     reaction, 20.6.10          query2, 21.8.1
enumeration, 10.32.4     cheminformatics, 21.8
eps, 10.2.6     clipping plane, 21.2.11
epsilon, 21.4.15     closest, 21.4.22
eraser, 10.4.11     color carbon, 21.2.4
errno, 21.1.3          skin, 21.2.16

     convert chemical from pdb, 21.4.1     pockets, 21.2.14
     covalent bond, 21.4.2     preserve coordinates, 21.8.6
     delete, 21.4.9     quad buffer, 21.1.7
     descriptors, 21.8.15     receptor selection, 21.5.14
     deselect, 21.2.7     reload dock, 21.5.4
     dihedral, 21.2.18     remove salt, 21.8.14
     dock charge groups, 21.5.22          select, 21.2.6
          probe, 21.5.13     renumber, 21.4.4
          racemic, 21.5.21     residue number selection, 21.2.36
          repeat, 21.5.5     rmsd, 21.4.7
          working directory, 21.5.23     rmsdtips, 21.4.8
     docking, 21.5     rocking active ppt, 21.3.1
     docktime, 21.5.11          speed, 21.3.2
     dollar, 21.10.3     rotate chemical, 21.8.13
     download install, 21.1.1     scale display, 21.2.38
     druglikeness, 21.8.9     scanScoreExternal, 21.5.17
     energy, 21.5.1     scanScoreExternal2, 21.5.18
     error admin, 21.1.10     score, 21.5.8
     extract ligand, 21.8.8     script, 21.10
     flexible dock, 21.5.15     sequence secondary structure, 21.6.1
          ring docking, 21.5.20          alignments, 21.6
     font size, 21.2.1     smiles, 21.8.11
     foreground table, 21.10.4     solvent accessible surface table, 21.4.19
     gl failure, 21.1.11     ss, 21.4.17
     gui, 21.2     structure, 21.4
     guided dock, 21.5.3     superimpose, 21.4.6
     hitlist, 21.5.7     surface display, 21.2.37
     hydrogen bond acceptors, 21.8.17     thoroughness, 21.5.12
     iSee, 21.2.30     transparent ribbon, 21.2.3
     icmPocketFinder, 21.5.10     truncate mesh, 21.2.15
     insert column, 21.8.7     view stack, 21.9.8
     installation, 21.1     weak hydrogen bonds, 21.4.20
     interactions, 21.2.12     write pdb, 21.4.3
     ligandbox, 21.5.9faqcontour, 21.2.28
     measure distance ring, 21.8.16faqhbondstrength, 21.2.29
     merge, 21.4.5faqmaps, 21.2.27
     modeling, 21.7faqoda, 21.2.26
     molcart 64bit, 21.1.3faqstereo, 21.1.14
          query, 21.9.5fasta, 8.1.5
          sdf, 21.9.4fbdd, 13.2
          text search, 21.9.6fft, 12.7.1
     molecule c, 21.2.5     protein protein docking, 12.7.1
     moledit, 21.8.2file, 3.6.1.3
     movie planes, 21.2.19     close, 3.6.1.13
     newscript, 21.10.1     compatible, 3.6.1.10
     nmr, 21.4.18     export, 3.6.1.12
     nvidia error, 21.1.2     high quality image, 6.15.1
     origin, 21.2.10     load, 3.6.1.7
     plist, 21.1.9     menu, 3.6.1
     pmf score, 21.5.6     password, 3.6.1.11

     quick image, 3.6.1.14fuzzy, 12.3
     icb, 4.1.10gap, 9.3
     recent, 3.6.1.17general preferences, 4.7.5
     bak, 3.6.2.11generalselecttools, 4.6.1
filter, 17.2, 21.2.4generator, 5.3.3, 10.20
     selection, 4.6.8getting started, 4
filters, 13.1.5giga search, 10.5.5
find chemical, 10.3.32          enamine, 10.5.5
fingerprint, 11, 11.3, 20.13, 21.8.1, 21.9.5glasses, 6.6, 21.1.6, 21.1.14
     method, 11.3glutamine proline, 9.20.2
fingerprints, 21.8.15google, 3.6.1.7
firefox, 21.3     objects, 6.3.7
fit, 10.3.34, 12.5, 21.5.15     3D, 3.7.6, 6.3.7
fitting, 12.5, 16.4.16gpcr_model, 20.5.1
flex super, 10.34.3graft loop, 9.4
flexibility, 5.6.4, 12.2.3, 20.12graphical, 21.2.4
flexible, 10.34, 12.2, 12.2.1, 12.2.2, 20.12.1, 21.5.15     display, 5.1.3.1, 5.1.3.2, 10.7.2, 10.7.3
     docking, 15.14          tutorial, 20.1
     receptor groups, 15.14               2D3D labels, 20.1.4
     ring sampling level, 12.1.6               annotation, 20.1.2
flood, 9.20.17               color representation, 20.1.1
fog, 3.6.3.5, 6, 6.10.1               labels, 20.1.3
font, 4.7, 4.7.7, 5.2.3.1, 6.8.2, 6.8.3, 8.7.7, 8.7.7.1, 10.3.28, 16.1.40, 16.7.4     user interface, 21.2
     preferences, 4.7.7graphics, 4.1
     size, 8.7, 21.1.16, 21.2.1     card, 21.1.2
form view, 16.1.5     controls, 6
formal, 5.1.3, 21.4.21     defects, 21.1.12
     charge, 6.1.9, 10.15, 10.16     effects, 6.10
format, 16.1.2, 16.1.40     panel, 6.2
formula, 10.4.9, 10.11     preferences, 4.7.3
fragment, 10.3.35, 10.33.1, 13, 13.2, 15.11     shadow, 3.6.3.13, 6.10.2
     linking, 15.11green arrows, 8.7.16, 21.6.2
     screening, 13.2     lines, 8.2, 21.6.1
fragments, 10.8grid, 10.3.3, 10.34, 20.12.1, 21.8.4
frame, 8.3.3grob, 4.7.5, 5.3.4, 5.3.6, 5.3.7, 6.3
free energy, 9.12, 9.13group, 10.33.1, 15.6
     radical, 10.4.7     column, 16.1.46
     wilson regression analysis, 10.33.2groups, 10.8, 10.11, 10.12
freeze column, 16.1.30guanidinium, 10.15
     row, 16.1.31gui, 4.1.1, 4.7.4
frequency, 10.3.35     menus, 3.6
front, 6.3.10, 6.13.1     preferences, 4.7.4
full model, 9.1.3     tabs, 3.7
          builder, 9.1.3guided docking, 12.1.7, 21.5.3
          multiple chain, 9.1.3.1h-bond, 5.2.3, 5.2.3.1, 5.2.3.2, 21.2.12
     refinement, 9.1.3halogen, 10.11.2
     scene antialias, 3.6.3.10hardware stereo, 3.6.3.7, 21.1
     screen, 3.6.3.8hbond, 5.2, 20.3.6, 21.2.29
function, 16.1.26, 16.1.32     strength, 21.2.29
functional.groups, 10.13header, 4.2.1.6, 16.4.9

heatmap, 16.4.7     markush, 20.6.8
     example, 16.4.7.1          structure, 20.6.7
helix, 21.2.20     merge tables, 10.3.23
help, 2     properties, 10.3.19
     videos, 2     reactions, 20.6.10
hetero, 10.3.28     reorder, 10.25.3
     scan, 15.7     sdf, 10.3.9
hidden block format, 8.7.11     show hide, 10.3.8
          width, 8.7.11     sort column, 10.3.5
hide, 16.1.39     standardize, 10.3.18
     column, 16.1.28     table hyperlinks, 10.3.15
high, 3.6.1.15          print, 10.3.11
     quality, 3.6.3.11          activeicm, 3.3
highlight new data, 10.3.7.1               create molecular documents, 3.3.3
his, 21.4.15                    slides, 3.3.2
histidine, 9.20.2, 21.4.15               getting started, 3.3.1
     tautomer, 21.4.15               ppt, 3.3.4
histogram, 13.1.9.2, 13.1.9.3, 16.4, 16.4.1, 16.4.9, 16.4.11, 16.4.13, 16.4.14, 16.4.15, 16.4.16, 16.4.17, 16.4.18, 16.4.20, 16.4.22               web, 3.3.5
     bins, 16.4.3          chemical clusering, 10.25.1
     options, 16.4.2          icm browser convert display pocket, 3.1.4
     bin.size, 16.4.2                    distances angles, 3.1.9
     bins, 16.4.3                    get started, 3.1.1
     color, 16.4.2                    graphical display, 3.1.2
     source, 16.4.2                         effects, 3.1.5
     style, 16.4.2                    images, 3.1.7
     title, 16.4.2                    labels annotation, 3.1.6
hitlist, 12.1.12, 12.1.13, 13.1.8, 13.1.9.1, 13.1.9.3, 13.1.9.7, 21.5.7                    pro crystallographic tools, 3.2.6
     cluster apf, 13.1.9.7                         get started, 3.2.1
     columns, 12.1.13.1                         graphics, 3.2.2
     export, 12.1.14                         plots, 3.2.8
homology, 4.2.1.2, 4.2.5, 9, 9.1, 9.1.1, 9.1.1.1, 9.1.2.1, 9.1.2.2, 9.1.3.1, 9.2, 9.7, 20.5                         sequence analysis, 3.2.7
     model, 9.1, 9.1.1.2                         structure analysis, 3.2.3
          introduction, 9.1.1                         superimpose, 3.2.5
     older versions, 9.1.1.3                         surfaces, 3.2.4
hover, 16.4.26                    selections, 3.1.3
     3D editor, 20.7                    superimpose, 3.1.8
     add columns, 10.3.4          search, 4.2
     cluster center, 10.25.2          use gui, 4.1
     color 2D by ph4, 10.5.6.5hrydrogen.bond, 21.2.29
     copy 2D, 10.3.16html, 3.6.1.12, 4.3, 7.6.1, 7.6.7, 21.3
          paste, 10.3.6html-doc font size, 21.2.1
     decompose, 20.6.9hybridization, 10.4.3, 10.5.1
     duplicate chemicals, 10.3.21hydrogen, 5.2.3, 5.2.3.1, 5.2.3.2, 6.1.8, 10.4.3, 10.5.1, 20.3.6, 21.2.12, 21.8.7, 21.8.10
     edit table, 10.3.17     atom display, 15.3.3
          tree, 10.25.4     bond, 5.2, 6.1.8, 10.6, 13.1.9.5, 20.3.6
     excel, 10.3.10          acceptors, 21.8.17
     extract 3D ph4, 10.5.6.4          donor, 10.36.1
     filter, 10.3.12          label edit, 5.2.3.1
     find replace, 10.3.13               move, 5.2.3.2
     mark row, 10.3.14     bonds, 5.2.4, 12.1.1.6

hydrogens, 10.3.28induced, 21.5.15
     remove, 10.3.18     fit, 12.2, 12.2.1, 12.2.3, 15.14, 20.12, 20.12.1
hyperlink, 7.6.1, 7.6.2, 16.1.40insert, 7.6.4
hyrophobic, 10.36.1     column, 16.1.26
iSee, 3.6.1.5, 3.6.1.12, 4.1.10, 6.15.3, 20.2, 21.2.30, 21.2.31, 21.3.3     image, 7.6.3, 16.1.34
icb, 4.4.2, 4.5, 21.2.30, 21.3.3          table, 16.1.34
icm, 21.3.3     row, 16.1.33
     chemist howto chemical search, 3.4.3     script, 7.6.4
               cluster, 3.4.5install, 1, 10.10.1, 18.1, 21.1.3, 21.1.4
               combi library, 3.4.7installation, 21.1
               ph4, 3.4.4interactio, 21.5.2
               plots, 3.4.8interaction, 5.5.3, 10.6, 21.2.12
               sketch, 3.4.1     fingerprint, 13.1.9.8
               spreadsheets, 3.4.2     fingerprints, 13.1.9.8
               stereoisomers tautomers, 3.4.6     restraint, 12.1.7
          pro 3D ligand editor, 3.5.1     restraints, 12.1.7
               chem3D, 3.5.2interactions, 15.3.12
               chemsuper, 3.5.4interactive, 12.1.9, 20.2
               energy, 3.5.3     loaded ligand, 12.1.9.2
               qsar, 3.5.5     loop, 9.1.4.2
               tutorials, 3.5     modeling, 9.1.4
          tutorials, 3.4          table ligand, 12.1.9.1
     hanging, 21.1.13     modeling, 9.1.4
     object, 5.1, 20.3.2interface prediction, 20.10
     script, 16.1.40internal hydrogen bonds, 12.1.1.6
icm-crash, 21.1.13internet explorer, 21.3
icmFastAlignment, 8.4interrupt, 6.10.7.3
icmPocketFinder, 5.6.6, 21.2.14, 21.5.10     animation, 6.10.7.3
icmdb, 18introduction, 1
icmjs, 7.16invert selection, 16.1.23
icmpocketfinder, 20.3.7invisible residue label, 21.1.12
id, 16.1.27iqr, 16.4.23
identity, 4.2.1.2isee, 7.6.5
image, 4.1.14, 4.7, 4.7.5, 6.15.3, 7.6.3, 10.2, 10.2.6, 16.4.21, 21.1.20isis, 10.4.18
     advanced, 6.15.3isostere, 13.4
     distortion, 21.1.20isotope, 10.4.3, 10.5.1
     preferences, 4.7.6iupac, 10.2.7, 10.3.20
     problem, 21.1.20javascript, 7.16
     multiple, 3.6.1.7job, 21.5.19
     quality, 3.6.3.11join, 10.29
     quick, 3.6.1.14, 6.15.2jpg, 6.15
images, 6.15     means, 16.7.1
impose, 12.2.2kcc, 14.3.1, 14.5
improve model, 11.1.3keep carboxyls neutral, 12.1.6
in-a-window, 21.1.7kernel regression, 14.3.1
inchi, 10.17.3     chemical, 10.4.10
increment, 16.1.27keyboard mouse, 6.11
     id, 16.1.27keystokes in chem-edit, 10.4.10
index, 21.9.6kmz, 3.7.6, 6.3.7
     models, 14.1.2knime, 19

     atoms, 6.8.2          preferences, 3.6.2.18
     color, 6.8.7     energetics, 10.24
     move, 6.8.4          conformational entropy, 10.24.1
     residues, 6.8.3          strain, 10.24.2
     sites, 6.8.6     pocket, 5.2.4, 21.4.11
     variables, 6.8.5          surface, 15.3.2
     2D, 3.7.3     receptor contacts, 15.3.12
     3D, 3.7.3, 6.8.1          display, 5.2
     atom, 6.8.1          interaction, 10.6
     atoms, 6.8.2     strain, 15.3.10
     color, 6.8.7     surface, 5.2.2
     custom, 6.8.8     tether, 15.12
     delete, 6.8.1, 6.8.9ligand-based, 13, 13.3
     distance, 6.8.10     convert, 9.20.1
     drag, 3.6.3.16     editor, 15, 15.1
     move, 3.6.3.16, 6.8.4          binding.re-dock ligand, 15.9
     residue, 6.8.1          display, 15.3
     residues, 6.8.3          edit, 15.5
     site, 6.8.1          energy, 15.3
     sites, 6.8.6          hydrogen.bond, 15.3
     variable, 6.8.1          pocket, 15.3
     variables, 6.8.5, 21.2.18          preferences, 15.2
labeling, 6.8.1          restraint, 15.12
labels, 6.8, 10.3.28          surface, 15.3
     distances, 6.8.10          tether, 15.12
     tab, 3.7.3     optimization, 20.11.3
landscape, 4.7.6     pocket, 4.1.8
large chemical space, 20.6.4     receptor.contact, 5.5.3
     font, 21.1.16ligand_pocket_interactions, 5.2.4
          size, 21.1.9ligedit distance restraint, 15.12.2
     sdf, 10.1.2     tab, 3.7.5
layer, 6.14     tether, 15.12.1
layers, 6.14light, 3.7.2
learn, 10.18, 10.19, 11, 11.1, 16.6, 21.8.12     tab, 3.7.2
learning, 11lighting, 6.3.9.4, 6.5
     theory, 11.5likeness, 10.11, 21.8.9
least.squares, 16.4.16line, 4.7.5, 16.7.4, 21.2.12
library, 10.32.4lineWidth, 4.7.3
     reaction, 20.6.10link, 8.3.9
license, 21.1.4     structure to alignment, 20.4
ligand, 5.2.2, 10.6, 10.24, 10.24.1, 10.24.2, 12.1.1, 12.2, 12.7.6, 12.7.7, 15.3.12, 15.3.13, 15.5.8, 15.10, 15.11, 21.4.5, 21.4.11, 21.5.2, 21.5.9, 21.8.8links, 4.6.20
     based screen, 10.36.3, 13.3linux, 10.10.1
     best replace, 15.6lipinski rule, 10.31
     binding, 9.15list, 4.6.18
     code, 4.2.1.3, 4.2.7lmhostid, 21.1.18
     considerations, 12.1.1.2load, 3.6.1.3, 3.6.1.17, 5.3.4, 5.3.6, 5.3.7, 8.1
     editor, 15, 15.10, 15.10.1, 15.17, 15.18     example alignment, 8.3.14
          bioisostere, 15.8     nmr model, 4.2.1.4
          covalent docking, 15.17     protein structure, 5.1.1
          mrc, 15.16     sequence, 8.1

          from file, 8.1.4     object, 3.6.1.1
          paste, 8.1.2making molecular slides, 7.1
          swissprot, 8.1.1     html, 7.6
     libraries, 9.20.6     color, 16.4.14
local, 21.2.24, 21.2.25manual change torsion, 15.5.4
     databases, 17map, 4.7.7, 5.3.4, 5.3.6, 5.3.7
     database.browse, 17.2     cel, 5.3.5
          edit, 17.3maps, 12.1.4, 12.1.5, 12.7.8, 20.12.1, 21.2.27, 21.2.28, 21.5.9
          query, 17.4mark, 16.1.45
          row, 17.3     row, 16.1.45
localpdb, 21.2.24     shape, 16.4.13
localseq, 21.2.25     size, 16.4.13
lock, 6.3.10, 6.13.1, 10.3.31markush, 10.25.7, 10.32.1, 10.32.3, 10.33.1, 20.11.3
log, 16.4.6, 16.4.11     docking, 20.11.3
logD, 10.11.6     library, 20.6.8
logP, 10.4.9, 10.11mass, 21.4.22
logS, 10.4.9, 10.11matched pair, 10.33.6, 20.6.11
logarithmic, 16.4.11          analysis, 10.33.6
logout, 3.6.1.19materials, 3.7.6
loop, 9.2, 9.4, 21.2.20max, 16.7.1
     analysis, 9.6maxColorPotential, 4.7.10
     design, 9.3maximum common substructure, 10.25.6, 10.27, 10.27.1
     find pdb segments, 9.6               dendrogram, 10.27.1
     model, 9.2, 9.3, 20.5.2mcs, 10.25.6, 10.27.1
          tutorial, 20.5.2     rgroup decomposition, 10.25.7
     modeling, 9.1.4.2, 9.5, 9.6, 9.20.10mean, 16.4.6, 16.4.23, 21.4.7
     preferred residues, 9.5measure distance, 21.8.16
     model, 9.20.9          to ring, 21.8.16
     sample, 9.20.9median, 16.4.6, 16.4.23
     energy water, 9.20.17memory, 10.1.2
mac, 10.10.1, 21.1.9, 21.1.16menu, 7.6.5
     font, 21.1.16     chemistry, 3.6.14
          size, 21.1.16     docking, 3.6.15
machine learning, 20.13     homology, 3.6.13
macrocycles, 9.19     molmechanics, 3.6.16
macros, 7.14     tools chemical search, 3.6.11
macroshape, 3.6.3.22, 6.3, 6.3.6          molecular editor, 3.6.12
make, 6.10.7.1, 16.1.1     windows, 3.6.17
     alignment, 8.6.1merge, 10.29, 21.4.5
     animation, 6.10.7.1     two sets, 10.29
     apf docking sar model, 14.6mesh, 5.2.1, 5.2.2, 5.3.4, 5.3.6, 5.3.7, 6.3, 6.3.9.1, 6.3.9.2, 6.3.9.4, 6.3.10, 6.3.11, 6.3.12, 6.13.1
     complex, 13.1.9.6, 15.21     clip, 6.3.10
     flat, 21.8.13     color lighting, 6.3.9.4
     molecular document, 7.6     options, 6.3.9
     molt, 17.1     representation, 6.3.9.3
     receptor maps, 12.1.5     save, 6.3.11
     selection, 4.6     options, 6.3.9
     bond, 21.4.2meshes, 6.3.2, 6.10.5
     disulfide, 9.9, 21.4.17     surfaces grobs, 6.3
     molecule, 3.6.1.1     tab, 3.7.6

min, 16.7.1          generate normal mode stack, 9.20.14
minimization, 9.17          his asn, 9.20.2
     cartesian, 9.20.8          ic table, 9.20.13
     global, 9.20.8          impose conformation, 9.20.4
     local, 9.20.8          minimize, 9.20.8
minimum specifications, 1          mmff, 9.20.6
mmff, 9.20.6, 10.4.16, 21.2.17, 21.8.5          regularization, 9.20.3
     type, 6.8.2          sample loop, 9.20.9
mmp, 20.6.11               peptide, 9.20.12
mnSolutions, 4.7.10               protein, 9.20.11
model, 9, 9.1, 9.1.1, 9.1.1.1, 9.1.2, 9.1.2.1, 9.1.2.2, 9.1.3.1, 9.2, 9.7, 9.17, 20.5          terms, 9.20.18
     domain interaction, 9.17          view stack, 9.20.15
     start, 9.1.1.2     modeling, 9
     weight, 11.1.2     table, 10.17.2
modelers view, 9.1.4.1     weight, 10.4.9
     view, 9.1.4.1molecule, 21.2.8, 21.8.3
modeling, 9.20.3     editor, 10.4
     options, 9.1.1.1moledit, 10.4.8
modeller view, 9.1.4molmechanics, 21.9.8
modification history, 15.5.6     minimize, 9.20.8
modify, 9.11     mmff, 9.20.6
     amino acid, 9.11molscreen, 13, 14
     group, 9.10     custom model panel, 14.4
mol, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6, 10.4.13, 20.11.2     load models, 14.1.1
mol2, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6               run, 14.1
molcart, 10.10, 10.10.1, 10.10.2, 10.10.3, 10.10.4, 10.10.5, 17, 18, 21.1.3, 21.8, 21.8.1, 21.9.3, 21.9.4, 21.9.5, 21.9.6     model type, 14.3
     add database, 10.10.3     results, 14.2
     administration, 10.10.5molskin, 6.3.2
     connect, 21.9.2molsynth, 10.11.5
     download dbs, 21.9.3molt, 17, 17.4
     hostid, 21.9.1monitor, 21.8.10
     installation, 10.10.1monochrome, 10.3.28
     license, 21.1.4montecarlo, 21.9.7
     search, 10.10.4mouse, 4.1.3, 6.11, 6.12
     start, 10.10.2mov, 6.16, 6.16.2
     connect, 21.9.2move, 3.6.3.19, 4.1.11, 4.1.13, 5.2.3.2, 6.3.9.1, 6.3.9.2, 6.12, 6.12.7, 9.17, 21.4.5
     hostid, 21.9.1     column, 16.1.28
     license, 21.9.1     mesh, 6.3.9.2
molclart, 21.1.4     slide, 7.4.2
molecular, 10.3.30, 10.3.31, 10.3.34, 10.3.35, 10.20, 21.8.7, 21.8.10     structure, 6.12
     animations slides, 7     tools, 6
     documents, 20.2     rotate, 6.11
     editor, 21.8.2     slab, 6.11
     graphics, 6     translate, 6.11
     matched pairs, 20.6.11     z-rotation, 6.11
     mechanics, 9.20     zoom, 6.11
          convert, 9.20.1movie, 6.16.1, 21.2.19, 21.9.7
          design loop, 9.20.10     montecarlo, 21.9.7
          edit structure, 9.20.5     making, 6.16, 6.16.2
          gamess, 9.20.16     open, 6.16, 6.16.2

mpeg, 6.16, 6.16.1, 6.16.2oda, 5.6.5, 12.7, 12.7.2, 12.7.3
mpg, 6.16, 6.16.2older version, 3.6.1.10
mpo, 10.31omega, 6.8.5, 21.2.18
multi apf super, 10.35.3online databases, 10.5.5
     panel, 6.2open, 3.6.1.3, 4.4, 16.1.2
     parameter optimization, 10.31     file, 4.4
     template, 9.1.4.3     password, 4.4.1
     windows, 6.2     with password, 3.6.1.4
multiple, 12.2.2, 20.12.1     movie, 6.16, 6.16.2
     chain, 9.1.2.2, 9.1.3.1     password, 3.6.1.4, 4.4.1
     position group scan, 15.7optimal, 5.6.5, 12.7, 12.7.2, 12.7.3
     rec, 12.2.2optimize, 9.20.2
     receptor, 4.2.2, 20.12oracle, 18
          docking, 15.16orange, 4.6.5
     protein, 21.2.5     selection, 4.6.5
mutant, 9.10, 21.4.13, 21.4.14origin, 6.8.11, 21.2.10
mutate, 9.12, 9.13, 21.4.15orthosteric, 5.6.6
     residue, 21.4.13other selection, 4.6.19
          N C, 21.4.14outside, 21.5.9
mutation, 9.10, 9.12, 9.13, 9.15, 20.5.3, 20.5.4, 21.4.13, 21.4.14overlay, 20.3.3, 21.2.5, 21.4.6
     protein binding, 9.12package.activeicm, 7.13
          ligand, 9.15packing, 5.3.1
          peptide, 9.14pages, 18.7
          stability, 9.13pairwise, 10.35.1, 10.35.2
mysql, 18     apf score, 10.36
navigate workspace, 4.6.10parallelization, 13.1.7
nearest, 21.4.22password, 10.10.5
neural network, 12.1.13.1paste, 10.4.11, 10.4.18, 16.1.35
new, 8.1pca, 16.5
     icm session, 3.6.1.2pdb, 3.6.1.7, 4.2, 4.2.1.1, 4.2.7, 4.5, 5.1.3, 10.7.1, 20.3, 21.2.24, 21.2.25, 21.4.4
     table, 16.1.1     chem gl, 10.7.3
     table, 16.1.1          iw, 10.7.2
nmr, 21.4.18     dormat, 4.5
     model, 4.2.1.4     file, 21.4.3
nof, 10.11.2     html, 4.2.1.6
     chemical, 10.11.2     preparation, 20.3.11
non-contiguous selection, 4.6.18     search, 4.2.1, 4.2.1.2, 4.2.1.3, 20.3.1
normal modes, 9.20.14     convert, 9.20.1
number of sp3, 10.11.2     recent, 3.6.1.18
numbers, 10.3.28     search, 3.7.4, 4.1.2
nvidia, 21.1.2pdbsearchfield, 3.6.2.13
object, 4.1.11, 4.5, 20.3, 21.2.8pdbsearchhomology, 3.6.2.15
objects, 5.1.2pdbsearchidentity, 3.6.2.14
     in table, 16.3pdbsearcsequence, 3.6.2.16
     in.table, 16.3peptide, 4.3, 9.14, 9.19, 12.6
occlusion, 6.3.12, 6.10.5     docking, 12.6
     shading, 6.3.12     modeling, 9.19
          effect, 6.10.5percentage similarity, 8.7.15, 20.4.4
occupancy, 6.1.3, 20.3.10perspective, 3.6.3.9, 6.10.6
     display, 4.2.1.5ph4, 10.5.6

          3d, 10.5.6.2     logarithmic, 16.4.12
     search, 10.5.6.3pls, 10.18, 10.19, 11, 16.6, 20.13
pharmacophore, 10.3.35, 10.5.6.5, 20.8.2pmf, 21.5.6
     2D, 20.6.6png, 3.6.1.14, 6.15, 6.15.2, 7.6.3, 10.2, 10.2.6
     3D, 20.6.5pocket, 4.1.8, 5.2, 5.2.1, 5.2.2, 5.6.6, 12.1, 20.3.7, 21.2.14, 21.4.11, 21.5.10
     clone, 10.5.6.2     conservation, 21.4.12
     draw2D, 10.5.6.1     surface, 5.2.1, 13.1.10
     draw3D, 10.5.6.2     peptide, 4.1.8
     edit, 10.5.6.1, 10.5.6.2     properties, 4.1.8
     move, 10.5.6.2pocketome, 4.2, 4.2.2
     new, 10.5.6.2pockets, 5.6.6
     search, 10.5.6, 10.5.6.3, 20.6.5, 20.6.6point label, 16.4.19
phi, 6.8.5, 21.2.18portait, 4.7.6
phylogenetic, 8.7.8post edit ligand, 15.5.8
phylogeny, 8.7.8     screen, 13.1.9
pi, 5.2.5postscript, 4.7.6
     pi, 5.2.5potential mean force, 13.1.4
picking, 6powerpoint, 20.2, 21.3
picture, 3.6.1.14, 4.1.14, 6.15.2, 7.6.3ppbatch, 12.7.9
     tips, 4.1.14ppepitope, 12.7.7
     chart, 16.4.8ppmaps, 12.7.8
pipi, 5.2.5pprefine, 12.7.11
pka, 10.15ppresults, 12.7.10
planar, 5.5.7, 6.8.5, 21.2.18pproc, 12.7.3
     angle, 5.5ppsetligand, 12.7.6
     angle, 6.9.2ppsetproject, 12.7.4
plane, 6.3.10, 6.13, 6.13.1, 6.14, 21.2.11, 21.2.19, 21.2.21ppsetreceptor, 12.7.5
     faq, 21.2.21ppt, 7.12, 7.14, 21.3.3
plot, 4.7, 4.7.8, 13.1.9.2, 16.4, 16.4.1, 16.4.4, 16.4.9, 16.4.11, 16.4.13, 16.4.14, 16.4.15, 16.4.16, 16.4.17, 16.4.18, 16.4.20, 16.4.21, 16.4.22, 16.4.23predict, 8.3.2, 10.18, 10.19, 11, 11.2, 16.6, 21.8.9, 21.8.12
     R group sar, 10.33.4     disulfide, 9.16
     axis, 16.4.11     metabolic oxidation, 14.7
     color, 16.4.14predicting bioassays, 11.2
     columns, 16.4.6     compound properties, 11.2
     function, 3.6.9, 3.6.9.1prediction binding, 9.12
     grid, 16.4.15preferences, 4.7, 13.1.5, 21.2.24, 21.2.25
     header, 16.4.9preferred residues, 9.5
     inline, 16.4.22presentatio, 7.6.5
     logarithmic, 16.4.12presentation, 7.7, 7.12
     mark, 16.4.13presentations, 7
     mean median iqr, 16.4.23preserve, 21.8.6
     point label, 16.4.19press-and-hold to rotate, 10.4.8
     preferences, 4.7.8pretty view, 15.3.6
          groups, 16.4.25primary aliphatic amines, 10.15
     regression, 16.4.16principal component analysis, 16.5
     selection, 16.4.18          regression, 11
     zoom translate, 16.4.17     components, 11.5
     axis, 16.4.15print, 6.7, 16.4.20, 16.7.3
     display, 16.4.15     alignment, 8.7.4
     grid, 16.4.15     plot, 16.4.20
     inline, 16.4.22     alignment, 8.7.4

pro-drug, 10.23protein-proteindocking, 12.7.7
probe, 12.1.4, 21.5.13protein-protin, 20.10
problem, 21.1.14     convert, 9.20.1
     with selection, 21.1.12protonated, 21.4.15
prodrug, 10.23protonation, 12.1.1.5
profile, 8.3.8     state, 12.1.1.5
project, 3.6.1.5, 12.7.4, 18.6, 20.6.4.6protprot, 12.7
     close, 3.6.1.13proximity, 6.3.3, 6.3.4
     rename, 3.6.1.9psa, 10.4.9
properties, 6.8.2, 10.11, 10.11.1, 21.8.7psi, 6.8.5, 21.2.18
property, 10.4.9, 21.8.7, 21.8.8, 21.8.9, 21.8.10pubchem, 10.1
     expression, 13.1.9.6publication quality images, 6.3.2
     monitor, 10.4.9pubmed, 4.2.1.7
protect, 7.6.8purple box, 3.6.3.23, 12.1.4, 15.9.1
protein, 5.4.6, 8, 9.14, 21.4.5qs hydrogen bond, 5.2.3
     chain, 9.3     pdb chem gl, 5.1.3.2
     health, 5.6.3               iw, 5.1.3.1
     model, 9.18qsar, 10.18, 10.19, 11.1, 20.13
     protein docking, 20.10     learn predict, 10.18
               tutorial, 20.10     predict, 10.19
     sculpting, 9.17quad buffer stereo, 21.1
     sequence, 10.4.17     buffer, 21.1.7
     structure, 5quality, 3.6.1.15, 4.7.5
          analysis, 5.5query, 9.1.2, 18, 18.3, 21.8.1, 21.9.5, 21.9.6
               closed cavities, 5.5.4     molt, 17.4
               contact areas, 5.5.3     processing, 10.5.3
               distance, 5.5.6     setup, 10.5.1
               find related chains, 5.5.1quick, 4.1.14
               finding dihedral angle, 5.5.8     image, 6.15.2
                    planar angle, 5.5.7     model multiple chain, 9.1.2.2
               rama export, 5.5.10          single chain, 9.1.2.1
               ramachandran plot, 5.5.9     start move structure, 4.1.3
               rmsd, 5.5.2          read pdb, 4.1.2
               surface area, 5.5.5          representation, 4.1.6
          tutorials, 20.3          selection, 4.1.5
               analysis, 20.3.4               level, 4.6.3
               contact area, 20.3.5          what is selected, 4.6.4
               convert, 20.3.2     dispalay.distance, 6.9.1
               hydrogen bond, 20.3.6     start color, 4.1.7
               icmpocketfinder, 20.3.7quit, 3.6.1.19
               search, 20.3.1     group, 10.25.7, 10.32.4
               superimpose, 20.3.3          table, 10.32.2
     superposition, 5.4     groups, 10.32.2
          select, 5.4.1r-group, 10.25.7, 10.32.2
          sites by apf, 5.4.6     decomposition, 10.25.7
          superimpose 3D, 5.4.3     enumeration, 10.25.7
               grid, 5.4.5r-groups, 16.4.25
               multiple proteins, 5.4.4racemic, 10.3.28, 10.17.5, 21.5.21
protein-protein, 5.6.5, 12.7, 12.7.1, 12.7.2, 12.7.3, 12.7.4, 12.7.5, 12.7.6, 12.7.8, 12.7.9, 12.7.10radar, 16.4.6
     docking refinement, 12.7.11rainbow, 4.7.5, 6.8.15, 10.3.35, 21.2.38

random forest, 11, 20.13renumber, 21.4.4
range, 6.10.7.2reorder column, 16.1.29
rapid isostere replacement, 13.4replace chemical, 10.3.32
ratio.selection, 4.7.5replacement, 15.6
     dock ligand, 15.9     group, 15.8
reactions, 10.8, 10.32.5report, 18.3
reactive cysteine, 5.6.2representation, 3.6.3.19
reactivity, 10.11.3residue, 4.7.7, 21.2.8, 21.4.15, 21.4.22
read, 3.6.1.3, 3.6.1.17, 4.4, 8.1, 10.3.1     alternative orientaiton, 20.3.11
     chemical, 10.1     content, 8.3.1
          spreadsheet, 10.3.1     number selection, 21.2.36
     table, 16.1.2     range, 4.6.18
     pdb, 4.1.2     content, 3.6.4, 8.3, 8.3.1
     table, 16     mutate, 21.4.13, 21.4.14
reagent, 10.32.5residues, 5.2.1, 5.2.2, 21.2.14
rear, 6.3.10, 6.13.1resize, 6.3.9.1, 6.15.3
recent files, 3.6.1.17     mesh, 6.3.9.1
     pdb codes, 3.6.1.18resolution, 4.2.1.3
receptor, 5.2.1, 5.2.2, 10.6, 12.1.1, 12.2.2, 12.7.5, 12.7.7, 15.3.12, 20.12.1, 21.5.2, 21.5.14, 21.5.15restore, 3.6.2.11, 6.3.10, 6.13.1
     considertations, 12.1.1.1     default, 21.1.9
     flexibility, 15.16     recent backup, 3.6.2.11
     pocket, 15.3.1restrained docking, 12.1.7
          surface, 15.3.1, 15.3.2restraing, 15.12.1, 15.12.2
     flexibility, 20.12.2results, 12.7.10
recover, 3.6.2.11     stack, 12.1.12.2
     cylinders, 8.7.16, 21.6.2retrieve columns, 21.5.24
     lines, 8.2, 21.6.1          from original database, 21.5.24
redo, 3.6.2.10, 10.4.11, 15.5.5review and adjust binding site, 12.1.4
refine, 9.7, 9.8rgroup, 10.32.4
     loops, 9.1.3ribbon, 3.7.1, 4.7.9, 6.1.3, 21.2.23, 21.2.34
     side chain, 9.8     as a mesh object, 21.2.3
     sidechains, 9.1.3     faq, 21.2.23
refinement, 12.2.4     preferences, 4.7.9
region, 12.7.7     style, 4.7.9
regresion, 16.4.16     breaks, 6.1.3
regression, 10.33.2, 11.1, 11.5, 20.13     cylinders, 6.1.3
regul, 9.7     smooth, 6.1.3
regularization, 9.7, 9.20.3     worm, 6.1.3
relationship, 11, 16.6ribbonColorStyle, 4.7.9
     covalent geometry, 12.1.6ride, 13.4
relaxed ligand, 15.3.9     gpu benchmark, 13.4.1.2
reload, 12.1.16, 21.5.4     server setup, 13.4.1.1
     dock results, 12.1.16     setup, 13.4.1
remove, 21.2.6, 21.2.7, 21.2.10right, 4.1.12
     salt, 21.8.14     click, 4.1.12
     explixit.hydrogens, 10.12rigid, 10.34
     salt, 10.12     super, 10.34.2
rename, 16.1.25          table, 10.34.1
     colunn, 16.1.25ring, 5.2.5, 10.4.3, 10.4.6, 10.5.1
     project, 3.6.1.9     stacking, 5.2.5

rmsd, 5.5, 5.5.2, 21.4.7, 21.4.8     project icb, 4.1.10
rock, 3.6.3.15, 6.10.7, 6.10.7.1, 7     sequence, 8.1.5
     speed, 6.10.7.2     slide, 7.4
root, 21.4.7     smiles string, 10.4.15
     mean square deviation, 5.5.2     table, 16.1.21
rotate, 3.6.3.15, 4.1.3, 6, 6.10.7, 6.10.7.1, 6.12, 6.12.1, 6.12.2, 7, 10.3.34, 21.8.13          spreadsheet, 15.5.7
     chemical, 10.3.34     tree, 16.7.3
     when pasting, 10.4.8          sdf, 10.4.14
     easy, 3.6.3.12     image, 3.6.1.15, 4.1.14
     speed, 6.10.7.2     object, 4.1.9
rotating fragment in editor, 10.4.8     password, 3.6.1.11
rotation, 6.12.1     picture, 3.6.1.15
rough surface, 21.2.37     project, 3.6.1.8, 3.6.1.9, 3.6.1.10, 4.1.10
row, 16, 16.1.22, 16.1.35, 16.1.45     table.view, 16.1.8
     flag, 16.1.13saving, 3.6.1.8
     height, 16.1.7, 21.2.39     project, 3.6.1.8
     mark, 16.1.13scaffold, 10.14
     hide, 10.3.8     hopping, 15.8
     show, 10.3.8scale, 4.7.5, 21.2.38
ruler, 6.8.15scan, 9.20.7, 12.1.12.1
     molscreen, 14.1.3     hits, 12.1.12.1
rundock, 21.5.16          group, 15.7
rxn, 10.4.13scarab, 18
safari, 21.3     add user, 18.5
sali, 10.33.5     browse export data, 18.4
     bridge, 20.3.6     installation, 18.1
salts, 10.3.18     new project, 18.6
sample, 9.18, 10.34     pages, 18.7
     double bond cis trans, 12.1.6     query, 18.3
     peptide, 9.19, 9.20.12     upload data, 18.2
     protein, 9.18, 9.20.11scare, 12.2.4
     racemic centers, 12.1.6scatter, 13.1.9.2
sar, 10.25.7, 10.33, 16.4.25scatterplot, 13.1.9.4
     analysis, 10.33score, 12.1.13.1, 13.1.8, 15.4, 20.8.3, 20.8.5, 21.5.7, 21.5.8, 21.5.18
     table, 10.33.3     threshold, 13.1.4
save, 4.5, 6.3.11, 6.10.7.4, 8.1.5, 10.2.3, 16.4.21, 16.7.3, 21.2.33screen, 10.36, 20.8.4, 20.9, 20.11.1
     SMILES, 10.4.15screening, 13.1, 13.1.1, 13.1.2, 20.12
     alignment, 8.7.3screenshot, 6.16, 6.16.2
          PDB, 4.5     movie, 6.16.2
          pdb, 4.5script, 4.3, 7.6.4, 7.6.5, 21.4.19, 21.10, 21.10.1, 21.10.2, 21.10.3
     chemical mol, 10.4.13sculpting, 9.17
          spreadsheet workspace, 10.2.1sdf, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6, 10.3.35, 10.10, 10.10.3, 10.17.1, 15.10, 17.1, 18.2, 20.11.2, 21.9.3, 21.9.4
          to chemical spreadsheet, 10.4.14search, 10.10, 10.10.4, 17.2, 18.3, 21.9.6
     docked ligand, 15.19     chembl, 4.2.3
     file, 4.5     drugbank, 4.2.8
     hits, 15.5.7     filter, 10.5.2
     image plot, 16.4.21     in workspace, 3.6.2.4
     ligand receptor complex, 15.19     pdb, 4.2.1
     object, 4.1.9          chemical, 4.2.1
     pdb, 4.5          ligand code, 4.2.7

     pubchem, 4.2.9     neighbors, 3.6.2.5, 3.6.2.8, 4.6.15, 4.6.17
     surechembl, 4.2.4     object, 4.6.11
     tab field, 4.2.1.3     other, 4.6.19
          pdb chemical, 4.2.1.1     properties, 3.6.2.5
               sequence, 4.2.1.2     range, 16.1.23
     tautomer, 10.5.3     residue, 3.6.2.5
     uniprot, 4.2.6     row, 16.1.23
     in.workspace, 3.6.2.4     sphere, 4.6.15
secondary aliphatic amines, 10.15     spherical, 3.6.2.8
     structure, 5.6.1, 21.2.20     superposition, 5.4.1
     sctructure, 8.3.2     table, 4.6.19, 16.1.23
     structure, 3.6.4, 6.1.3, 8.3          elements, 16.1.23
select, 4.6.12, 4.6.13, 16, 16.1.45, 21.4.22     tools, 4.6.1, 4.6.2, 4.6.7, 4.6.8
     a tree branch, 16.7.2     whole, 4.6.11
     all, 4.6.14     workspace, 4.6.9, 4.6.17
     amino acid, 4.6.13selectioninvert, 3.6.2.6
     duplicates, 10.30selections, 4.6
     molecule, 4.6.12     links, 8.3.9
     neighbors, 4.6.15selectneighbors workspace, 4.6.17
          graphic, 4.6.16     organized network, 10.27
     object, 4.6.11sequence, 3.6.4, 4.2, 4.2.1.2, 4.2.5, 4.2.6, 4.3, 8, 8.1, 8.1.5, 8.2, 8.3, 8.3.7, 8.6.1, 8.6.5, 9.1.2, 10.4.17, 20.3, 20.4, 20.4.4, 21.4.12, 21.6, 21.6.1
     residue, 4.6.13, 4.6.18     analysis, 8.3
          by number, 4.6.18     editor, 8.5
          number, 4.6.18     identity, 8.7.15
     tree, 16.7.2     pattern, 4.2.1.2
     atom, 4.1.5, 4.6.3     reordering, 8.7.8
     graphical, 4.1.5, 4.6.3     secondary structure, 8.2, 21.6.1
     object, 4.1.5, 4.6.3     similarity, 8.7.15
     purple.box, 3.6.3.23     sites, 8.5
     residue, 4.1.5, 4.6.3     structure, 8.3.6
     workspace, 4.1.5, 4.6.3     type, 8.3.4
selectall, 3.6.2.3     DNA, 8.3.4
selecting.neighbors, 4.6.16     alignment, 8.3.5, 8.6.2, 8.6.6
selection, 4.6.4, 4.6.5, 4.6.21, 6.3.4, 10.4.11, 16.4.18, 16.7.2, 16.7.4, 21.2.4, 21.2.6, 21.2.7, 21.2.8, 21.2.13, 21.2.32, 21.4.9, 21.4.10, 21.4.22, 21.5.14     nucleotide, 8.3.4
     clear, 3.6.2.7     protein, 8.3.4
     neighbors, 3.6.2.8     search, 8.4
     alignment, 4.6.19     structure.alignment, 8.3.6, 8.6.3
     all, 3.6.2.3sequences, 8, 21.2.25
     alter, 4.6.7     unique, 8.3.13
     atom, 3.6.2.5     extract, 8.3.13
     basic, 4.6.2     unique, 8.3.13
     change, 4.6.7server, 13.1.7.2
     clear, 3.6.2.7     error, 21.1.17
     column, 16.1.23set, 10.3.31, 21.4.21
     filter, 3.6.2.5, 4.6.8     formal charges, 10.15
     graphical, 4.6.16     server, 21.1.17
     invert, 3.6.2.6, 16.1.23     bond type, 9.20.5
     level, 3.6.3.3     charges, 9.20.6
     mode, 3.6.3.4     chirality, 9.20.5
     near atoms, 3.6.2.8     disulfide, 9.9, 21.4.17

     formal charge, 9.20.5     show, 7.3
     tether, 9.20.5     blend, 7.5
     types, 9.20.6     edit, 7.4.1
setAPFparams, 21.8.12     effect, 7.5
setup, 12.7.6     smooth, 7.5
     ligand receptor, 15.1     transition, 7.5
shade, 8.7.7, 8.7.7.1slides, 6.16.1, 7, 7.1, 7.3, 21.2.30
     alignment, 20.4.4smiles, 10.4.9, 10.11, 10.17, 10.17.3, 10.17.4
shading, 6.3.12smooth, 6.3.9.3
shadow, 6.10.2     surface, 21.2.37
share model, 11.1.4solid, 6.3.9.3
sheet, 21.2.20solvent.accessible.area, 21.4.19
shell preferences, 4.7.10sort hitlist, 13.1.9.1
shift, 6.8.3     table, 3.6.10.4
shine, 3.7.2, 4.7.5sorting, 13.1.9.1
shineStyle, 4.7.3     compounds, 16.7
show, 7.3.1, 16.1.39sp3, 10.11.2
     hide column, 16.1.39spec, 3.7.2
side, 10.3.29specifications, 21.1.5
     by side, 10.3.29specs, 1
               error, 21.1.19     faq, 21.1.5
               stereo, 3.6.3.6speed, 6.10.7.2
     chain refinement, 15.15sphere, 21.4.11
     chains, 9.8spherical, 21.4.9, 21.4.12
side-by-side, 21.1.19split, 10.33.1
side-chain sampling, 12.7.11spreadsheet, 10.17.2
side-chains, 12.2.1square, 21.4.7
sigmaLevel, 5.3.6, 5.3.7squence.amino acid, 8.3.4
similarity, 10.28stability, 9.13, 20.5.3, 20.5.4
simulation, 21.9.8stack, 9.18, 12.1.12, 12.7.10, 21.9.8
     length, 21.5.12stacking, 5.2.5
simulations, 21.7standalone hitlist, 12.1.14
single, 10.4.10standard table, 16.1
     chain, 9.1.2.1standardize, 10.12
singlet, 10.4.7     table, 10.12
sites, 5.4.6start, 10.10.2
size, 5.2.3.1     dock, 12.1
sketch accents, 6.10.3startup, 21.10.2
     markush, 10.32.1static, 21.4.8
     reaction, 12.4.1stereo, 4.7.6, 6.6, 10.3.28, 10.4.2, 21.1, 21.1.6, 21.1.7, 21.1.14
     smiles, 10.4.12     bond, 10.4.2
     accents, 3.6.3.14, 6.10.3     hardware, 3.6.3.7
skin, 3.7.1, 6.1.4, 21.2.16     side-by-side, 3.6.3.6
slab, 6.3.10, 6.13.1stereohard faq, 21.1.6
slice, 6.13stereoisomer, 10.17.5
slide, 6.10.7.4, 7.2, 7.3.1, 7.6.1, 21.2.31stereoisomers, 10.22
     effects, 7.5stick, 4.7.5
     movie, 6.16.1stl, 6.7
          file, 7.2stop, 6.10.7.3
     navigation, 7.3.2store, 3.6.3.19, 6.10.7.4, 21.2.22

               faq, 21.2.22     filter, 16.1.43
strain, 5.6.3, 10.24, 10.24.2, 12.1.1.7, 15.4     find, 16.1.9
strip, 21.4.9          replace, 10.3.32
structure, 5.3.3, 11, 16.6, 20.3, 21.4     font, 16.1.11
     analysis, 20.3.4          size, 21.2.1
     ensemble, 9.20.14     grid, 16.1.5
     representation, 6.1     histogram, 16.4.1
     smiles, 10.17.4     insert, 16.1.26
structure-based, 13     layout, 16.1.5
structures, 10, 10.1     learning, 16.6
style, 4.7.5     mark, 16.1.13
substituent, 10.9.1, 10.9.2, 10.32.2, 15.5.2          row, 16.1.13
substructure, 10.10.4, 10.13, 12.3, 21.8.1, 21.9.5     mouse, 16.1.47
     template, 15.13     navigation, 16.1.4
     alerts, 10.13     new column, 16.1.26
suface, 21.4.19     plot, 16.4
sulfur, 9.9     print, 16.1.19
superimpose, 3.6.8, 5.4.2, 5.4.6, 20.3.3, 21.2.5, 21.4.6, 21.4.7, 21.4.8     rename, 16.1.15
     3D, 5.4.3     rightclick, 16.1.14
     Calpha, 5.4.3     row height, 21.2.39
     arrange.grid, 5.4.5     save, 16.1.3
     backbone, 5.4.3          selection, 16.1.3
     flexible, 10.34.3     search, 16.1.9
     heavy atoms, 5.4.3     select, 16.1.23
     multiple, 5.4.4     setup, 16.1.18
     rigid, 10.34.1, 10.34.2     sort, 16.1.42
     substructure, 10.34.1, 10.34.2, 10.34.3     split fragments, 10.3.33
superposition, 10.34, 10.35.1, 10.35.2, 20.3.3, 20.8.1     view, 16.1.5
surface, 3.7.1, 4.7.5, 5.2.1, 5.2.2, 6.1.6, 6.3, 6.3.3, 6.3.4, 21.2.16, 21.2.37          save, 16.1.8
     area, 5.5     zoom translate, 10.3.30
     area, 5.5.5     action, 16.1.47
surfaces, 5.2, 6.3.1, 6.3.2, 6.10.5     alignment, 16.1.12
surrounding, 21.4.11     append, 16.1.43
swissprot, 8.1, 8.5     clone, 16.1.16
sxstrace, 21.1.19     color, 16.1.10
symmetric oligomer, 9.1.3     column, 10.3.4, 16.1.26, 16.1.32, 16.1.39
symmetry, 5.3.1, 5.3.3, 20.3.8, 20.3.9     columns, 10.3.8
synthesize, 10.11.5     compare, 10.3.22
synthetic feasibility, 10.11.5     copy, 10.3.6
system preferences, 4.7.11     cursor, 16.1.47
tab, 16.1.2, 16.1.21     delete, 16.1.14, 16.1.17
     pdb, 3.7.4     display, 21.10.4
table, 4.3, 10.1.3, 10.3.24, 10.3.25, 10.3.28, 10.3.30, 10.3.31, 10.3.34, 10.3.35, 10.17.2, 10.20, 10.34.1, 15.10, 16, 16.1.6, 16.1.35, 16.1.40, 16.1.45, 16.4, 16.4.1, 16.4.4, 16.4.9, 16.4.11, 16.4.13, 16.4.14, 16.4.15, 16.4.16, 16.4.17, 16.4.18, 16.4.20, 16.7.1, 21.4.19, 21.8.4, 21.8.5, 21.8.7, 21.8.8     double.click, 16.1.47
     alignment, 16.1.12     edit, 10.3.17
     clone, 16.1.16     excel, 10.3.10, 16.1.20
     color, 16.1.10     filter, 10.3.12, 16.1.43
     column format, 16.1.40     find-replace, 10.3.13
     copy, 16.1.36, 16.1.37          to screen, 16.1.4
     delete, 16.1.17     font, 16.1.11
     edit, 16.1.24     foreground, 21.10.4

     hide, 16.1.39     machine, 21.1.15
     hyperlink, 10.3.15     racemic, 10.17
     insert, 16.1.33tools 3D, 3.6.6
     join, 3.6.10.5     analysis, 3.6.7
     label, 10.3.14     append rows, 3.6.10.7
     landscape, 16.1.18     extras, 3.6.9
     mark, 10.3.14          plot function, 3.6.9.1
     merge, 3.6.10.5, 10.3.23, 10.29     superimpose, 3.6.8
     mouse, 16.1.47     table, 3.6.10
     name, 16.1.15          Learn, 3.6.10.1
     new, 16.1.1          clustering, 3.6.10.3
     options, 16.1.14          merge, 3.6.10.5
     orientation, 16.1.18          predict, 3.6.10.2
     portrait, 16.1.18tooltip, 16.4.26
     print, 10.3.11, 16.1.4, 16.1.19     balloons, 16.4.26
     read, 16.1.2torsion, 6.12.6, 9.20.7, 15.5.4, 21.4.16
     rename, 16.1.15     angles, 6.12, 6.12.6
     right click, 16.1.14     scan, 9.20.7
     row, 16.1.33toxscore, 10.11.3
     rows, 3.6.10.7trace, 6.1.10
     save, 10.3.9, 16.1.3, 16.1.4, 16.1.21transition.blend, 21.2.31
     scale, 16.1.18transitions, 7, 21.2.30
     scroll, 16.1.4translate, 4.1.3, 6, 6.12, 10.3.30
     sdf, 10.3.9translation, 6.12.3, 8.3.3, 16.4.17
     select, 16.1.23transparent, 6.3.9.3
     setup, 16.1.18     background, 6.15.3
     sort, 3.6.10.4, 10.3.5, 16.1.42     ribbon, 21.2.3
     standard, 16.1     surface, 21.2.37
     view, 10.3.29tree, 8.7.8, 10.25.7, 16.7.2, 16.7.3, 16.7.4
     width, 16.1.4     branch swapping, 8.7.8
tables, 10.28, 16     distance, 10.25.3
tag, 4.6.21, 15.5.7, 16.1.46     edit, 10.25.4
tags, 4.6.21     reorder, 10.25.3
tautomer, 10.21, 21.4.15triplet, 10.4.7
tautomers, 10.21trouble shooting, 21.1.11
temperature, 5.6.4trouble-shooting, 21.1.12
template, 9.1.2, 10.4.6, 10.34truncating a mesh object, 21.2.15
     docking, 21.5.3     crash qlock, 21.1.13
templates, 10.4.6tsv, 16.1.21
terminal, 10.3.28tut analyze alternative orientations, 20.3.11
     font size, 21.2.1          occupancy, 20.3.10
tether, 12.1.7, 15.12.1, 15.12.2          symmetry, 20.3.9
text, 4.7.7, 7.6, 7.6.1, 7.6.7, 10.3.28, 10.10.4, 16.4.24, 21.9.6     multiple receptor, 20.12.1
     search, 10.5.4tut3, 20.5
texture, 3.7.6tut3e, 20.3.12
thoroughness, 10.20, 10.34, 21.5.12tut5a, 20.9.1
three, 10.3.24, 21.8.6tut5b, 20.9.2
threshold, 4.7.5tut5c, 20.11.1
tier, 4.1.13tut5e, 20.11.2
time, 21.5.11tutorial 2D pharmacophore, 20.6.6

     chemical clustering, 20.6.3     sketch accents, 3.6.3.14
          search, 20.6.2     slide show, 7.3.1
     molecular documents, 20.2     tools, 3.6.3
     sequence alignment, 20.4     tree, 16.7.4
               link, 20.4.2     undisplay all, 3.6.3.1
               load sequence, 20.4.1     stach, 9.20.15
               sequence conservation, 20.4.3virtual, 13.1, 13.1.1, 13.1.2, 20.9, 20.11.1
tutorials, 20     ligand screening, 14
two, 10.3.24, 21.8.6     screen, 13.3, 13.4
ubuntu, 21.1.18     screening, 13, 13.2
unclip, 6.3.10, 6.13.1          examples, 20.11
undisplay, 4.1.4, 6.1.7, 21.2.10, 21.2.32virus, 5.3.3
     box shade font, 8.7.7.1visualize, 10.27
     origin, 6.8.11     apf fields, 15.3.11
undo, 3.6.2.9, 4.7, 10.4.11, 15.5.5     chemical space, 10.27
     redo, 15.5.5     ligand strain, 15.3.10
uniprot, 4.2.6, 8.5vls, 12.2, 12.2.3, 13, 13.1, 13.1.6, 13.1.7.2, 13.1.9.6, 13.3, 20.11.2, 21.5.7, 21.5.8, 21.5.24
unique, 10.3.28, 10.30     analysis, 13.1.9.6
unit, 5.3.3          display, 13.1.9.5
units, 21.5.1     command line, 13.1.7.2
unix, 21.10.2     getting started, 13.1.2
unsatisfied hydrogen bonds, 15.3.8     histogram, 13.1.9.3
     hyrdrogen bonds, 15.3.8          scatter plot, 13.1.9.2
unusual peptide, 4.3     introduction, 13.1.1
upload, 18.2     preferences, 13.1.4
use activeicm, 7.12     results, 13.1.8
user, 10.10.5, 18.5     run, 13.1.6
     defined groups, 15.5.3     scatterplot, 13.1.9.4
     modifiers, 15.5.3     score, 12.1.1.3
user-defined groups, 10.4.5     visualization, 13.1.10
uundisplay-all, 3.6.3.1     results, 13.1.8
van der waal, 6.8.14volume, 10.4.9
variable, 4.7.7, 21.2.8water, 9.20.17
verbose, 10.20waters, 9.20.17
     large sdf files, 10.1.2wavefront, 3.7.6, 6.3.11
vicinity, 10.20weak, 21.4.20
video, 2, 6.16, 6.16.1, 6.16.2web, 20.2
view, 3.6.3.19, 7.3.1, 10.3.28, 21.2.22, 21.9.8     browser, 3.6.1.12
     animate view, 3.6.3.15weight, 10.11, 21.8.7, 21.8.10
     center, 3.6.3.20weighted, 16.7.1
     color background, 3.6.3.18width, 16.1.22
     dock results, 12.1.12window, 4.1.13
     fog, 3.6.3.5windows, 4.1.13.1, 10.10.1
     macroshape, 3.6.3.22wire, 3.7.1, 4.7.5, 6.1.1, 21.2.4, 21.2.21
     menu, 3.6.3wireBondSeparation, 4.7.1
     mesh clip, 6.13.1working directory, 21.5.23
     perspective, 3.6.3.9workspace, 4.1.4, 5.1.3.1, 10.7.2
     selection level, 3.6.3.3     panel, 4.1.4
          mode, 3.6.3.4     selection, 4.6.9
     shadow, 3.6.3.13     navigation, 4.6.10

     alignment, 8.7.3 
     excel, 10.2.3 
     image, 3.6.1.15, 21.1.20 
     images, 6.15 
     pdb, 4.5 
     image, 3.6.1.15 
     object, 4.1.9 
     picture, 3.6.1.15 
     project, 3.6.1.8, 4.1.10 
     table, 16.1.3 
writing a pdb file, 21.4.3 
     ray, 3.6.5 
xi, 6.8.5, 21.2.18 
xls, 10.2.3 
xlsx, 10.2.3 
xml, 18.2 
xstick, 6.1.2, 21.2.21 
xyz, 21.2.10 
youtube, 2 
zoom, 4.1.3, 6, 6.12, 6.12.4, 10.3.30, 16.4.17 

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