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Contents
 
Help Videos
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Cheminformatics
Learn and Predict
Molecular Dynamics
MolScreen
3D Ligand Editor
Tables and Plots
Local Databases
KNIME
Tutorials
 
Index

Index

2D, 5.8.8, 7.3.24, 7.3.28, 7.14, 7.20.2, 7.20.4Drug Bank, 3.2.8
     Chemical Label, 5.8.11Editor, 3.7.2
     Interaction Diagram, 11.3.7FILTER.Z, 3.7.2
     bioisostere, 7.9.1     gz, 3.7.2
     chemical label, 5.8.11     uue, 3.7.2
     from PDB, 7.1.1FTP.createFile, 3.7.11
     interaction diagram, 7.6     keep File, 3.7.11
     screening, 10     proxy, 3.7.11
     to 3D, 7.20, 7.20.3Filter.zip, 3.7.2
     depiction, 7.20.2Force Auto Bond Typing, 3.7.11
3D, 5.6, 5.8.8, 7.1.3, 7.3.24, 7.3.28, 7.3.31, 7.20.2, 15.2Free Wilson, 7.36.2
     QSAR, 7.38.4, 8.4, 15.8GIF, 2.6.1.15, 5.16, 5.16.2
     chemical, 7.4.16, 7.20.1GINGER, 7.23
     interactive ligand editor, 2.7.5GRAPHIC.store Display, 3.7.3
     ligand editor, 11.3.4     NtoC Rainbow, 3.7.4
     object, 5.3.9     alignment Rainbow, 3.7.4
     pharmacophore, 11.3.11     atomLabelShift, 3.7.7
     print, 5.7     ballStickRatio, 3.7.1
     printing, 5.7     center Follows Clipping, 3.7.3
     screening, 10     clash Style, 3.7.3
     stereo, 5.6     clashWidth, 3.7.3
3DMOLT, 13.5     clip Grobs, 3.7.3
3DQsar, 8.4          Skin, 3.7.3
3D_Similarity_PDB_Search, 4.6          Static, 3.7.3
3Dqsar tutorial, 15.8     discrete Rainbow, 3.7.4
     bioisostere, 7.9.2     displayLineLabels, 3.7.7
     predict local flexibility, 4.5.13     displayMapBox, 3.7.3
          protein health, 4.5.12     distance Label Drag, 3.7.1
          tools identify ligand binding pocket, 4.5.15     dnaBallRadius, 3.7.9
               oda, 4.5.14     dnaRibbonRatio, 3.7.9
4D dock, 11.15     dnaRibbonWidth, 3.7.9
     docking, 3.2.2     dnaRibbonWorm, 3.7.9
APF, 7.37.4, 7.37.7, 7.38.4, 8.4, 10, 10.6, 15.8     dnaStickRadius, 3.7.9
     template, 7.37.3     dnaWormRadius, 3.7.9
ActiveICM, 2.6.1.12     font Scale, 3.7.7
Atom Single Style, 3.7.3     fontColor, 3.7.7
Atomic Property Fields, 8.4, 15.8     fontLineSpacing, 3.7.7
Baell, 7.4.9     grobLineWidth, 3.7.3
Beep, 3.7.11     hbond Ball Period, 3.7.1
BlastDB Directory, 3.7.2               Style, 3.7.1
     alphas, 5.8.3     hbondAngleSharpness, 3.7.1
COLLADA, 2.6.1.7     hbondMinStrength, 3.7.1
CPK, 2.7.1     hbondStyle, 3.7.1
ChEMBL, 3.2.3, 7.1     hbondWidth, 3.7.1
Chemical Cluster, 15.4.3     hetatmZoom, 3.7.1
     Search, 15.4.2     hydrogenDisplay, 3.7.1
Clash Threshold, 3.7.10     light, 3.7.3
DNA, 3.3     lightPosition, 3.7.3
Decomposition, 7.36.3     mapLineWidth, 3.7.3
Dock Directory, 3.7.2     occupancy Radius Ratio, 3.7.3
     quality, 3.7.3ICM Browser How To, 2.1
     rainbow Bar Style, 3.7.4          Pro How To, 2.2
     resLabelDrag, 3.7.7IMAGE.bondLength2D, 3.7.6
     resize Keep Scale, 3.7.3     color, 3.7.6
     ribbonRatio, 3.7.9     compress, 3.7.6
     ribbonWidth, 3.7.9     gammaCorrection, 3.7.6
     ribbonWorm, 3.7.9     generateAlpha, 3.7.6
     rocking, 3.7.4     lineWidth, 3.7.6
          Range, 3.7.4     lineWidth2D, 3.7.6
          Speed, 3.7.4     orientation, 3.7.6
     selectionStyle, 3.7.3     paper Size, 3.7.6
     site Label Drag, 3.7.7     previewResolution, 3.7.6
               Shift, 3.7.7     previewer, 3.7.6
     siteArrow, 3.7.7     print, 3.7.6
     stereoMode, 3.7.3     printerDPI, 3.7.6
     stickRadius, 3.7.1     scale, 3.7.6
     surfaceDotDensity, 3.7.3     stereoAngle, 3.7.6
     surfaceDotSize, 3.7.3     stereoBase, 3.7.6
     surfaceProbeRadius, 3.7.3     stereoText, 3.7.6
     transparency, 3.7.3INCHI, 7.20.3
     wire Width, 3.7.1IQR, 12.4.6
     wormRadius, 3.7.9Icm Prompt, 3.7.10
     xstick Backbone Ratio, 3.7.1InChi, 7.3.20, 7.4.12, 7.20.3
          Hydrogen Ratio, 3.7.1     key, 7.3.20
          Style, 3.7.1Interaction Diagram 2D, 11.3.7
          Vw Ratio, 3.7.1     Directory, 3.7.2
GROB.arrowRadius, 3.7.3JPEG, 2.6.1.15
     atomSphereRadius, 3.7.3KMZ, 2.6.1.7
     contourSigmaIncrement, 3.7.3Log Directory, 3.7.2
     relArrow Size, 3.7.3LogP, 8, 12.6
     relArrowHead, 3.7.3LogS, 8, 12.6
GUI.auto Save, 3.7.4MD, 9, 9.1, 9.2, 9.3, 9.4
               Interval, 3.7.4MOL, 7, 7.3.3, 7.3.24, 7.3.25, 7.3.26, 7.3.27, 12.2
     enumeration Memory Limit, 3.7.11MOLT, 13.1
     max Nof Recent Files, 3.7.11MOVIE.frame Grab Mode, 3.7.4
          Sequence Length, 3.7.4MPO, 7.34
     splash Screen Delay, 3.7.11Map Atom Margin, 3.7.10
               Image, 3.7.11     Sigma Level, 3.7.10
     table Row Mark Colors, 3.7.4Markush, 15.4.9
     workspace Folder Style, 3.7.4     create, 15.4.7
     workspaceTabStyle, 3.7.4     File Size Mb, 3.7.11
GigaScreen, 13.5Max_Fused_Rings, 7.11
HTTP.proxy, 3.7.11Mnconf, 3.7.10
     support Cookies, 3.7.11Model, 8.4
     user Agent, 3.7.11MolPSA, 7.11
Hbonds, 11.3.4MolScreen, 10
How To Guide, 2MolVol, 7.11
Html, 3.2.1.6Molcart, 7.5.3
Http Read Style, 3.7.11MoldHf, 7.11
Hydrogen.bond, 3.7.5Movie.fade Nof Frames, 3.7.4
          Auto, 3.7.4R, 7.8, 7.36.1
Nof_Atoms, 7.11R-Group, 7.36.3
Nof_Chirals, 7.11R-groups, 11.5.3
Nof_HBA, 7.11REAL, 7.5.5
Nof_HBD, 7.11RIDE, 13.5
Nof_Rings, 7.11RIDGE, 13.5
Nof_RotBonds, 7.11RMSD, 4.4.2
Output Directory, 3.7.2RNA, 3.3
PAINS, 7.4.9, 7.11.3Ramachandran Plot, 4.5.9
     chemicals, 7.4.9Real Format, 3.7.10
PCA, 8.1, 8.5, 15.4.4     Label Shift, 3.7.7
     analysis, 7.29          Style, 3.7.7
PDB, 3.2.1.6, 4.1.2, 4.3.3, 4.6, 7.1.1, 11.18SALI, 7.36.5, 15.4.11
     Directory, 3.7.2SAR, 8, 10.6, 12.4.25, 12.6
          Style, 3.7.2     table, 7.36.3, 15.4.9
     link, 12.1.40SDF, 7, 7.3.24, 7.3.25, 7.3.26, 7.3.27, 12.2
     Search, 2.6.2.12, 2.6.2.13, 2.6.2.14, 2.6.2.15, 2.6.2.16SEQUENCE.site Colors, 3.7.4
          Field, 2.6.2.13SITE.label Style, 3.7.7
          Homology, 2.6.2.15     labelOffset, 3.7.7
          Identity, 2.6.2.14     wrap Comment, 3.7.7
          Sequence, 2.6.2.16SLIDE.ignore Background Color, 3.7.4
     convert, 4.1.2          Fog, 3.7.4
PFAM, 2.6.1.7SMILES, 7.1.2, 7.2.4, 7.4.12
PLOT.Yratio, 3.7.8Select Min Grad, 3.7.10
     color, 3.7.8Show Res Code In Selection, 3.7.7
     date, 3.7.8Special Cases, 7.34.1.1
     draw Tics, 3.7.8SureChEMBL, 3.2.4
     font, 3.7.8Swissprot, 2.6.1.7
     fontSize, 3.7.8     Dat, 3.7.2
     labelFont, 3.7.8     link, 12.1.40
     lineWidth, 3.7.8Temp Directory, 3.7.2
     logo, 3.7.8USER.email, 3.7.11
     markSize, 3.7.8     friends, 3.7.11
     orientation, 3.7.8     full Name, 3.7.11
     paper Size, 3.7.8     organization, 3.7.11
     previewer, 3.7.8     phone, 3.7.11
     rainbowStyle, 3.7.8Ultra Large Libraries, 13.5
     seriesLabels, 3.7.8Uniprot, 12.1.40
PLS, 8.1Van Drie, 7.36.5
PNG, 2.6.1.15, 3.1.14, 5.16, 5.16.2     Label Style, 3.7.7
PSA, 7.11.7Water Radius, 3.7.10
PowerPoint, 15.2Wilson, 7.36.2
Projects Directory, 3.7.2Wire Style, 3.7.1
Prosite Dat, 3.7.2XPDB Directory, 3.7.2
     Viewer, 3.7.2Xstick, 2.7.1
Pub Chem, 3.2.9a-bright, 2.7.2
PubMed, 3.2.1.7about model, 8.1.1
     Reference, 12.1.40acceptor, 7.4.9, 7.38.1
Pubchem, 3.2.9active, 6.7
QSAR, 8, 8.1, 12.6, 15.8activeICM, 6.8
     advanced, 6.14          cluster, 15.6.5
     background images, 6.15          consensus, 15.6.2
     control, 6.13          score, 15.6.3
activeicmjs, 6.16          screen, 15.6.4
activity, 8, 12.6          superposition, 15.6.1
     cliff, 7.36.5, 7.36.6, 15.4.11     alignment, 7.37.7
          tutorial, 15.4.11append, 12.1.44
add database, 7.10.3     table, 12.1.44
     new data, 7.3.7     rows, 2.6.10.7
     to table, 11.5.7applying prediction models, 8.2
adding fragment, 7.4.8area, 4.5.3, 4.5.14, 15.3.5
          in editor, 7.4.8aromatic, 7.3.28, 7.38.1
administration, 7.10.5arrange, 3.1.13.1
album, 5.15.3     window, 3.1.13.1
alias, 7.4.5as2_graph, 3.6.5
align, 3.1.11, 7.14assign, 5.1.3
     color 2D scaffold, 7.14     2D coordinates, 7.20.2
alignment, 7.37.5, 7.37.6atom, 3.7.5, 7.3.28
allosteric, 4.5.15atomLabelStyle, 3.7.7
alpha, 2.7.2atomic energy circles, 11.3.5
     channel, 3.7.6     property field, 7.37.5, 7.37.6, 11.3.11
ambient, 2.7.2               score, 7.38.2
amidinium, 7.15          fields, 4.4.6, 4.7, 7.38, 7.38.1, 7.38.3, 15.6
amino acid, 3.3attachment, 7.4.3, 7.5.1
     acids, 7.4.6     point, 7.35.4
anaglyph, 5.6author, 3.2.1.3
analysis, 2.6.4     close tree, 7.28.5
angle, 4.5.7, 4.5.8, 5.8.5, 5.9, 5.12.6, 7.16     play slide, 6.13
animate, 2.6.3.15, 5.10.7available properties, 7.11.1
     view, 5.10.7ave, 12.7.1
animation, 5.10.7.1, 5.10.7.2, 5.10.7.3, 5.10.7.4avi, 5.16, 5.16.2
     store, 5.10.7.4axes, 12.4.15
animations, 6axis, 12.4.11
annotate, 3.6.21, 7.13     options, 12.4.10
     by substructure, 7.13     grid, 12.4.10
     plot, 12.4.24     range, 12.4.10
antialias, 2.6.1.15, 2.6.3.10     title, 12.4.10
     lines, 2.6.3.17b-factor, 4.5.13, 15.3.10
     lines, 2.6.3.17backbone, 5.1.10
apf, 4.4.6, 4.7, 7.37.5, 7.37.6, 7.38, 8, 11.3.11, 11.17, 15.6, 15.6.1, 15.6.2, 15.6.3, 15.6.4, 15.6.5background, 5.4.2, 5.4.3
     flexible template, 7.37.6     images activeicm, 6.15
     pairwise, 7.37.5     image, 5.4.3
     super, 7.37.3backup, 2.6.2.11
     template, 11.12.3bad, 7.11
     tools, 7.38     groups, 7.4.9
          3DQSAR, 7.38.4ball, 3.7.5
          consensus ph4, 7.38.1     and stick, 2.7.1
          pairwise score, 7.38.2balloon, 12.4.26
          screen, 7.38.3bases, 7.4.6
     tutorial, 15.6basicsel, 3.6.2
bbb, 7.11.4          editor, 7.2.4
best, 7.3.34          image, 7.2.6
bicyclics, 7.4.6          table, 7.2.2
binding properties, 5.3.1     super, 7.37
bioinfo menu, 2.6.4     view, 7.3.28
bioisoester, 7.9chembl, 3.2.3, 3.2.4
bioisostere, 7.9, 7.9.1, 7.9.2, 11.8chemical, 7, 7.3.28, 7.3.30, 7.3.31, 7.3.34, 7.3.35, 7.4.10, 7.8, 7.10.4, 7.11.3, 7.20.2, 7.24, 7.35.4, 7.35.5, 7.37, 7.37.5, 7.37.6, 12.7.1, 15.4.4
biological, 4.3.3     clustering, 7.28, 7.28.6
biomolecule, 2.6.5, 4.3.3, 15.3.8, 15.3.12     dictionary, 7.4.4, 7.4.5, 7.4.6
blast, 3.2.5     draw, 15.4.1
     search, 3.2.5          spreadsheet tutorial, 15.4.1
blood brain barrier, 7.11.4     edit buttons, 7.4.11
bond, 4.2.3, 4.2.3.1, 4.2.3.2, 7.4.10     editor, 7.4, 7.4.8
     type, 7.7.1, 7.7.2, 7.7.3     fingerprint, 10
bonding, 5.1.8     fragments, 7.3.33
     preferences, 3.7.1     group, 7.4.5
box, 3.7.7, 5.8.16     groups, 7.4.5, 7.4.8
     size, 11.9.1     modifiers, 7.35.2
browse, 7.3.31     properties, 15.4.4
     mode, 7.3.31     right click, 7.4.3
     molt, 13.2     search, 7.5
build, 5.10.7.1          filter, 7.5.2
buttons, 6.14          text, 7.5.4
bye, 2.6.1.19     sketch, 15.4.1
     alpha, 5.1.10     space, 7.30
     trace, 5.1.10     spreadsheet, 3.2.3, 7.1.3, 7.3.1, 7.4.14, 15.4.1
ca-trace, 5.1.10          compare, 7.3.22
cache, 6.14.1          template, 7.3.2
calculate, 7.11     spreadsheets, 7.3
     properties, 7.11     substituent, 7.9
carboxylic acid, 7.15     substructure, 3.2.1.1
cartesian, 7.23     table, 11.10
cation, 4.2.5          display, 7.3.3
cavities, 4.5     tables, 12.2
     closed, 4.5.4     toxicity, 7.11.3
cell, 4.3.2     2D, 7.7
center, 2.6.3.20, 3.1.3, 5.12, 5.12.5, 11.3.13, 12.1.40     3D, 7.7
     on ligand, 11.3.13     append, 7.4.13
     and representative members, 12.7.2     clustering, 7.28, 7.28.1
change box size, 11.9.1     convert, 7.7, 7.7.1, 7.7.2, 7.7.3
     height of all rows, 12.1.7     draw, 7.4.1
     ligand, 11.5.1     duplicates, 7.3.21
     row height, 12.1.7     editor, 7.2, 7.2.2, 7.2.4, 7.2.5, 7.2.6
     selection, 3.6.7     load, 7.1
     speed range, 5.10.7.2     merge, 7.32
charge, 2.6.3.21, 5.8.2, 7.4.3, 7.5.1, 7.7.1, 7.7.2, 7.7.3, 7.38.1     new, 7.4.1
check box, 6.6.6     properties, 7.3.19
     export excel, 7.2.3     query, 7.4.3, 7.5.1, 7.5.3
     save, 7.2     read, 7.1
          3D, 7.2.5     save, 7.2, 7.2.2, 7.2.4, 7.2.5, 7.2.6, 7.4.13
     similarity, 7.4.3, 7.5, 7.5.1, 7.5.3     chemical, 7.3.35
     spreadsheet, 7.2, 7.2.2, 7.2.4, 7.2.5, 7.2.6, 7.3     surface by proximity, 5.3.3
     structure, 7.4.13               selection, 5.3.4
     superposition, 7.37.3, 7.37.7     table, 7.3.27
     table, 7.3, 12.2     2D sketch, 7.5.6.5
cheminformatics, 7, 7.3     background, 2.6.3.18, 5.4.2
     tutorials, 15.4     distance, 5.8.10
chemistry, 7.24     mesh, 5.3.9.3
     convert, 7.20     table, 7.3.27
          2dto3d, 7.20.1coloring, 5.4.1
     pca, 7.29column, 12, 12.1.6, 12.1.22, 12.1.25, 12.1.39, 12.1.40, 12.4, 12.4.1
     smiles, 7.20.3     annotation, 12.1.41
     duplicates, 7.33     order, 12.1.29
     remove.redundant, 7.33     plot, 12.4.6
chemspace append, 15.4.4.4     row width, 12.1.22
     build visualize, 15.4.4.1     statistics, 12.1.32
     compare, 15.4.4.8     visibility order, 12.1.28
     delete row, 15.4.4.3     color, 12.1.10
     distinguish, 15.4.4.7     hide, 7.3.8
     export, 15.4.4.5     show, 7.3.8
     project, 15.4.4.6combinatorial chemistry, 7.35
     select, 15.4.4.2     library, 15.4.8
chi, 5.8.5combine, 2.6.10.5
chiral, 7.25     display style, 3.7.9
chirality, 7.25common substructure, 7.37.1
clash, 3.7.5, 5.8.15compact tree, 7.28.5
classes, 7.3.28compare, 7.3.29, 7.31, 7.32
classification model, 10.5     table, 7.3.22
clear display and planes, 2.6.3.2     tables, 7.31
     selection, 3.6.6compatible, 2.6.1.10
     planes, 2.6.3.2complex, 7.6
click, 3.1.12, 5.11, 5.12compound, 3.2.1.3, 7.24, 12.2
clip, 5.3.10, 5.13.1compress, 3.7.6
clipboard, 5.15.3, 12.7.3compressed, 12.1.6
clipping planes, 5     table view, 12.1.6
     tool, 5.13conditions, 7.5.2
     tools, 5.13     gen, 7.23
clone, 2.6.1.2conformation, 7.23
close, 5.3.3, 5.3.4, 11.20conformational entropy, 7.27
     downstream cluster, 7.28.5conformers, 7.23
     project, 11.20connect, 5.3.9.1, 5.12, 5.12.7
     cavities, 4.5.15     object, 5.12.7
cluster, 12.7.1connectivity, 7.4.3, 7.5.1
     representative.center, 7.28.2consensus, 7.38, 15.6.2
clustering, 12.7, 15.4.3     pharmacophore, 7.38.1
cns, 7.34construct, 2.6.1.1, 5.10.7.1
collada, 2.7.6, 5.3.7     molecule, 2.6.1.1
color, 4.5.12, 5.3.2, 5.3.3, 5.3.4, 5.3.9.4, 5.4, 5.4.1, 5.8.2, 5.8.3, 7.3.35, 7.14, 12.1.45, 12.7.4     object, 2.6.1.1
     background, 5.4.2contact, 4.5, 4.5.3, 15.3.5
     by, 5.4     surface, 5.3.2
contour, 4.3.6, 4.3.7     fragments, 7.13
convert, 4.1.2, 7.20.1, 7.20.5     label, 5.8.8
     chemical, 7.3.24     rotation, 5.12.2
          2D 3D, 7.7customized MPO score, 7.34.1
          3D molecular editor, 7.4.16cut, 12.1.35
     local database, 2.6.1.6cys, 4.5.11
     pdb, 15.3.2cysteine reactivity, 4.5.11
          chem, 7.7.1database, 7.10, 7.35.4, 13.1
     local.database, 2.6.1.6decompose.library, 15.4.9
     smiles, 7.20, 7.20.3, 7.20.4decomposition, 7.35.4, 7.36.1, 12.4.25
converting pdb, 4.1.2default, 3.1.13
coordinates, 7.1.3delete, 2.6.2.1, 3.6.6, 6.6.8
copy, 7.3.25, 7.4.11, 7.4.18, 7.5.6.2, 12.1.35     all, 2.6.2.2
     cell, 12.1.36     column row, 12.1.38
     chemical, 7.3.25     label, 5.8.9
     paste row, 12.1.35     all, 2.6.2.2
     row, 12.1.36     angle.label, 5.9.4
     rows, 12.1.44     column, 12.1.38
     selection to table, 12.1.37     distance.label, 5.9.4
     chemical, 7.3.16     label, 5.8.9
covalent, 11.10.1     row, 12.1.38
     bond, 4.5.11     selection, 2.6.2.1
     docking, 11.16dendrogram, 7.30.1
cpk, 5.1.5density, 4.3.4, 4.3.6, 4.3.7
crash, 2.6.2.11depth, 5.3.12, 5.10.5
creat, 6.6.1dfa, 10.3.3
create, 12.1.1dfz, 10.3.2
     markush, 7.35.3dialog, 6.6.5
     new objects, 3.3diffuse, 2.7.2
cross section, 5.13dihedral, 4.5.8, 5.8.5
cryptic, 4.5.15     angle, 4.5
crystal, 4.3.2directories preferences, 3.7.2
crystallographic analysis, 4.3directory, 3.7
          biomolecule, 4.3.3dislay ligand receptor interaction, 7.6
          contour map, 4.3.6display, 3.1.4, 3.1.13.1, 3.7, 4.2.3, 4.2.3.1, 4.2.3.2, 5.8.15, 5.14, 7.25
          convert2grid, 4.3.7     chemical, 5.8.11
          crystallographic cell, 4.3.2     delete distances, 5.9.4
          load eds, 4.3.4     dihedral, 5.9.3
          maps cell, 4.3.5     distance restraints, 5.8.14
          symmetry packing, 4.3.1     distance2, 5.9.1
          tools, 15.3.8          angles, 5.9
     cell, 2.6.5     formal charge, 5.1.9
     neigbor, 4.3.1     gradient, 5.8.17
     neighbors, 2.6.5     hbonds, 11.3.4
crystallography, 4.3.4, 4.3.6, 4.3.7     hydrogen, 5.1.7
csv, 7.2.3, 12.1.2, 12.1.3, 12.1.21          atoms ligand editor, 11.3.3
current.slide, 6.13     mesh, 5.3.5
curves, 12.4.5     meshes, 5.3.8
custom, 5.12, 7.3.3, 7.37     options, 11.3
     actions, 12.1.40     planar angle, 5.9.2
     tether, 5.8.13draw, 7.4.18, 7.35.5
     toggle, 5.8.16     chemical, 7.4.1
     CPK, 5.1.5drop, 3.1.11, 6.6.4
     angle, 5.9.2drug, 7.11
     chemical, 7.3.3     bank, 3.2, 3.2.8, 7.1
     dihedral.angle, 5.9.3     like, 7.11.4
     distance, 5.8.10, 5.8.14, 5.9.1drugbank, 7.1
     electrostatic, 2.6.3.21druglikeness, 7.4.9
     energy.gradient, 5.8.17dsPocket, 3.1.8
     hydrogen, 5.1.7easy rotate, 2.6.3.12
          polar, 5.1.7ecfp, 8.3
     macroshape, 5.3.6edit, 4.2.3.1, 11.5.8
     meshes, 5.3.5     2D, 11.5.1
          and display.macroshape, 2.7.6     add sequence, 7.4.17
     molecule, 7.3.24     chemical moledit, 7.3.26
     origin, 5.8.12     ligand, 11.5, 11.5.1
     potential, 2.6.3.21          2D, 11.5.1
     representations, 2.7.1          editor preferences, 11.2
     restraints, 5.8.14          multiple substituents, 11.5.2
     ribbon, 5.1.3          tools, 2.6.2.17
     skin, 5.1.4     menu, 2.6.2
     surface, 5.1.6, 5.3.1     molecular document, 6.6.1
     surfaces, 2.7.6     molecule, 7.4
     table, 7.3.3     molt, 13.3
     tethers, 5.8.13     selection, 2.6.2.5
     wire, 5.1.1     slide, 6.4.1
     xstick, 5.1.2     table row, 12.1.24
distance, 4.5, 4.5.6, 5.8.10, 5.9, 7.31     molecule, 7.3.26
     label, 3.7.7     structure, 7.3.26
distances, 2.7.3editpdbsearch, 2.6.2.12
diverse set, 12.7eds, 4.3.4, 4.3.6, 4.3.7
dock, 11.10, 11.10.1effort, 7.23, 7.37
     apf, 11.17electron, 4.3.4, 4.3.6, 4.3.7
     table, 11.10     denisty map, 4.3.5
          covalent, 11.10.1     density map, 2.6.1.7, 2.6.5, 4.3.4, 4.3.6
docking, 4.5.14, 11.10, 11.10.1, 11.11               contour, 2.6.5
     templates, 11.12.3electrostatic potential, 2.6.3.21
document, 6.6.4, 6.6.5     surface, 5.3
     navigation, 6.6.7electrostatics, 5.3.1
documents, 5.15.3elegant sketch, 5.10.4
donator, 7.4.9element, 7.4.10
     envelope, 2.7.1embed browser, 6.11
     surface, 3.7.5     powerpoint03, 6.8
dotted line, 5.1.3     powerpoint07, 6.9
double, 7.4.10     powerpoint10, 6.10
doublet, 7.4.7     activeicm, 6.13
dpc, 10.3.4          script, 6.13
drag, 3.1.11, 3.7.7, 5.8.3, 6.6.4     browser, 6.7, 6.11
     residue label, 2.6.3.16     firefox, 6.7, 6.11
draganddrop, 3.1.11     internet.explorer, 6.7, 6.11
     powerpoint, 6.7, 6.8, 6.9, 6.10     docking, 11.13
enamine, 7.5.5     receptor groups, 11.13
energy, 4.5.12, 5.8.15, 7.27, 7.27.2fog, 2.6.3.5, 5, 5.10.1
entropy, 7.17, 7.27.1font, 3.7, 3.7.7, 4.2.3.1, 5.8.2, 5.8.3, 7.3.28, 12.1.40, 12.7.4
enumerate formal charge states, 7.18     preferences, 3.7.7
     reaction, 15.4.10form view, 12.1.5
enumeration, 7.35.4formal charge, 5.1.9, 7.15, 7.18
eps, 7.2.6format, 12.1.2, 12.1.40
eraser, 7.4.11formula, 7.4.9, 7.11
evaluate score strain, 11.4fragment, 7.3.35, 7.36.1, 11.11
exact, 7.31     linking, 11.11
excel, 7.2.3fragments, 7.8
exclude fragment, 7.5.2free radical, 7.4.7
     volume, 11.3.11     wilson regression analysis, 7.36.2
exit, 2.6.1.19freeze column, 12.1.30
explicit, 7.3.28     row, 12.1.31
export, 4.5.10frequency, 7.3.35
     dock project, 11.19front, 5.3.10, 5.13.1
     pdb, 3.5full scene antialias, 2.6.3.10
extra windows, 5.2     screen, 2.6.3.8
extract, 3.4.2, 7.1.3function, 12.1.26, 12.1.32
     2D, 7.1.1functional.groups, 7.13
     3d coordinates to spreadsheet, 7.1.3general preferences, 3.7.5
     icb, 2.6.1.5generalselecttools, 3.6.1
     object icb, 3.4.2generator, 4.3.3, 7.23
     icb, 2.6.1.5getting started, 3
     pharmacophore, 7.5.6.4giga search, 7.5.5
file, 2.6.1.3          enamine, 7.5.5
     close, 2.6.1.13ginger, 7.23
     compatible, 2.6.1.10glasses, 5.6
     export, 2.6.1.12google, 2.6.1.7
     high quality image, 5.15.1     objects, 5.3.7
     load, 2.6.1.7     3D, 2.7.6, 5.3.7
     menu, 2.6.1graphical display, 7.7.2, 7.7.3
     password, 2.6.1.11          tutorial, 15.1
     preferences, 2.6.1.16               2D3D labels, 15.1.4
     quick image, 2.6.1.14               annotation, 15.1.2
     icb, 3.1.10               color representation, 15.1.1
     recent, 2.6.1.17               labels, 15.1.3
     bak, 2.6.2.11graphics, 3.1
filter, 13.2     controls, 5
     selection, 3.6.8     effects, 5.10
find chemical, 7.3.32     panel, 5.2
fingerprint, 8, 8.3, 15.7     preferences, 3.7.3
     method, 8.3     shadow, 2.6.3.13, 5.10.2
fit, 7.3.34grid, 7.3.3, 7.37
fitting, 12.4.16grob, 3.7.5, 4.3.4, 4.3.6, 4.3.7, 5.3
flexibility, 4.5.13group, 7.36.1, 11.6
flexible, 7.37     column, 12.1.46
     APF superposition to template, 7.37.4groups, 7.8, 7.11, 7.12
gui, 3.1.1, 3.7.4          structure, 15.4.7
     menus, 2.6     merge tables, 7.3.23
     preferences, 3.7.4     properties, 7.3.19
     tabs, 2.7     reactions, 15.4.10
h-bond, 4.2.3, 4.2.3.1, 4.2.3.2     reorder, 7.28.3
halogen, 7.11.2     sdf, 7.3.9
hardware stereo, 2.6.3.7     show hide, 7.3.8
hbond, 4.2, 15.3.6     sort column, 7.3.5
header, 3.2.1.6, 12.4.9     standardize, 7.3.18
health, 4.5.12     table hyperlinks, 7.3.15
heatmap, 12.4.7          print, 7.3.11
     example, 12.4.7.1          activeicm, 2.3
help, 1               create molecular documents, 2.3.3
     videos, 1                    slides, 2.3.2
hetero, 7.3.28               getting started, 2.3.1
     scan, 11.7               ppt, 2.3.4
hide, 12.1.39               web, 2.3.5
     column, 12.1.28          chemical clusering, 7.28.1
high, 2.6.1.15          icm browser convert display pocket, 2.1.4
     quality, 2.6.3.11                    distances angles, 2.1.9
highlight new data, 7.3.7.1                    get started, 2.1.1
histogram, 12.4, 12.4.1, 12.4.9, 12.4.11, 12.4.13, 12.4.14, 12.4.15, 12.4.16, 12.4.17, 12.4.18, 12.4.20, 12.4.22                    graphical display, 2.1.2
     bins, 12.4.3                         effects, 2.1.5
     options, 12.4.2                    images, 2.1.7
     bin.size, 12.4.2                    labels annotation, 2.1.6
     bins, 12.4.3                    pro crystallographic tools, 2.2.6
     color, 12.4.2                         get started, 2.2.1
     source, 12.4.2                         graphics, 2.2.2
     style, 12.4.2                         plots, 2.2.8
     title, 12.4.2                         sequence analysis, 2.2.7
historeceptomics, 3.2.10                         structure analysis, 2.2.3
hitlist, 9.4                         superimpose, 2.2.5
homology, 3.2.1.2, 3.2.5                         surfaces, 2.2.4
hover, 12.4.26                    selections, 2.1.3
     3D editor, 15.5                    superimpose, 2.1.8
     add columns, 7.3.4          search, 3.2
     cluster center, 7.28.2          use gui, 3.1
     color 2D by ph4, 7.5.6.5html, 2.6.1.12, 3.3, 6.6.1, 6.6.7
     copy 2D, 7.3.16hybridization, 7.4.3, 7.5.1
          paste, 7.3.6hydrogen, 4.2.3, 4.2.3.1, 4.2.3.2, 5.1.8, 7.4.3, 7.5.1, 15.3.6
     decompose, 15.4.9     atom display, 11.3.3
     duplicate chemicals, 7.3.21     bond, 4.2, 5.1.8, 7.6, 15.3.6
     edit table, 7.3.17          donor, 7.38.1
          tree, 7.28.4          label edit, 4.2.3.1
     excel, 7.3.10               move, 4.2.3.2
     extract 3D ph4, 7.5.6.4     bonds, 4.2.4
     filter, 7.3.12     bond, 7.4.9
     find replace, 7.3.13hydrogens, 7.3.28
     mark row, 7.3.14     remove, 7.3.18
     markush, 15.4.8hyperlink, 6.6.1, 6.6.2, 12.1.40
iSee, 2.6.1.5, 2.6.1.12, 3.1.10, 5.15.3, 15.2isee, 6.6.5
icb, 3.4.2, 3.5isis, 7.4.18
     chemist howto chemical search, 2.4.3isotope, 7.4.3, 7.5.1
               cluster, 2.4.5iupac, 7.2.7, 7.3.20
               combi library, 2.4.7javascript, 6.16
               ph4, 2.4.4join, 7.32
               plots, 2.4.8jpg, 5.15
               sketch, 2.4.1     means, 12.7.1
               spreadsheets, 2.4.2kcc, 10.3.1, 10.5
               stereoisomers tautomers, 2.4.6kernel regression, 10.3.1
          pro 3D ligand editor, 2.5.1     chemical, 7.4.10
               chem3D, 2.5.2keyboard mouse, 5.11
               chemsuper, 2.5.4keystokes in chem-edit, 7.4.10
               energy, 2.5.3kmz, 2.7.6, 5.3.7
               qsar, 2.5.5knime, 14
               tutorials, 2.5label, 3.7.7, 12.7.4
          tutorials, 2.4     atoms, 5.8.2
     object, 4.1, 15.3.2     color, 5.8.7
     script, 12.1.40     move, 5.8.4
icmPocketFinder, 4.5.15     residues, 5.8.3
icmjs, 6.16     sites, 5.8.6
icmpocketfinder, 15.3.7     variables, 5.8.5
id, 12.1.27     2D, 2.7.3
identity, 3.2.1.2     3D, 2.7.3, 5.8.1
image, 3.1.14, 3.7, 3.7.5, 5.15.3, 6.6.3, 7.2, 7.2.6, 12.4.21     atom, 5.8.1
     advanced, 5.15.3     atoms, 5.8.2
     preferences, 3.7.6     color, 5.8.7
     multiple, 2.6.1.7     custom, 5.8.8
     quality, 2.6.3.11     delete, 5.8.1, 5.8.9
     quick, 2.6.1.14, 5.15.2     distance, 5.8.10
images, 5.15     drag, 2.6.3.16
inchi, 7.20.3     move, 2.6.3.16, 5.8.4
increment, 12.1.27     residue, 5.8.1
     id, 12.1.27     residues, 5.8.3
index models, 10.1.2     site, 5.8.1
induced fit, 11.13     sites, 5.8.6
insert, 6.6.4     variable, 5.8.1
     column, 12.1.26     variables, 5.8.5
     image, 6.6.3, 12.1.34labeling, 5.8.1
          table, 12.1.34labels, 5.8, 7.3.28
     row, 12.1.33     distances, 5.8.10
     script, 6.6.4     tab, 2.7.3
install, 7.10.1landscape, 3.7.6
interaction, 4.5.3, 7.6large chemical space, 15.4.4
interactions, 11.3.12     sdf, 7.1.2
interactive, 15.2layer, 5.14
interrupt, 5.10.7.3layers, 5.14
     animation, 5.10.7.3learn, 7.21, 7.22, 8, 8.1, 12.6
invert selection, 12.1.23learning, 8
iqr, 12.4.23     theory, 8.5
library, 7.35.4     nmr model, 3.2.1.4
     reaction, 15.4.10     protein structure, 4.1.1
ligand, 4.2.2, 7.6, 7.27, 7.27.1, 7.27.2, 11.3.12, 11.3.13, 11.5.8, 11.10, 11.11local databases, 13
     based screen, 7.38.3     database.browse, 13.2
     best replace, 11.6          edit, 13.3
     code, 3.2.1.3, 3.2.7          query, 13.4
     editor, 11, 11.10, 11.10.1, 11.16, 11.17          row, 13.3
          bioisostere, 11.8lock, 5.3.10, 5.13.1, 7.3.31
          covalent docking, 11.16log, 12.4.6, 12.4.11
          mrc, 11.15logD, 7.11.6
          preferences, 2.6.2.18logP, 7.4.9, 7.11
     energetics, 7.27logS, 7.4.9, 7.11
          conformational entropy, 7.27.1logarithmic, 12.4.11
          strain, 7.27.2logout, 2.6.1.19
     pocket, 4.2.4mac, 7.10.1
          surface, 11.3.2machine learning, 15.7
     receptor contacts, 11.3.12macros, 6.14
          display, 4.2macroshape, 2.6.3.22, 5.3, 5.3.6
          interaction, 7.6make, 5.10.7.1, 12.1.1
     strain, 11.3.10     animation, 5.10.7.1
     surface, 4.2.2     apf docking sar model, 10.6
     tether, 11.12     complex, 11.20
     editor, 11, 11.1     molecular document, 6.6
          binding.re-dock ligand, 11.9     molt, 13.1
          display, 11.3     selection, 3.6
          edit, 11.5     molecule, 2.6.1.1
          energy, 11.3     object, 2.6.1.1
          hydrogen.bond, 11.3making molecular slides, 6.1
          pocket, 11.3     html, 6.6
          preferences, 11.2manual change torsion, 11.5.4
          restraint, 11.12map, 3.7.7, 4.3.4, 4.3.6, 4.3.7
          surface, 11.3     cel, 4.3.5
          tether, 11.12mark, 12.1.45
     pocket, 3.1.8     row, 12.1.45
     receptor.contact, 4.5.3     color, 12.4.14
ligand_pocket_interactions, 4.2.4     shape, 12.4.13
ligedit distance restraint, 11.12.2     size, 12.4.13
     tab, 2.7.5markush, 7.28.7, 7.35.1, 7.35.3, 7.36.1
     tether, 11.12.1     library, 15.4.8
light, 2.7.2matched pair, 7.36.6, 15.4.11
     tab, 2.7.2          analysis, 7.36.6
lighting, 5.3.9.4, 5.5materials, 2.7.6
likeness, 7.11max, 12.7.1
line, 3.7.5, 12.7.4maxColorPotential, 3.7.10
lineWidth, 3.7.3maximum common substructure, 7.28.6, 7.30, 7.30.1
links, 3.6.20               dendrogram, 7.30.1
linux, 7.10.1mcs, 7.28.6, 7.30.1
lipinski rule, 7.34     rgroup decomposition, 7.28.7
list, 3.6.18mean, 12.4.6, 12.4.23
load, 2.6.1.3, 2.6.1.17, 4.3.4, 4.3.6, 4.3.7median, 12.4.6, 12.4.23
memory, 7.1.2moledit, 7.4.8
menu, 6.6.5molscreen, 10
     chemistry, 2.6.14     custom model panel, 10.4
     docking, 2.6.15     load models, 10.1.1
     homology, 2.6.13               run, 10.1
     molmechanics, 2.6.16     model type, 10.3
     tools chemical search, 2.6.11     results, 10.2
          molecular editor, 2.6.12molskin, 5.3.2
     windows, 2.6.17molsynth, 7.11.5
merge, 7.32molt, 13, 13.4
     two sets, 7.32monochrome, 7.3.28
mesh, 4.2.1, 4.2.2, 4.3.4, 4.3.6, 4.3.7, 5.3, 5.3.9.1, 5.3.9.2, 5.3.9.4, 5.3.10, 5.3.11, 5.3.12, 5.13.1mouse, 3.1.3, 5.11, 5.12
     clip, 5.3.10mov, 5.16, 5.16.2
     color lighting, 5.3.9.4move, 2.6.3.19, 3.1.11, 3.1.13, 4.2.3.2, 5.3.9.1, 5.3.9.2, 5.12, 5.12.7
     options, 5.3.9     column, 12.1.28
     representation, 5.3.9.3     mesh, 5.3.9.2
     save, 5.3.11     slide, 6.4.2
     options, 5.3.9     structure, 5.12
meshes, 5.3.2, 5.10.5     tools, 5
     surfaces grobs, 5.3     rotate, 5.11
     tab, 2.7.6     slab, 5.11
metabolic oxidation, 10.7     translate, 5.11
min, 12.7.1     z-rotation, 5.11
mmff, 7.4.16     zoom, 5.11
     type, 5.8.2movie, 5.16.1
mmp, 15.4.11     making, 5.16, 5.16.2
mnSolutions, 3.7.10     open, 5.16, 5.16.2
model weight, 8.1.2mpa, 15.4.11
modification history, 11.5.6mpeg, 5.16, 5.16.1, 5.16.2
mol, 7.2, 7.2.2, 7.2.4, 7.2.5, 7.2.6, 7.4.13mpg, 5.16, 5.16.2
mol2, 7.2, 7.2.2, 7.2.4, 7.2.5, 7.2.6mpo, 7.34
molcart, 7.10, 7.10.1, 7.10.2, 7.10.3, 7.10.4, 7.10.5, 13     binary classification, 7.34.2
     add database, 7.10.3     custom step function, 7.34.1.2
     administration, 7.10.5     customized, 7.34.1
     installation, 7.10.1     save, 7.34.1.3
     search, 7.10.4     special cases, 7.34.1.1
     start, 7.10.2mtl, 5.7
molecular, 7.3.30, 7.3.31, 7.3.34, 7.3.35, 7.23multi apf super, 7.37.7
     animations slides, 6     panel, 5.2
     documents, 15.2     parameter optimization, 7.34
     dynamics, 9, 9.1, 9.2, 9.3, 9.4     windows, 5.2
          membrane, 9.3multiple position group scan, 11.7
          restraints, 9.2     receptor, 3.2.2
          run, 9.1          docking, 11.15
          vls, 9.4navigate workspace, 3.6.10
     graphics, 5neural network Torsion Profile Neural Network Prediction Engine, 5.12.6.1
     matched pairs, 15.4.11     icm session, 2.6.1.2
     table, 7.20.2     table, 12.1.1
     weight, 7.4.9     table, 12.1.1
     editor, 7.4nmr model, 3.2.1.4
nntorsion, 5.12.6.1pdbsearchfield, 2.6.2.13
nof, 7.11.2pdbsearchhomology, 2.6.2.15
     chemical, 7.11.2pdbsearchidentity, 2.6.2.14
non-contiguous selection, 3.6.18pdbsearcsequence, 2.6.2.16
number of sp3, 7.11.2peptide, 3.3
numbers, 7.3.28perspective, 2.6.3.9, 5.10.6
obj, 5.7ph4, 7.5.6
object, 3.1.11, 3.5, 15.3     draw 2d, 7.5.6.1
objects, 4.1.2          3d, 7.5.6.2
     in table, 12.3     search, 7.5.6.3
     in.table, 12.3pharmacophore, 7.3.35, 7.5.6.5, 15.6.2
occlusion, 5.3.12, 5.10.5     2D, 15.4.6
     shading, 5.3.12     3D, 15.4.5
          effect, 5.10.5     clone, 7.5.6.2
occupancy, 5.1.3, 15.3.10     draw2D, 7.5.6.1
     display, 3.2.1.5     draw3D, 7.5.6.2
oda, 4.5.14     edit, 7.5.6.1, 7.5.6.2
older version, 2.6.1.10     move, 7.5.6.2
omega, 5.8.5     new, 7.5.6.2
online databases, 7.5.5     search, 7.5.6, 7.5.6.3, 15.4.5, 15.4.6
open, 2.6.1.3, 3.4, 12.1.2phi, 5.8.5
     file, 3.4pi, 4.2.5
     password, 3.4.1     cation, 4.2.5
     with password, 2.6.1.4     pi, 4.2.5
     movie, 5.16, 5.16.2picking, 5
     password, 2.6.1.4, 3.4.1picture, 2.6.1.14, 3.1.14, 5.15.2, 6.6.3
optimal, 4.5.14     tips, 3.1.14
orange, 3.6.5     chart, 12.4.8
     selection, 3.6.5pipi, 4.2.5
origin, 5.8.12pka, 7.15
orthosteric, 4.5.15planar, 4.5.7, 5.8.5
other selection, 3.6.19     angle, 4.5
overlay, 15.3.3     angle, 5.9.2
pH, 7.19plane, 5.3.10, 5.13, 5.13.1, 5.14
package.activeicm, 6.13plot, 3.7, 3.7.8, 12.4, 12.4.1, 12.4.4, 12.4.9, 12.4.11, 12.4.13, 12.4.14, 12.4.15, 12.4.16, 12.4.17, 12.4.18, 12.4.20, 12.4.21, 12.4.22, 12.4.23
packing, 4.3.1     R group sar, 7.36.4
pairwise, 7.37.5, 7.37.6     axis, 12.4.11
     apf score, 7.38     color, 12.4.14
password, 7.10.5     columns, 12.4.6
paste, 7.4.11, 7.4.18, 12.1.35     function, 2.6.9, 2.6.9.1
pca, 12.5     grid, 12.4.15
pdb, 2.6.1.7, 3.2, 3.2.1.1, 3.2.7, 3.5, 7.7.1, 15.3     header, 12.4.9
     chem gl, 7.7.3     inline, 12.4.22
          iw, 7.7.2     logarithmic, 12.4.12
     dormat, 3.5     mark, 12.4.13
     html, 3.2.1.6     mean median iqr, 12.4.23
     preparation, 15.3.11     point label, 12.4.19
     search, 3.2.1, 3.2.1.2, 3.2.1.3, 15.3.1     preferences, 3.7.8
     recent, 2.6.1.18          groups, 12.4.25
     search, 2.7.4, 3.1.2     regression, 12.4.16
     zoom translate, 12.4.17          analysis, 4.5
     axis, 12.4.15               closed cavities, 4.5.4
     display, 12.4.15               contact areas, 4.5.3
     grid, 12.4.15               distance, 4.5.6
     inline, 12.4.22               find related chains, 4.5.1
     logarithmic, 12.4.12               finding dihedral angle, 4.5.8
pls, 7.21, 7.22, 8, 12.6, 15.7                    planar angle, 4.5.7
png, 2.6.1.14, 5.15, 5.15.2, 6.6.3, 7.2, 7.2.6               rama export, 4.5.10
pocket, 3.1.8, 4.2, 4.2.1, 4.2.2, 4.5.15, 15.3.7               ramachandran plot, 4.5.9
     properties, 4.7               rmsd, 4.5.2
     surface, 4.2.1               surface area, 4.5.5
     peptide, 3.1.8          similarity, 4.6
     properties, 3.1.8          tutorials, 15.3
pocketome, 3.2, 3.2.2, 4.7               analysis, 15.3.4
pockets, 4.5.15               contact area, 15.3.5
point label, 12.4.19               convert, 15.3.2
portait, 3.7.6               hydrogen bond, 15.3.6
post edit ligand, 11.5.8               icmpocketfinder, 15.3.7
postscript, 3.7.6               search, 15.3.1
ppt, 6.12, 6.14               superimpose, 15.3.3
predict, 7.21, 7.22, 8, 8.2, 12.6     superposition, 4.4
     metabolic oxidation, 10.7          select, 4.4.1
predicting bioassays, 8.2          sites by apf, 4.4.6
     compound properties, 8.2          superimpose 3D, 4.4.3
preferences, 3.7               grid, 4.4.5
presentation, 6.6.5, 6.7, 6.12               multiple proteins, 4.4.4
presentations, 6protein-protein, 4.5.14
press-and-hold to rotate, 7.4.8protonation, 7.19
pretty view, 11.3.6protonation_ph, 7.19
primary aliphatic amines, 7.15protonation_ph_charge, 7.19.2
principal component analysis, 12.5protonation_ph_concentration, 7.19.1
          regression, 8proximity, 5.3.3, 5.3.4
     components, 8.5psa, 7.4.9, 7.11.7
print, 5.7, 12.4.20, 12.7.3psi, 5.8.5
     plot, 12.4.20pubchem, 7.1
printer.resolution, 3.7.6publication quality images, 5.3.2
pro-drug, 7.26pubmed, 3.2.1.7
prodrug, 7.26purple box, 2.6.3.23, 11.9.1
profile, 3.2.10qs hydrogen bond, 4.2.3
project, 2.6.1.5, 15.4.4.6qsar, 7.21, 7.22, 8.1, 15.7
     close, 2.6.1.13     learn predict, 7.21
     rename, 2.6.1.9     predict, 7.22
properties, 5.8.2, 7.11, 7.11.1quality, 2.6.1.15, 3.7.5
property, 7.4.9query molt, 13.4
     monitor, 7.4.9     processing, 7.5.3
protect, 6.6.8     setup, 7.5.1
protein, 4.4.6quick, 3.1.14
     health, 4.5.12     image, 5.15.2
     sequence, 7.4.17     start move structure, 3.1.3
     structure, 4          read pdb, 3.1.2
          selection, 3.1.5replacement, 11.6
               level, 3.6.3     group, 11.8
          what is selected, 3.6.4representation, 2.6.3.19
     display.distance, 5.9.1residue, 3.7.7
     start color, 3.1.7     alternative orientation, 15.3.11
quit, 2.6.1.19     range, 3.6.18
     group, 7.28.7, 7.35.4     content, 2.6.4
          table, 7.35.2residues, 4.2.1, 4.2.2
     groups, 7.35.2resize, 5.3.9.1, 5.15.3
r-group, 7.28.7, 7.35.2     mesh, 5.3.9.1
     decomposition, 7.28.7resolution, 3.2.1.3
     enumeration, 7.28.7restore, 2.6.2.11, 5.3.10, 5.13.1
r-groups, 12.4.25     recent backup, 2.6.2.11
racemic, 7.3.28, 7.20.5restraint, 11.12.1, 11.12.2
radar, 12.4.6restraints, 9.2
rainbow, 3.7.5, 5.8.16, 7.3.35rgroup, 7.35.4
ramachandran plot, 4.5, 4.5.10ribbon, 2.7.1, 3.7.9, 5.1.3
random forest, 8, 15.7     preferences, 3.7.9
range, 5.10.7.2     style, 3.7.9
ratio.selection, 3.7.5     breaks, 5.1.3
     dock ligand, 11.9     cylinders, 5.1.3
reactions, 7.8, 7.35.5     smooth, 5.1.3
reactive cysteine, 4.5.11     worm, 5.1.3
reactivity, 7.11.3ribbonColorStyle, 3.7.9
read, 2.6.1.3, 2.6.1.17, 3.4, 7.3.1right, 3.1.12
     chemical, 7.1     click, 3.1.12
          spreadsheet, 7.3.1rigid, 7.37
     table, 12.1.2     substructure superposition to template, 7.37.2
     pdb, 3.1.2ring, 4.2.5, 7.4.3, 7.4.6, 7.5.1
     table, 12     stacking, 4.2.5
reagent, 7.35.5rings, 7.3.28, 7.23, 7.37
rear, 5.3.10, 5.13.1rmsd, 4.5, 4.5.2
recent files, 2.6.1.17rock, 2.6.3.15, 5.10.7, 5.10.7.1, 6
     pdb codes, 2.6.1.18     speed, 5.10.7.2
receptor, 4.2.1, 4.2.2, 7.6, 11.3.12root mean square deviation, 4.5.2
     flexibility, 11.15rotate, 2.6.3.15, 3.1.3, 5, 5.10.7, 5.10.7.1, 5.12, 5.12.1, 5.12.2, 6, 7.3.34
     pocket, 11.3.1     chemical, 7.3.34
          surface, 11.3.1, 11.3.2     torsion, 5.12.6.1
recover, 2.6.2.11     when pasting, 7.4.8
redo, 2.6.2.10, 7.4.11, 11.5.5     easy, 2.6.3.12
regression, 7.36.2, 8.1, 8.5, 12.4.16, 15.7     speed, 5.10.7.2
relationship, 8, 12.6rotating fragment in editor, 7.4.8
relaxed ligand, 11.3.9rotation, 5.12.1
remove.explixit.hydrogens, 7.12row, 12, 12.1.22, 12.1.35, 12.1.45
     salt, 7.12     flag, 12.1.13
rename, 12.1.25     height, 12.1.7
     column, 12.1.25     mark, 12.1.13
     project, 2.6.1.9     hide, 7.3.8
reorder column, 12.1.29     show, 7.3.8
replace chemical, 7.3.32ruler, 5.8.16
rxn, 7.4.13     chembl, 3.2.3
sali, 7.36.5     drugbank, 3.2.8
     bridge, 15.3.6     filter, 7.5.2
salts, 7.3.18     in workspace, 2.6.2.4
sample, 7.37     pdb, 3.2.1
sar, 7.28.7, 7.36, 12.4.25          chemical, 3.2.1
     analysis, 7.36          ligand code, 3.2.7
     table, 7.36.3     pocketome, 3.2.2
save, 3.5, 5.3.11, 5.10.7.4, 7.2.3, 12.4.21, 12.7.3     pubchem, 3.2.9
     SMILES, 7.4.15     surechembl, 3.2.4
     as PDB, 3.5     tab field, 3.2.1.3
          pdb, 3.5          pdb chemical, 3.2.1.1
     chemical mol, 7.4.13               sequence, 3.2.1.2
          spreadsheet workspace, 7.2.1     tautomer, 7.5.3
          to chemical spreadsheet, 7.4.14     uniprot, 3.2.6
     docked ligand, 11.18     in.workspace, 2.6.2.4
     file, 3.5secondary aliphatic amines, 7.15
     hits, 11.5.7     structure, 2.6.4, 5.1.3
     image plot, 12.4.21select, 3.6.12, 3.6.13, 12, 12.1.45
     ligand receptor complex, 11.18     a tree branch, 12.7.2
     object, 3.1.9     all, 3.6.14
     pdb, 3.5     amino acid, 3.6.13
     project icb, 3.1.10     duplicates, 7.33
     slide, 6.4     molecule, 3.6.12
     smiles string, 7.4.15     neighbors, 3.6.15
     table, 12.1.21          graphic, 3.6.16
          spreadsheet, 11.5.7     object, 3.6.11
     tree, 12.7.3     residue, 3.6.13, 3.6.18
          sdf, 7.4.14          by number, 3.6.18
     image, 2.6.1.15, 3.1.14          number, 3.6.18
     object, 3.1.9     tree, 12.7.2
     password, 2.6.1.11     atom, 3.1.5, 3.6.3
     picture, 2.6.1.15     graphical, 3.1.5, 3.6.3
     project, 2.6.1.8, 2.6.1.9, 2.6.1.10, 3.1.10     object, 3.1.5, 3.6.3
     table.view, 12.1.8     purple.box, 2.6.3.23
saving, 2.6.1.8     residue, 3.1.5, 3.6.3
     project, 2.6.1.8     workspace, 3.1.5, 3.6.3
scaffold, 7.14selectall, 2.6.2.3
     hopping, 11.8selecting.neighbors, 3.6.16
scale, 3.7.5selection, 3.6.4, 3.6.5, 3.6.21, 5.3.4, 7.4.11, 12.4.18, 12.7.2, 12.7.4
     r group, 11.7     clear, 2.6.2.7
scan_pockets, 4.7     neighbors, 2.6.2.8
score, 11.4, 15.6.3, 15.6.5     alignment, 3.6.19
screen, 7.38, 15.6.4     all, 2.6.2.3
screening, 9.4     alter, 3.6.7
screenshot, 5.16, 5.16.2     atom, 2.6.2.5
     movie, 5.16.2     basic, 3.6.2
script, 3.3, 6.6.4, 6.6.5     change, 3.6.7
sdf, 7.2, 7.2.2, 7.2.4, 7.2.5, 7.2.6, 7.3.35, 7.10, 7.10.3, 7.20.1, 11.10, 13.1     clear, 2.6.2.7
search, 4.6, 7.10, 7.10.4, 13.2     column, 12.1.23
     graphical, 3.6.16     markush, 7.35.1
     invert, 2.6.2.6, 12.1.23     smiles, 7.4.12
     level, 2.6.3.3     accents, 2.6.3.14, 5.10.3
     mode, 2.6.3.4skin, 2.7.1, 5.1.4
     near atoms, 2.6.2.8slab, 5.3.10, 5.13.1
     neighbors, 2.6.2.5, 2.6.2.8, 3.6.15, 3.6.17slice, 5.13
     object, 3.6.11slide, 5.10.7.4, 6.2, 6.3.1, 6.6.1
     other, 3.6.19     effects, 6.5
     properties, 2.6.2.5     movie, 5.16.1
     range, 12.1.23          file, 6.2
     residue, 2.6.2.5     navigation, 6.3.2
     row, 12.1.23     show, 6.3
     sphere, 3.6.15     blend, 6.5
     spherical, 2.6.2.8     edit, 6.4.1
     superposition, 4.4.1     effect, 6.5
     table, 3.6.19, 12.1.23     smooth, 6.5
          elements, 12.1.23     transition, 6.5
     tools, 3.6.1, 3.6.2, 3.6.7, 3.6.8slides, 5.16.1, 6, 6.1, 6.3
     whole, 3.6.11smiles, 7.4.9, 7.11, 7.20, 7.20.3, 7.20.4
     workspace, 3.6.9, 3.6.17smooth, 5.3.9.3
selectioninvert, 2.6.2.6solid, 5.3.9.3
selections, 3.6sort table, 2.6.10.4
selectneighbors workspace, 3.6.17sorting compounds, 12.7
     organized network, 7.30sp3, 7.11.2
sequence, 2.6.4, 3.2, 3.2.1.2, 3.2.5, 3.2.6, 3.3, 7.4.17, 15.3spec, 2.7.2
     pattern, 3.2.1.2speed, 5.10.7.2
set, 7.3.31split, 7.36.1
     formal charges, 7.15spreadsheet, 7.20.2
setup ligand receptor, 11.1stacking, 4.2.5
shading, 5.3.12standard table, 12.1
shadow, 5.10.2standardize, 7.12
share model, 8.1.3     table, 7.12
shell preferences, 3.7.10start, 7.10.2
shift, 5.8.3stereo, 3.7.6, 5.6, 7.3.28, 7.4.2
shine, 2.7.2, 3.7.5     bond, 7.4.2
shineStyle, 3.7.3     hardware, 2.6.3.7
show, 6.3.1, 12.1.39     side-by-side, 2.6.3.6
     hide column, 12.1.39stereoisomer, 7.20.5
side, 7.3.29stereoisomers, 7.25
     by side, 7.3.29stick, 3.7.5
               stereo, 2.6.3.6stl, 5.7
     chain refinement, 11.14stop, 5.10.7.3
sigmaLevel, 4.3.6, 4.3.7store, 2.6.3.19, 5.10.7.4
similarity, 7.31     current view, 2.6.3.19
simulation, 9, 9.1, 9.2, 9.3, 9.4strain, 4.5.12, 5.12.6.1, 7.17, 7.27, 7.27.2, 11.4
single, 7.4.10structure, 4.3.3, 8, 12.6, 15.3
singlet, 7.4.7     analysis, 15.3.4
sites, 4.4.6     representation, 5.1
size, 4.2.3.1     smiles, 7.20.4
sketch accents, 5.10.3structures, 7, 7.1
substituent, 7.9.1, 7.9.2, 7.35.2, 11.5.2     search, 12.1.9
substructure, 7.10.4, 7.13, 7.37.1, 7.37.2     select, 12.1.23
     template, 11.12.3     setup, 12.1.18
     alerts, 7.13     sort, 12.1.42
superimpose, 2.6.8, 4.4.2, 4.4.6, 7.37.4, 15.3.3     split fragments, 7.3.33
     3D, 4.4.3     view, 12.1.5
     Calpha, 4.4.3          save, 12.1.8
     arrange.grid, 4.4.5     zoom translate, 7.3.30
     backbone, 4.4.3     action, 12.1.47
     heavy atoms, 4.4.3     alignment, 12.1.12
     multiple, 4.4.4     append, 12.1.43
superposition, 7.37, 7.37.1, 7.37.2, 7.37.5, 7.37.6, 15.3.3, 15.6.1     clone, 12.1.16
surface, 2.7.1, 3.7.5, 4.2.1, 4.2.2, 5.1.6, 5.3, 5.3.3, 5.3.4     color, 12.1.10
     area, 4.5     column, 7.3.4, 12.1.26, 12.1.32, 12.1.39
     area, 4.5.5     columns, 7.3.8
surfaces, 4.2, 5.3.1, 5.3.2, 5.10.5     compare, 7.3.22
symmetry, 4.3.1, 4.3.3, 15.3.8, 15.3.9     copy, 7.3.6
synthesize, 7.11.5     cursor, 12.1.47
synthetic feasibility, 7.11.5     delete, 12.1.14, 12.1.17
system preferences, 3.7.11     double.click, 12.1.47
tab, 12.1.2, 12.1.21     edit, 7.3.17
     pdb, 2.7.4     excel, 7.3.10, 12.1.20
table, 3.3, 7.1.3, 7.3.24, 7.3.25, 7.3.28, 7.3.30, 7.3.31, 7.3.34, 7.3.35, 7.20.2, 7.23, 11.10, 12, 12.1.6, 12.1.35, 12.1.40, 12.1.45, 12.4, 12.4.1, 12.4.4, 12.4.9, 12.4.11, 12.4.13, 12.4.14, 12.4.15, 12.4.16, 12.4.17, 12.4.18, 12.4.20, 12.7.1     filter, 7.3.12, 12.1.43
     alignment, 12.1.12     find-replace, 7.3.13
     clone, 12.1.16          to screen, 12.1.4
     color, 12.1.10     font, 12.1.11
     column format, 12.1.40     grid lines, 12.1.4
     copy, 12.1.36, 12.1.37     hide, 12.1.39
     delete, 12.1.17     hyperlink, 7.3.15
     edit, 12.1.24     insert, 12.1.33
     filter, 12.1.43     join, 2.6.10.5
     find, 12.1.9     label, 7.3.14
          replace, 7.3.32     landscape, 12.1.18
     font, 12.1.11     mark, 7.3.14
     grid, 12.1.5     merge, 2.6.10.5, 7.3.23, 7.32
     histogram, 12.4.1     mouse, 12.1.47
     insert, 12.1.26     name, 12.1.15
     layout, 12.1.5     new, 12.1.1
     learning, 12.6     options, 12.1.14
     mark, 12.1.13     orientation, 12.1.18
          row, 12.1.13     portrait, 12.1.18
     mouse, 12.1.47     print, 7.3.11, 12.1.4, 12.1.19
     navigation, 12.1.4     read, 12.1.2
     new column, 12.1.26     rename, 12.1.15
     plot, 12.4     right click, 12.1.14
     print, 12.1.19     row, 12.1.33
     rename, 12.1.15     rows, 2.6.10.7
     rightclick, 12.1.14     save, 7.3.9, 12.1.3, 12.1.4, 12.1.21
     save, 12.1.3     scale, 12.1.18
          selection, 12.1.3     scroll, 12.1.4
     select, 12.1.23     distance, 7.28.3
     setup, 12.1.18     edit, 7.28.4
     sort, 2.6.10.4, 7.3.5, 12.1.42     reorder, 7.28.3
     standard, 12.1triplet, 7.4.7
     view, 7.3.29tsv, 12.1.21
     width, 12.1.4tut analyze alternative orientations, 15.3.11
tables, 7.31, 12          occupancy, 15.3.10
tag, 3.6.21, 11.5.7, 12.1.46          symmetry, 15.3.9
tags, 3.6.21tut3e, 15.3.12
tautomer, 7.24tutorial 2D pharmacophore, 15.4.6
tautomers, 7.24     3D pharmacophore, 15.4.5
temperature, 4.5.13     chemical clustering, 15.4.3
template, 7.4.6, 7.37          search, 15.4.2
templates, 7.4.6     molecular documents, 15.2
terminal, 7.3.28tutorials, 15
tether, 11.12.1, 11.12.2two, 7.3.24
text, 3.7.7, 6.6, 6.6.1, 6.6.7, 7.3.28, 7.10.4, 12.4.24unclip, 5.3.10, 5.13.1
     search, 7.5.4undisplay, 3.1.4, 5.1.7
texture, 2.7.6undisplay-all, 2.6.3.1
thoroughness, 7.23, 7.37     origin, 5.8.12
three, 7.3.24undo, 2.6.2.9, 3.7, 7.4.11, 11.5.5
threshold, 3.7.5     redo, 11.5.5
tier, 3.1.13uniprot, 3.2.6
tissue, 3.2.10unique, 7.3.28, 7.33
     racemic, 7.20unit, 4.3.3
tools 3D, 2.6.6unsatisfied hydrogen bonds, 11.3.8
     analysis, 2.6.7unusual peptide, 3.3
     append rows, 2.6.10.7     activeicm, 6.12
     extras, 2.6.9user, 7.10.5
          plot function, 2.6.9.1     defined groups, 11.5.3
     superimpose, 2.6.8     modifiers, 11.5.3
     table, 2.6.10user-defined groups, 7.4.5
          Learn, 2.6.10.1van der waal, 5.8.15
          clustering, 2.6.10.3variable, 3.7.7
          merge, 2.6.10.5verbose, 7.23
          predict, 2.6.10.2     large sdf files, 7.1.2
tooltip, 12.4.26vicinity, 7.23
     balloons, 12.4.26video, 1, 5.16, 5.16.1, 5.16.2
torsion, 5.12.6, 5.12.6.1, 7.17, 11.5.4view, 2.6.3.19, 6.3.1, 7.3.28
     analysis, 7.16     animate view, 2.6.3.15
     angles, 5.12, 5.12.6     center, 2.6.3.20
     free strain, 7.17     color background, 2.6.3.18
toxscore, 7.11.3     fog, 2.6.3.5
trace, 5.1.10     macroshape, 2.6.3.22
transitions, 6     menu, 2.6.3
translate, 3.1.3, 5, 5.12, 7.3.30     mesh clip, 5.13.1
translation, 5.12.3, 12.4.17     perspective, 2.6.3.9
transparent, 5.3.9.3     selection level, 2.6.3.3
     background, 5.15.3          mode, 2.6.3.4
tree, 7.28.7, 12.7.2, 12.7.3, 12.7.4     shadow, 2.6.3.13
     slide show, 6.3.1 
     tools, 2.6.3 
     tree, 12.7.4 
     undisplay all, 2.6.3.1 
virtual ligand screening, 10 
virus, 4.3.3 
visualize, 7.30 
     apf fields, 11.3.11 
     chemical space, 7.30 
     ligand strain, 11.3.10 
vls, 9.4 
volume, 7.4.9 
wavefront, 2.7.6, 5.3.11, 5.7 
web, 15.2 
     browser, 2.6.1.12 
weight, 7.11 
weighted, 12.7.1 
width, 12.1.22 
window, 3.1.13 
windows, 3.1.13.1, 7.10.1 
wire, 2.7.1, 3.7.5, 5.1.1 
wireBondSeparation, 3.7.1 
workspace, 3.1.4, 7.7.2 
     panel, 3.1.4 
     selection, 3.6.9 
     navigation, 3.6.10 
write, 3.1.14, 3.5, 12.4.21 
     excel, 7.2.3 
     image, 2.6.1.15 
     images, 5.15 
     pdb, 3.5 
     image, 2.6.1.15 
     object, 3.1.9 
     picture, 2.6.1.15 
     project, 2.6.1.8, 3.1.10 
     table, 12.1.3 
     ray, 2.6.5 
xi, 5.8.5 
xls, 7.2.3 
xlsx, 7.2.3 
xstick, 5.1.2 
youtube, 1 
zoom, 3.1.3, 5, 5.12, 5.12.4, 7.3.30, 12.4.17 

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