Mar 10 2017 Feedback.
Contents
 
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Cheminformatics
Learn and Predict
MolScreen
3D Ligand Editor
Tables and Plots
Local Databases
KNIME
Tutorials
 
Index

Index

2D, 4.8.8, 6.3.24, 6.3.28, 6.14, 6.17.2, 6.17.4     proxy, 2.7.11
     Interaction Diagram, 9.3.7Filter.zip, 2.7.2
     from PDB, 6.1.1Force Auto Bond Typing, 2.7.11
     screening, 8GIF, 1.6.1.15, 4.16, 4.16.2
     to 3D, 6.17, 6.17.3GRAPHIC.store Display, 2.7.3
     depiction, 6.17.2     NtoC Rainbow, 2.7.4
3D, 4.6, 4.8.8, 6.1.3, 6.3.24, 6.3.28, 6.3.31, 6.17.2, 13.2     alignment Rainbow, 2.7.4
     QSAR, 6.35.4, 7.4, 13.8     atomLabelShift, 2.7.7
     chemical, 6.4.16, 6.17.1     ballStickRatio, 2.7.1
     interactive ligand editor, 1.7.5     center Follows Clipping, 2.7.3
     ligand editor, 9.3.4     clash Style, 2.7.3
     object, 4.3.9     clashWidth, 2.7.3
     pharmacophore, 9.3.11     clip Grobs, 2.7.3
     print, 4.7          Skin, 2.7.3
     printing, 4.7          Static, 2.7.3
     screening, 8     discrete Rainbow, 2.7.4
     stereo, 4.6     displayLineLabels, 2.7.7
3DQsar, 7.4     displayMapBox, 2.7.3
3Dqsar tutorial, 13.8     distance Label Drag, 2.7.1
     predict local flexibility, 3.5.12     dnaBallRadius, 2.7.9
          protein health, 3.5.11     dnaRibbonRatio, 2.7.9
          tools identify ligand binding pocket, 3.5.14     dnaRibbonWidth, 2.7.9
               oda, 3.5.13     dnaRibbonWorm, 2.7.9
4D dock, 9.14     dnaStickRadius, 2.7.9
     docking, 2.2.2     dnaWormRadius, 2.7.9
APF, 6.34.3, 6.35.4, 7.4, 8, 8.7, 13.8     font Scale, 2.7.7
     template, 6.34     fontColor, 2.7.7
ActiveICM, 1.6.1.12     fontLineSpacing, 2.7.7
Atom Single Style, 2.7.3     grobLineWidth, 2.7.3
Atomic Property Fields, 7.4, 13.8     hbond Ball Period, 2.7.1
Baell, 6.4.9               Style, 2.7.1
Beep, 2.7.11     hbondAngleSharpness, 2.7.1
BlastDB Directory, 2.7.2     hbondMinStrength, 2.7.1
     alphas, 4.8.3     hbondStyle, 2.7.1
COLLADA, 1.6.1.7     hbondWidth, 2.7.1
CPK, 1.7.1     hetatmZoom, 2.7.1
ChEMBL, 2.2.3, 6.1     hydrogenDisplay, 2.7.1
Chemical Cluster, 13.4.3     light, 2.7.3
     Search, 13.4.2     lightPosition, 2.7.3
Clash Threshold, 2.7.10     mapLineWidth, 2.7.3
DNA, 2.3     occupancy Radius Ratio, 2.7.3
Decomposition, 6.32.2     occupancyDisplay, 2.7.3
Dock Directory, 2.7.2     quality, 2.7.3
Drug Bank, 2.2.8     rainbow Bar Style, 2.7.4
Editor, 2.7.2     resLabelDrag, 2.7.7
FILTER.Z, 2.7.2     resize Keep Scale, 2.7.3
     gz, 2.7.2     ribbonRatio, 2.7.9
     uue, 2.7.2     ribbonWidth, 2.7.9
FTP.createFile, 2.7.11     ribbonWorm, 2.7.9
     keep File, 2.7.11     rocking, 2.7.4

          Speed, 2.7.4     paper Size, 2.7.6
     selectionStyle, 2.7.3     previewResolution, 2.7.6
     site Label Drag, 2.7.7     previewer, 2.7.6
               Shift, 2.7.7     print, 2.7.6
     siteArrow, 2.7.7     printerDPI, 2.7.6
     stereoMode, 2.7.3     scale, 2.7.6
     stickRadius, 2.7.1     stereoAngle, 2.7.6
     surfaceDotDensity, 2.7.3     stereoBase, 2.7.6
     surfaceDotSize, 2.7.3     stereoText, 2.7.6
     surfaceProbeRadius, 2.7.3Icm Prompt, 2.7.10
     transparency, 2.7.3InChi, 6.3.20, 6.4.12
     wire Width, 2.7.1     key, 6.3.20
     wormRadius, 2.7.9Interaction Diagram 2D, 9.3.7
     xstick Backbone Ratio, 2.7.1     Directory, 2.7.2
          Hydrogen Ratio, 2.7.1JPEG, 1.6.1.15
          Style, 2.7.1KMZ, 1.6.1.7
          Vw Ratio, 2.7.1Log Directory, 2.7.2
GROB.arrowRadius, 2.7.3LogP, 7, 10.6
     atomSphereRadius, 2.7.3LogS, 7, 10.6
     contourSigmaIncrement, 2.7.3MOL, 6, 6.3.3, 6.3.24, 6.3.25, 6.3.26, 6.3.27, 10.2
     relArrow Size, 2.7.3MOLT, 11.1
     relArrowHead, 2.7.3MOVIE.frame Grab Mode, 2.7.4
GUI.auto Save, 2.7.4MPO, 6.30
               Interval, 2.7.4Map Atom Margin, 2.7.10
     enumberation Memory Limit, 2.7.11     Sigma Level, 2.7.10
     max Nof Recent Files, 2.7.11Markush, 13.4.9
          Sequence Length, 2.7.4     create, 13.4.7
     splash Screen Delay, 2.7.11     File Size Mb, 2.7.11
               Image, 2.7.11Max_Fused_Rings, 6.11
     table Row Mark Colors, 2.7.4Mnconf, 2.7.10
     workspace Folder Style, 2.7.4Model, 7.4
     workspaceTabStyle, 2.7.4MolPSA, 6.11
HTTP.proxy, 2.7.11MolScreen, 8
     support Cookies, 2.7.11MolVol, 6.11
     user Agent, 2.7.11Molcart, 6.5.3
Hbonds, 9.3.4MoldHf, 6.11
How To Guide, 1Movie.fade Nof Frames, 2.7.4
Html, 2.2.1.6     quality, 2.7.4
Http Read Style, 2.7.11          Auto, 2.7.4
Hydrogen.bond, 2.7.5Nof_Atoms, 6.11
ICM Browser How To, 1.1Nof_Chirals, 6.11
          Pro How To, 1.2Nof_HBA, 6.11
IMAGE.bondLength2D, 2.7.6Nof_HBD, 6.11
     color, 2.7.6Nof_Rings, 6.11
     compress, 2.7.6Nof_RotBonds, 6.11
     gammaCorrection, 2.7.6Output Directory, 2.7.2
     generateAlpha, 2.7.6PAINS, 6.4.9, 6.11.2
     lineWidth, 2.7.6     chemica, 6.4.9
     lineWidth2D, 2.7.6PCA, 7.1, 7.5, 13.4.4
     orientation, 2.7.6     analysis, 6.26

     Directory, 2.7.2     labelOffset, 2.7.7
          Style, 2.7.2     wrap Comment, 2.7.7
     link, 10.1.37SLIDE.ignore Background Color, 2.7.4
     Search, 1.6.2.12, 1.6.2.13, 1.6.2.14, 1.6.2.15, 1.6.2.16          Fog, 2.7.4
          Field, 1.6.2.13SMILES, 6.1.2, 6.2.4, 6.4.12
          Homology, 1.6.2.15Select Min Grad, 2.7.10
          Identity, 1.6.2.14Show Res Code In Selection, 2.7.7
          Sequence, 1.6.2.16SureChEMBL, 2.2.4
     convert, 3.1.2Swissprot, 1.6.1.7
PFAM, 1.6.1.7     Dat, 2.7.2
PLOT.Yratio, 2.7.8     link, 10.1.37
     color, 2.7.8Temp Directory, 2.7.2
     date, 2.7.8USER.email, 2.7.11
     draw Tics, 2.7.8     friends, 2.7.11
     font, 2.7.8     full Name, 2.7.11
     fontSize, 2.7.8     organization, 2.7.11
     labelFont, 2.7.8     phone, 2.7.11
     lineWidth, 2.7.8Uniprot, 10.1.37
     logo, 2.7.8Van Drie, 6.32.3
     markSize, 2.7.8     Label Style, 2.7.7
     orientation, 2.7.8Water Radius, 2.7.10
     paper Size, 2.7.8Wire Style, 2.7.1
     previewer, 2.7.8XPDB Directory, 2.7.2
     rainbowStyle, 2.7.8Xstick, 1.7.1
     seriesLabels, 2.7.8a-bright, 1.7.2
PLS, 7.1about model, 7.1.1
PNG, 1.6.1.15, 2.1.14, 4.16, 4.16.2acceptor, 6.4.9, 6.35.1
Projects Directory, 2.7.2active, 5.7
Prosite Dat, 2.7.2activeICM, 5.8
     Viewer, 2.7.2activeicm, 5.7, 5.12, 5.14, 5.14.1
Pub Chem, 2.2.9     advanced, 5.14
PubMed, 2.2.1.7     background images, 5.15
     Reference, 10.1.37     control, 5.13
Pubchem, 2.2.9activeicmjs, 5.16
QSAR, 7, 7.1, 10.6, 13.8activity cliff, 6.32.3, 6.32.4
R, 6.8, 6.32.1activityy, 7, 10.6
R-Group, 6.32.2add database, 6.10.3
R-groups, 9.5.3     new data, 6.3.7
RMSD, 3.4.2     to table, 9.5.7
RNA, 2.3adding fragment, 6.4.8
Ramachandran Plot, 3.5.9          in editor, 6.4.8
Real Format, 2.7.10administration, 6.10.5
     Label Shift, 2.7.7album, 4.15.3
          Style, 2.7.7alias, 6.4.5
SALI, 6.32.3align, 2.1.11, 6.14
SAR, 7, 8.7, 10.6     color 2D scaffold, 6.14
     table, 6.32.2, 13.4.9alignment, 6.34.1, 6.34.2
SDF, 6, 6.3.24, 6.3.25, 6.3.26, 6.3.27, 10.2alpha, 1.7.2
SEQUENCE.site Colors, 2.7.4     channel, 2.7.6
SITE.label Style, 2.7.7ambient, 1.7.2

amino acid, 2.3     point, 6.31.4
     acids, 6.4.6author, 2.2.1.3
anaglyph, 4.6     close tree, 6.25.5
analysis, 1.6.4     play slide, 5.13
angle, 3.5.7, 3.5.8, 4.8.5, 4.9, 4.12.6ave, 10.7.1
animate, 1.6.3.15, 4.10.7avi, 4.16, 4.16.2
     view, 4.10.7axes, 10.4.13
animation, 4.10.7.1, 4.10.7.2, 4.10.7.3, 4.10.7.4axis, 10.4.9
     store, 4.10.7.4     options, 10.4.8
animations, 5     grid, 10.4.8
annotate, 2.6.21, 6.13     range, 10.4.8
     by substructure, 6.13     title, 10.4.8
     plot, 10.4.20b-factor, 3.5.12, 13.3.10
antialias, 1.6.1.15, 1.6.3.10backbone, 4.1.10
     lines, 1.6.3.17background, 4.4.2, 4.4.3
     lines, 1.6.3.17     images activeicm, 5.15
apf, 3.4.6, 6.34.1, 6.34.2, 6.35, 7, 9.3.11, 9.16, 13.6, 13.6.1, 13.6.2, 13.6.3, 13.6.4, 13.6.5     image, 4.4.3
     flexible template, 6.34.2backup, 1.6.2.11
     pairwise, 6.34.1bad, 6.11
     super, 6.34     groups, 6.4.9
     tools, 6.35ball, 2.7.5
          3DQSAR, 6.35.4     and stick, 1.7.1
          consensus ph4, 6.35.1balloon, 10.4.21
          pairwise score, 6.35.2bases, 6.4.6
          screen, 6.35.3basicsel, 2.6.2
     tutorial, 13.6bayesian classifier, 7
          cluster, 13.6.5best, 6.3.34
          consensus, 13.6.2bicyclics, 6.4.6
          score, 13.6.3binding properties, 4.3.1
          screen, 13.6.4bioinfo menu, 1.6.4
          superposition, 13.6.1bioisoester, 6.9
     alignment, 6.34.3bioisostere, 6.9
append, 10.1.41biological, 3.3.3
     table, 10.1.41biomolecule, 1.6.5, 3.3.3, 13.3.8, 13.3.12
     rows, 1.6.10.7blast, 2.2.5
applying prediction models, 7.2     search, 2.2.5
area, 3.5.3, 3.5.13, 13.3.5bond, 3.2.3, 3.2.3.1, 3.2.3.2, 6.4.10
aromatic, 6.3.28, 6.35.1     type, 6.7.1, 6.7.2, 6.7.3
arrange, 2.1.13.1bonding, 4.1.8
     window, 2.1.13.1     preferences, 2.7.1
as2_graph, 2.6.5box, 2.7.7, 4.8.15
assign, 4.1.3     size, 9.8.1
     2D coordinates, 6.17.2browse, 6.3.31
atom, 2.7.5, 6.3.28     mode, 6.3.31
atomLabelStyle, 2.7.7     molt, 11.2
atomic energy circles, 9.3.5build, 4.10.7.1
     property field, 6.34.1, 6.34.2, 9.3.11buttons, 5.14
               score, 6.35.2bye, 1.6.1.19
          fields, 3.4.6, 6.35, 6.35.1, 6.35.3, 13.6     alpha, 4.1.10
attachment, 6.4.3, 6.5.1     trace, 4.1.10

cache, 5.14.1     substructure, 2.2.1.1
calculate, 6.11     table, 9.9
     properties, 6.11          display, 6.3.3
carboxylic acid, 6.15     tables, 10.2
cartesian, 6.20     toxicity, 6.11.2
cavities, 3.5     2D, 6.7
     closed, 3.5.4     3D, 6.7
cell, 3.3.2     append, 6.4.13
center, 1.6.3.20, 2.1.3, 4.12, 4.12.5, 9.3.13, 10.1.37     clustering, 6.25, 6.25.1
     on ligand, 9.3.13     convert, 6.7, 6.7.1, 6.7.2, 6.7.3
     and representative members, 10.7.2     draw, 6.4.1
change box size, 9.8.1     duplicates, 6.3.21
     height of all rows, 10.1.6     editor, 6.2, 6.2.2, 6.2.4, 6.2.5, 6.2.6
     ligand, 9.5.1     load, 6.1
     row height, 10.1.6     merge, 6.28
     selection, 2.6.7     new, 6.4.1
     speed range, 4.10.7.2     properties, 6.3.19
charge, 1.6.3.21, 4.8.2, 6.4.3, 6.5.1, 6.7.1, 6.7.2, 6.7.3, 6.35.1     query, 6.4.3, 6.5.1, 6.5.3
chem export excel, 6.2.3     read, 6.1
     save, 6.2     save, 6.2, 6.2.2, 6.2.4, 6.2.5, 6.2.6, 6.4.13
          3D, 6.2.5     search, 6.4.3, 6.5, 6.5.1, 6.5.3
          editor, 6.2.4     similarity, 6.4.3, 6.5, 6.5.1, 6.5.3
          image, 6.2.6     spreadsheet, 6.2, 6.2.2, 6.2.4, 6.2.5, 6.2.6, 6.3
          table, 6.2.2     structure, 6.4.13
     super, 6.33     superimpose, 6.33.1, 6.33.2, 6.33.3
     view, 6.3.28     superposition, 6.34, 6.34.3
chembl, 2.2.3, 2.2.4     table, 6.3, 10.2
chemical, 6, 6.3.28, 6.3.30, 6.3.31, 6.3.34, 6.3.35, 6.4.10, 6.8, 6.10.4, 6.11.2, 6.17.2, 6.21, 6.31.4, 6.31.5, 6.33, 6.34.1, 6.34.2, 10.7.1, 13.4.4cheminformatics, 6, 6.3
     clustering, 6.25, 6.25.6     tutorials, 13.4
     dictionary, 6.4.4, 6.4.5, 6.4.6chemistry, 6.21
     draw, 13.4.1     convert, 6.17
          spreadsheet tutorial, 13.4.1          2dto3d, 6.17.1
     edit buttons, 6.4.11     pca, 6.26
     editor, 6.4, 6.4.8     smiles, 6.17.3
     fingerprint, 8     duplicates, 6.29
     fragments, 6.3.33     remove.redundant, 6.29
     group, 6.4.5chemspace append, 13.4.4.4
     groups, 6.4.5, 6.4.8     build visualize, 13.4.4.1
     modifiers, 6.31.2     compare, 13.4.4.8
     properties, 13.4.4     delete row, 13.4.4.3
     right click, 6.4.3     distinguish, 13.4.4.7
     search, 6.5     export, 13.4.4.5
          filter, 6.5.2     project, 13.4.4.6
          text, 6.5.4     select, 13.4.4.2
     sketch, 13.4.1chi, 4.8.5
     spreadsheet, 2.2.3, 6.1.3, 6.3.1, 6.4.14, 13.4.1chiral, 6.22
          compare, 6.3.22chirality, 6.22
          template, 6.3.2clash, 2.7.5, 4.8.14
     spreadsheets, 6.3classes, 6.3.28
     substituent, 6.9classification model, 8.6

     selection, 2.6.6compress, 2.7.6
     planes, 1.6.3.2conditions, 6.5.2
click, 2.1.12, 4.11, 4.12     gen, 6.20
clip, 4.3.10, 4.13.1conformation, 6.20
clipboard, 4.15.3, 10.7.3conformational entropy, 6.24
clipping planes, 4conformers, 6.20
     tool, 4.13connect, 4.3.9.1, 4.12, 4.12.7
     tools, 4.13     object, 4.12.7
clone, 1.6.1.2connectivity, 6.4.3, 6.5.1
close, 4.3.3, 4.3.4, 9.19consensus, 6.35, 13.6.2
     downstream cluster, 6.25.5     pharmacophore, 6.35.1
     project, 9.19construct, 1.6.1.1, 4.10.7.1
     cavities, 3.5.14     molecule, 1.6.1.1
cluster, 10.7.1     object, 1.6.1.1
     representative.center, 6.25.2contact, 3.5, 3.5.3, 13.3.5
clustering, 10.7, 13.4.3     surface, 4.3.2
cns, 6.30contacts, 4.3.3, 4.3.4, 6.6, 9.3.12
collada, 1.7.6, 4.3.7contour, 3.3.6, 3.3.7
color, 3.5.11, 4.3.2, 4.3.3, 4.3.4, 4.3.9.4, 4.4, 4.4.1, 4.8.2, 4.8.3, 6.3.35, 6.14, 10.1.42, 10.7.4convert, 3.1.2, 6.17.1, 6.17.5
     background, 4.4.2     chemical, 6.3.24
     by, 4.4          2D 3D, 6.7
     chemical, 6.3.35          3D molecular editor, 6.4.16
     surface by proximity, 4.3.3     local database, 1.6.1.6
               selection, 4.3.4     pdb, 13.3.2
     table, 6.3.27          chem, 6.7.1
     2D sketch, 6.5.5.5     local.database, 1.6.1.6
     background, 1.6.3.18, 4.4.2     smiles, 6.17, 6.17.3, 6.17.4
     distance, 4.8.10converting pdb, 3.1.2
     mesh, 4.3.9.3coordinates, 6.1.3
     table, 6.3.27copy, 6.3.25, 6.4.11, 6.4.17, 6.5.5.2, 10.1.32
coloring, 4.4.1     cell, 10.1.33
coloumn, 10.1.24     chemical, 6.3.25
column, 10, 10.1.21, 10.1.36, 10.1.37, 10.4, 10.4.1     paste row, 10.1.32
     annotation, 10.1.38     row, 10.1.33
     row width, 10.1.21     rows, 10.1.41
     statistics, 10.1.29     selection to table, 10.1.34
     color, 10.1.9     chemical, 6.3.16
     hide, 6.3.8covalent, 9.9.1
     show, 6.3.8     docking, 9.15
combinatorial chemistry, 6.31cpk, 4.1.5
     library, 13.4.8crash, 1.6.2.11
combine, 1.6.10.5creat, 5.6.1
     display style, 2.7.9create, 10.1.1
compact tree, 6.25.5     markush, 6.31.3
compare, 6.3.29, 6.27, 6.28     new objects, 2.3
     table, 6.3.22cross section, 4.13
     tables, 6.27crystal, 3.3.2
compatible, 1.6.1.10crystallographic analysis, 3.3
complex, 6.6          biomolecule, 3.3.3
compound, 2.2.1.3, 6.21, 10.2          contour map, 3.3.6

          crystallographic cell, 3.3.2     gradient, 4.8.16
          load eds, 3.3.4     hbonds, 9.3.4
          maps cell, 3.3.5     hydrogen, 4.1.7
          symmetry packing, 3.3.1          atoms ligand editor, 9.3.3
          tools, 13.3.8     mesh, 4.3.5
     cell, 1.6.5     meshes, 4.3.8
     neigbor, 3.3.1     options, 9.3
     neighbors, 1.6.5     planar angle, 4.9.2
crystallography, 3.3.4, 3.3.6, 3.3.7     tab, 1.7.1
csv, 6.2.3, 10.1.2, 10.1.3, 10.1.20     tether, 4.8.12
current.slide, 5.13     toggle, 4.8.15
custom, 4.12, 6.3.3, 6.33     CPK, 4.1.5
     actions, 10.1.37     angle, 4.9.2
     fragments, 6.13     chemical, 6.3.3
     label, 4.8.8     dihedral.angle, 4.9.3
     rotation, 4.12.2     distace, 4.8.10
cut, 10.1.32     distance, 4.8.13, 4.9.1
database, 6.10, 6.31.4, 11.1     electrostatic, 1.6.3.21
decompose.library, 13.4.9     energy.gradient, 4.8.16
decomposition, 6.31.4, 6.32.1     hydrogen, 4.1.7
default, 2.1.13          polar, 4.1.7
delete, 1.6.2.1, 2.6.6, 5.6.7     macroshape, 4.3.6
     all, 1.6.2.2     meshes, 4.3.5
     column row, 10.1.35          and display.macroshape, 1.7.6
     label, 4.8.9     molecule, 6.3.24
     all, 1.6.2.2     origin, 4.8.11
     angle.label, 4.9.4     potential, 1.6.3.21
     column, 10.1.35     representations, 1.7.1
     distance.label, 4.9.4     restraints, 4.8.13
     label, 4.8.9     ribbon, 4.1.3
     row, 10.1.35     skin, 4.1.4
     selection, 1.6.2.1     surface, 4.1.6, 4.3.1
density, 3.3.4, 3.3.6, 3.3.7     surfaces, 1.7.6
depth, 4.3.12, 4.10.5     table, 6.3.3
dfa, 8.1.3     tethers, 4.8.12
dfz, 8.1.2     wire, 4.1.1
dialog, 5.6.5     xstick, 4.1.2
diffuse, 1.7.2distance, 3.5, 3.5.6, 4.8.10, 4.9, 6.27
dihedral, 3.5.8, 4.8.5     label, 2.7.7
     angle, 3.5distances, 1.7.3
directories preferences, 2.7.2diverse set, 10.7
directory, 2.7dock, 9.9, 9.9.1
dislay ligand receptor interaction, 6.6     apf, 9.16
display, 2.1.4, 2.1.13.1, 2.7, 3.2.3, 3.2.3.1, 3.2.3.2, 4.8.14, 4.14, 6.22     table, 9.9
     delete distances, 4.9.4          covalent, 9.9.1
     dihedral, 4.9.3docking, 3.5.13, 9.9, 9.9.1, 9.10
     distance restraints, 4.8.13document, 5.6.4, 5.6.5
     distance2, 4.9.1     navigation, 5.6.6
          angles, 4.9documents, 4.15.3
     formal charge, 4.1.9donator, 6.4.9

     surface, 2.7.5     powerpoint10, 5.10
dotted line, 4.1.3     activeicm, 5.13
double, 6.4.10          script, 5.13
doublet, 6.4.7     browser, 5.7, 5.11
dpc, 8.1.4     firefox, 5.7, 5.11
drag, 2.1.11, 2.7.7, 4.8.3, 5.6.4     internet.explorer, 5.7, 5.11
     residue label, 1.6.3.16     microsoft, 5.7
draganddrop, 2.1.11     powerpoint, 5.7, 5.8, 5.9, 5.10
draw, 6.4.17, 6.31.5energy, 3.5.11, 4.8.14, 6.24, 6.24.2
     chemical, 6.4.1entropy, 6.24.1
drop, 2.1.11, 5.6.4enumerate formal charge states, 6.16
drug, 6.11     reaction, 13.4.10
     bank, 2.2, 2.2.8, 6.1enumeration, 6.31.4
drugbank, 6.1eps, 6.2.6
druglikeness, 6.4.9eraser, 6.4.11
dsPocket, 2.1.8evaluate score strain, 9.4
easy rotate, 1.6.3.12exact, 6.27
ecfp, 7.3excel, 6.2.3
edit, 3.2.3.1, 9.5.8exclude fragment, 6.5.2
     2D, 9.5.1     volume, 9.3.11
     chemical moledit, 6.3.26exit, 1.6.1.19
     ligand, 9.5, 9.5.1explicit, 6.3.28
          2D, 9.5.1export, 3.5.10
          editor preferences, 9.2     dock project, 9.18
          multiple substituents, 9.5.2extra windows, 4.2
          tools, 1.6.2.17extract, 2.4.2, 6.1.3
     menu, 1.6.2     2D, 6.1.1
     molecular document, 5.6.1     3d coordinates to spreadsheet, 6.1.3
     molecule, 6.4     icb, 1.6.1.5
     molt, 11.3     object icb, 2.4.2
     selection, 1.6.2.5     icb, 1.6.1.5
     slide, 5.4.1     pharmacophore, 6.5.5.4
     table row, 10.1.23file, 1.6.1.3
     molecule, 6.3.26     close, 1.6.1.13
     structure, 6.3.26     compatible, 1.6.1.10
editpdbsearch, 1.6.2.12     export, 1.6.1.12
eds, 3.3.4, 3.3.6, 3.3.7     high quality image, 4.15.1
effort, 6.20, 6.33     load, 1.6.1.7
electron, 3.3.4, 3.3.6, 3.3.7     menu, 1.6.1
     denisty map, 3.3.5     password, 1.6.1.11
     densitry map.contour, 1.6.5     preferences, 1.6.1.16
          map, 1.6.1.7, 1.6.5, 3.3.4, 3.3.6     quick image, 1.6.1.14
electrostatic potential, 1.6.3.21     icb, 2.1.10
     surface, 4.3     recent, 1.6.1.17
electrostatics, 4.3.1     bak, 1.6.2.11
elegant sketch, 4.10.4filter, 11.2
element, 6.4.10     selection, 2.6.8
embed browser, 5.11find chemical, 6.3.32
     powerpoint03, 5.8fingerprint, 7, 7.3, 13.7
     powerpoint07, 5.9     method, 7.3

fitting, 10.4.14guanidinium, 6.15
flex super, 6.33.3gui, 2.1.1, 2.7.4
flexibility, 3.5.12     menus, 1.6
flexible, 6.33     preferences, 2.7.4
     docking, 9.12     tabs, 1.7
     receptor groups, 9.12h-bond, 3.2.3, 3.2.3.1, 3.2.3.2
fog, 1.6.3.5, 4, 4.10.1halogen, 6.11.1
font, 2.7, 2.7.7, 3.2.3.1, 4.8.2, 4.8.3, 6.3.28, 10.1.37, 10.7.4hardware stereo, 1.6.3.7
     preferences, 2.7.7hbond, 3.2, 13.3.6
form view, 10.1.5header, 2.2.1.6, 10.4.7
formal charge, 4.1.9, 6.15, 6.16health, 3.5.11
format, 10.1.2, 10.1.37heatmap, 10.4.5
formula, 6.4.9, 6.11hetero, 6.3.28
fragment, 6.3.35, 6.32.1, 9.10     scan, 9.7
     linking, 9.10hide, 10.1.36
fragments, 6.8high, 1.6.1.15
free radical, 6.4.7     quality, 1.6.3.11
freeze column, 10.1.27highlight new data, 6.3.7.1
     row, 10.1.28histogram, 10.4, 10.4.1, 10.4.7, 10.4.9, 10.4.11, 10.4.12, 10.4.13, 10.4.14, 10.4.15, 10.4.16, 10.4.17, 10.4.19
frequency, 6.3.35     bins, 10.4.3
front, 4.3.10, 4.13.1     options, 10.4.2
full scene antialias, 1.6.3.10     bin.size, 10.4.2
     screen, 1.6.3.8     bins, 10.4.3
function, 10.1.25, 10.1.29     color, 10.4.2
functional.groups, 6.13     source, 10.4.2
general preferences, 2.7.5     style, 10.4.2
generalselecttools, 2.6.1     title, 10.4.2
generator, 3.3.3, 6.20homology, 2.2.1.2, 2.2.5
getting started, 2hover, 10.4.21
glasses, 4.6     3D editor, 13.5
google, 1.6.1.7     add columns, 6.3.4
     objects, 4.3.7     cluster center, 6.25.2
     3D, 1.7.6, 4.3.7     color 2D by ph4, 6.5.5.5
graphical display, 6.7.2, 6.7.3     copy 2D, 6.3.16
          tutorial, 13.1          paste, 6.3.6
               2D3D labels, 13.1.4     decompose, 13.4.9
               annotation, 13.1.2     duplicate chemicals, 6.3.21
               color representation, 13.1.1     edit table, 6.3.17
               labels, 13.1.3          tree, 6.25.4
graphics, 2.1     excel, 6.3.10
     controls, 4     extract 3D ph4, 6.5.5.4
     effects, 4.10     filter, 6.3.12
     panel, 4.2     find replace, 6.3.13
     preferences, 2.7.3     mark row, 6.3.14
     shadow, 1.6.3.13, 4.10.2     markush, 13.4.8
grid, 6.3.3, 6.33          structure, 13.4.7
grob, 2.7.5, 3.3.4, 3.3.6, 3.3.7, 4.3     merge tables, 6.3.23
group, 6.32.1, 9.6     properties, 6.3.19
     column, 10.1.43     reactions, 13.4.10
groups, 6.8, 6.11, 6.12     reorder, 6.25.3

     show hide, 6.3.8               ph4, 1.4.4
     sort column, 6.3.5               plots, 1.4.8
     standardize, 6.3.18               sketch, 1.4.1
     table hyperlinks, 6.3.15               spreadsheets, 1.4.2
          print, 6.3.11               stereoisomers tautomers, 1.4.6
          activeicm, 1.3          pro 3D ligand editor, 1.5.1
               create molecular documents, 1.3.3               chem3D, 1.5.2
                    slides, 1.3.2               chemsuper, 1.5.4
               getting started, 1.3.1               energy, 1.5.3
               ppt, 1.3.4               qsar, 1.5.5
               web, 1.3.5               tutorials, 1.5
          chemical clusering, 6.25.1          tutorials, 1.4
          icm browser convert display pocket, 1.1.4     object, 3.1, 13.3.2
                    distances angles, 1.1.9     script, 10.1.37
                    get started, 1.1.1icmPocketFinder, 3.5.14
                    graphical display, 1.1.2icmjs, 5.16
                         effects, 1.1.5icmpocketfinder, 13.3.7
                    images, 1.1.7id, 10.1.26
                    labels annotation, 1.1.6identity, 2.2.1.2
                    pro crystallographic tools, 1.2.6image, 2.1.14, 2.7, 2.7.5, 4.15.3, 5.6.3, 6.2, 6.2.6, 10.4.18
                         get started, 1.2.1     advanced, 4.15.3
                         graphics, 1.2.2     preferences, 2.7.6
                         plots, 1.2.8     multiple, 1.6.1.7
                         sequence analysis, 1.2.7     quality, 1.6.3.11
                         structure analysis, 1.2.3     quick, 1.6.1.14, 4.15.2
                         superimpose, 1.2.5images, 4.15
                         surfaces, 1.2.4improve model, 7.1.3
                    selections, 1.1.3increment, 10.1.26
                    superimpose, 1.1.8     id, 10.1.26
          search, 2.2induced fit, 9.12
          use gui, 2.1insert, 5.6.4
html, 1.6.1.12, 2.3, 5.6.1, 5.6.6     column, 10.1.25
hybridization, 6.4.3, 6.5.1     image, 5.6.3, 10.1.31
hydrogen, 3.2.3, 3.2.3.1, 3.2.3.2, 4.1.8, 6.4.3, 6.5.1, 13.3.6          table, 10.1.31
     atom display, 9.3.3     row, 10.1.30
     bond, 3.2, 4.1.8, 6.6, 13.3.6     script, 5.6.4
          donor, 6.35.1install, 6.10.1
          label edit, 3.2.3.1interaction, 3.5.3, 6.6
               move, 3.2.3.2interactions, 9.3.12
     bonds, 3.2.4interactive, 13.2
     bond, 6.4.9interrupt, 4.10.7.3
hydrogens, 6.3.28     animation, 4.10.7.3
     remove, 6.3.18invert selection, 10.1.22
hyperlink, 5.6.1, 5.6.2, 10.1.37isee, 5.6.5
hyrophobic, 6.35.1isis, 6.4.17
iSee, 1.6.1.5, 1.6.1.12, 2.1.10, 4.15.3, 13.2isotope, 6.4.3, 6.5.1
icb, 2.4.2, 2.5iupac, 6.2.7, 6.3.20
     chemist howto chemical search, 1.4.3javascript, 5.16
               cluster, 1.4.5join, 6.28
               combi library, 1.4.7jpg, 4.15

kcc, 8.1.1, 8.6          covalent docking, 9.15
kernel regression, 8.1.1          mrc, 9.14
     chemical, 6.4.10          preferences, 1.6.2.18
keyboard mouse, 4.11     energetics, 6.24
keystokes in chem-edit, 6.4.10          conformational entropy, 6.24.1
kmz, 1.7.6, 4.3.7          strain, 6.24.2
knime, 12     pocket, 3.2.4
label, 2.7.7, 10.7.4          surface, 9.3.2
     atoms, 4.8.2     receptor contacts, 9.3.12
     color, 4.8.7          display, 3.2
     move, 4.8.4          interaction, 6.6
     residues, 4.8.3     strain, 9.3.10
     sites, 4.8.6     surface, 3.2.2
     variables, 4.8.5     tether, 9.11
     2D, 1.7.3     editor, 9, 9.1
     3D, 1.7.3, 4.8.1          binding.re-dock ligand, 9.8
     atom, 4.8.1          display, 9.3
     atoms, 4.8.2          edit, 9.5
     color, 4.8.7          energy, 9.3
     custom, 4.8.8          hydrogen.bond, 9.3
     delete, 4.8.1, 4.8.9          pocket, 9.3
     distance, 4.8.10          preferences, 9.2
     drag, 1.6.3.16          restraint, 9.11
     move, 1.6.3.16, 4.8.4          surface, 9.3
     residue, 4.8.1          tether, 9.11
     residues, 4.8.3     pocket, 2.1.8
     site, 4.8.1     receptor.contact, 3.5.3
     sites, 4.8.6ligand_pocket_interactions, 3.2.4
     variable, 4.8.1ligedit distance restraint, 9.11.2
     variables, 4.8.5     tab, 1.7.5
labeling, 4.8.1     tether, 9.11.1
labels, 4.8, 6.3.28light, 1.7.2
     distances, 4.8.10     tab, 1.7.2
     tab, 1.7.3lighting, 4.3.9.4, 4.5
landscape, 2.7.6likeness, 6.11
large chemical space, 13.4.4line, 2.7.5, 10.7.4
     sdf, 6.1.2lineWidth, 2.7.3
layer, 4.14links, 2.6.20
layers, 4.14linux, 6.10.1
learn, 6.18, 6.19, 7, 7.1, 10.6lipinski rule, 6.30
learning, 7list, 2.6.18
     theory, 7.5load, 1.6.1.3, 1.6.1.17, 3.3.4, 3.3.6, 3.3.7
least.squares, 10.4.14     nmr model, 2.2.1.4
library, 6.31.4     protein structure, 3.1.1
     reaction, 13.4.10local databases, 11
ligand, 3.2.2, 6.6, 6.24, 6.24.1, 6.24.2, 9.3.12, 9.3.13, 9.5.8, 9.9, 9.10     database.browse, 11.2
     based screen, 6.35.3          edit, 11.3
     best replace, 9.6          query, 11.4
     code, 2.2.1.3, 2.2.7          row, 11.3
     editor, 9, 9.9, 9.9.1, 9.15, 9.16lock, 4.3.10, 4.13.1, 6.3.31

logP, 6.4.9, 6.11     color lighting, 4.3.9.4
logS, 6.4.9, 6.11     options, 4.3.9
logarithmic, 10.4.9     representation, 4.3.9.3
logout, 1.6.1.19     save, 4.3.11
mac, 6.10.1     options, 4.3.9
machine learning, 13.7meshes, 4.3.2, 4.10.5
macros, 5.14     surfaces grobs, 4.3
macroshape, 1.6.3.22, 4.3, 4.3.6     tab, 1.7.6
make, 4.10.7.1, 10.1.1metabolic oxidation, 8.8
     animation, 4.10.7.1min, 10.7.1
     apf docking sar model, 8.7mmff, 6.4.16
     complex, 9.19     type, 4.8.2
     molecular document, 5.6mnSolutions, 2.7.10
     molt, 11.1model weight, 7.1.2
     selection, 2.6modification history, 9.5.6
     molecule, 1.6.1.1mol, 6.2, 6.2.2, 6.2.4, 6.2.5, 6.2.6, 6.4.13
     object, 1.6.1.1mol2, 6.2, 6.2.2, 6.2.4, 6.2.5, 6.2.6
making molecular slides, 5.1molcart, 6.10, 6.10.1, 6.10.2, 6.10.3, 6.10.4, 6.10.5, 11
     html, 5.6     add database, 6.10.3
     color, 10.4.12     administration, 6.10.5
manual change torsion, 9.5.4     installation, 6.10.1
map, 2.7.7, 3.3.4, 3.3.6, 3.3.7     search, 6.10.4
     cel, 3.3.5     start, 6.10.2
mark, 10.1.42molecular, 6.3.30, 6.3.31, 6.3.34, 6.3.35, 6.20
     row, 10.1.42     animations slides, 5
     shape, 10.4.11     documents, 13.2
     size, 10.4.11     graphics, 4
markush, 6.25.7, 6.31.1, 6.31.3, 6.32.1     table, 6.17.2
     library, 13.4.8     weight, 6.4.9
matched pair, 6.32.4     editor, 6.4
          analysis, 6.32.4moledit, 6.4.8
materials, 1.7.6molscreen, 8
max, 10.7.1     brief panel, 8.2
maxColorPotential, 2.7.10     custom model panel, 8.4
maximum common substructure, 6.25.6     full panel, 8.3
mcs, 6.25.6     model type, 8.1
     rgroup decomposition, 6.25.7     results, 8.5
memory, 6.1.2molskin, 4.3.2
menu, 5.6.5molt, 11, 11.4
     chemistry, 1.6.14monochrome, 6.3.28
     docking, 1.6.15mouse, 2.1.3, 4.11, 4.12
     homology, 1.6.13mov, 4.16, 4.16.2
     molmechanics, 1.6.16move, 1.6.3.19, 2.1.11, 2.1.13, 3.2.3.2, 4.3.9.1, 4.3.9.2, 4.12, 4.12.7
     tools chemical search, 1.6.11     mesh, 4.3.9.2
          molecular editor, 1.6.12     slide, 5.4.2
     windows, 1.6.17     structure, 4.12
merge, 6.28     tools, 4
     two sets, 6.28     rotate, 4.11
mesh, 3.2.1, 3.2.2, 3.3.4, 3.3.6, 3.3.7, 4.3, 4.3.9.1, 4.3.9.2, 4.3.9.4, 4.3.10, 4.3.11, 4.3.12, 4.13.1     slab, 4.11
     clip, 4.3.10     translate, 4.11

     zoom, 4.11pairwise, 6.34.1, 6.34.2
movie, 4.16.1     apf score, 6.35
     making, 4.16, 4.16.2password, 6.10.5
     open, 4.16, 4.16.2paste, 6.4.11, 6.4.17, 10.1.32
mpeg, 4.16, 4.16.1, 4.16.2pca, 10.5
mpg, 4.16, 4.16.2pdb, 1.6.1.7, 2.2, 2.2.1.1, 2.2.7, 2.5, 6.7.1, 13.3
mpo, 6.30     chem gl, 6.7.3
multi apf super, 6.34.3          iw, 6.7.2
     panel, 4.2     html, 2.2.1.6
     parameter optimization, 6.30     preparation, 13.3.11
     windows, 4.2     search, 2.2.1, 2.2.1.2, 2.2.1.3, 13.3.1
multiple position group scan, 9.7     recent, 1.6.1.18
     receptor, 2.2.2     search, 1.7.4, 2.1.2
          docking, 9.14pdbsearchfield, 1.6.2.13
navigate workspace, 2.6.10pdbsearchhomology, 1.6.2.15
new icm session, 1.6.1.2pdbsearchidentity, 1.6.2.14
     table, 10.1.1pdbsearcsequence, 1.6.2.16
     table, 10.1.1peptide, 2.3
nmr model, 2.2.1.4perspective, 1.6.3.9, 4.10.6
nof, 6.11.1ph4, 6.5.5
     chemical, 6.11.1     draw 2d, 6.5.5.1
non-contiguous selection, 2.6.18          3d, 6.5.5.2
number of sp3, 6.11.1     search, 6.5.5.3
numbers, 6.3.28pharmacophore, 6.3.35, 6.5.5.5, 13.6.2
object, 2.1.11, 2.5, 13.3     2D, 13.4.6
objects, 3.1.2     3D, 13.4.5
     in table, 10.3     clone, 6.5.5.2
     in.table, 10.3     draw2D, 6.5.5.1
occlusion, 4.3.12, 4.10.5     draw3D, 6.5.5.2
     shading, 4.3.12     edit, 6.5.5.1, 6.5.5.2
          effect, 4.10.5     move, 6.5.5.2
occupancy, 4.1.3, 13.3.10     new, 6.5.5.2
     display, 2.2.1.5     search, 6.5.5, 6.5.5.3, 13.4.5, 13.4.6
oda, 3.5.13phi, 4.8.5
older version, 1.6.1.10picking, 4
omega, 4.8.5picture, 1.6.1.14, 2.1.14, 4.15.2, 5.6.3
open, 1.6.1.3, 2.4, 10.1.2     tips, 2.1.14
     file, 2.4     chart, 10.4.6
     password, 2.4.1pka, 6.15
     with password, 1.6.1.4planar, 3.5.7, 4.8.5
     movie, 4.16, 4.16.2     angle, 3.5
     password, 1.6.1.4, 2.4.1     angle, 4.9.2
optimal, 3.5.13plane, 4.3.10, 4.13, 4.13.1, 4.14
orange, 2.6.5plot, 2.7, 2.7.8, 10.4, 10.4.1, 10.4.4, 10.4.7, 10.4.9, 10.4.11, 10.4.12, 10.4.13, 10.4.14, 10.4.15, 10.4.16, 10.4.17, 10.4.18, 10.4.19
     selection, 2.6.5     axis, 10.4.9
origin, 4.8.11     color, 10.4.12
other selection, 2.6.19     function, 1.6.9, 1.6.9.1
overlay, 13.3.3     grid, 10.4.13
package.activeicm, 5.13     header, 10.4.7
packing, 3.3.1     inline, 10.4.19

     mark, 10.4.11     structure, 3
     preferences, 2.7.8          analysis, 3.5
     regression, 10.4.14               closed cavities, 3.5.4
     selection, 10.4.16               contact areas, 3.5.3
     zoom translate, 10.4.15               distance, 3.5.6
     axis, 10.4.13               find related chains, 3.5.1
     display, 10.4.13               finding dihedral angle, 3.5.8
     grid, 10.4.13                    planar angle, 3.5.7
     inline, 10.4.19               rama export, 3.5.10
     logarithmic, 10.4.10               ramachandran plot, 3.5.9
pls, 6.18, 6.19, 7, 10.6, 13.7               rmsd, 3.5.2
png, 1.6.1.14, 4.15, 4.15.2, 5.6.3, 6.2, 6.2.6               surface area, 3.5.5
pocket, 2.1.8, 3.2, 3.2.1, 3.2.2, 3.5.14, 13.3.7          tutorials, 13.3
     surface, 3.2.1               analysis, 13.3.4
     peptide, 2.1.8               contact area, 13.3.5
     properties, 2.1.8               convert, 13.3.2
pocketome, 2.2, 2.2.2               hydrogen bond, 13.3.6
portait, 2.7.6               icmpocketfinder, 13.3.7
post edit ligand, 9.5.8               search, 13.3.1
postscript, 2.7.6               superimpose, 13.3.3
powerpoint, 13.2     superposition, 3.4
ppt, 5.12, 5.14          select, 3.4.1
predict, 6.18, 6.19, 7, 7.2, 10.6          sites by apf, 3.4.6
     metabolic oxidation, 8.8          superimpose 3D, 3.4.3
predicting bioassays, 7.2               grid, 3.4.5
     compound properties, 7.2               multiple proteins, 3.4.4
preferences, 2.7protein-protein, 3.5.13
presentatio, 5.6.5proximity, 4.3.3, 4.3.4
presentation, 5.7, 5.12psa, 6.4.9
presentations, 5psi, 4.8.5
press-and-hold to rotate, 6.4.8pubchem, 6.1
pretty view, 9.3.6publication quality images, 4.3.2
primary aliphatic amines, 6.15pubmed, 2.2.1.7
principal component analysis, 10.5purple box, 1.6.3.23, 9.8.1
          regression, 7qs hydrogen bond, 3.2.3
     components, 7.5qsar, 6.18, 6.19, 7.1, 13.7
print, 4.7, 10.4.17, 10.7.3     learn predict, 6.18
     plot, 10.4.17     predict, 6.19
printer.resolution, 2.7.6quality, 1.6.1.15, 2.7.5
pro-drug, 6.23query molt, 11.4
prodrug, 6.23     processing, 6.5.3
project, 1.6.1.5, 13.4.4.6     setup, 6.5.1
     close, 1.6.1.13quick, 2.1.14
     rename, 1.6.1.9     image, 4.15.2
properties, 4.8.2, 6.11     start move structure, 2.1.3
property, 6.4.9          read pdb, 2.1.2
     monitor, 6.4.9          representation, 2.1.6
protect, 5.6.7          selection, 2.1.5
protein, 3.4.6               level, 2.6.3
     health, 3.5.11          what is selected, 2.6.4

     start color, 2.1.7resize, 4.3.9.1, 4.15.3
quit, 1.6.1.19     mesh, 4.3.9.1
     group, 6.25.7, 6.31.4resolution, 2.2.1.3
          table, 6.31.2restore, 1.6.2.11, 4.3.10, 4.13.1
     groups, 6.31.2     recent backup, 1.6.2.11
r-group, 6.25.7, 6.31.2restraing, 9.11.1, 9.11.2
     decomposition, 6.25.7rgroup, 6.31.4
     enumeration, 6.25.7ribbon, 1.7.1, 2.7.9, 4.1.3
racemic, 6.3.28, 6.17.5     preferences, 2.7.9
rainbow, 2.7.5, 4.8.15, 6.3.35     style, 2.7.9
ramachandran plot, 3.5, 3.5.10     breaks, 4.1.3
random forest, 7, 13.7     cylinders, 4.1.3
range, 4.10.7.2     smooth, 4.1.3
ratio.selection, 2.7.5     worm, 4.1.3
     dock ligand, 9.8ribbonColorStyle, 2.7.9
reactions, 6.8, 6.31.5right, 2.1.12
reactivity, 6.11.2     click, 2.1.12
read, 1.6.1.3, 1.6.1.17, 2.4, 6.3.1rigid, 6.33
     chemical, 6.1     super, 6.33.2
          spreadsheet, 6.3.1          table, 6.33.1
     table, 10.1.2ring, 6.4.3, 6.4.6, 6.5.1
     pdb, 2.1.2rings, 6.3.28, 6.20, 6.33
     table, 10rmsd, 3.5, 3.5.2
reagent, 6.31.5rock, 1.6.3.15, 4.10.7, 4.10.7.1, 5
rear, 4.3.10, 4.13.1     speed, 4.10.7.2
recent files, 1.6.1.17root mean square deviation, 3.5.2
     pdb codes, 1.6.1.18rotate, 1.6.3.15, 2.1.3, 4, 4.10.7, 4.10.7.1, 4.12, 4.12.1, 4.12.2, 5, 6.3.34
receptor, 3.2.1, 3.2.2, 6.6, 9.3.12     chemical, 6.3.34
     flexibility, 9.14     when pasting, 6.4.8
     pocket, 9.3.1     easy, 1.6.3.12
          surface, 9.3.1, 9.3.2     speed, 4.10.7.2
recover, 1.6.2.11rotating fragment in editor, 6.4.8
redo, 1.6.2.10, 6.4.11, 9.5.5rotation, 4.12.1
regresion, 10.4.14row, 10, 10.1.21, 10.1.32, 10.1.42
regression, 7.1, 7.5, 13.7     flag, 10.1.12
relationship, 7, 10.6     height, 10.1.6
relaxed ligand, 9.3.9     mark, 10.1.12
remove.explixit.hydrogens, 6.12     hide, 6.3.8
     salt, 6.12     show, 6.3.8
rename, 10.1.24ruler, 4.8.15
     colunn, 10.1.24rxn, 6.4.13
     project, 1.6.1.9sali, 6.32.3
replace chemical, 6.3.32     bridge, 13.3.6
replacement, 9.6salts, 6.3.18
representation, 1.6.3.19sample, 6.33
residue, 2.7.7sar, 6.25.7, 6.32
     alternative orientaiton, 13.3.11     analysis, 6.32
     range, 2.6.18     table, 6.32.2
     content, 1.6.4save, 2.5, 4.3.11, 4.10.7.4, 6.2.3, 10.4.18, 10.7.3
residues, 3.2.1, 3.2.2     SMILES, 6.4.15

          spreadsheet workspace, 6.2.1     structure, 1.6.4, 4.1.3
          to chemical spreadsheet, 6.4.14select, 2.6.12, 2.6.13, 10, 10.1.42
     docked ligand, 9.17     a tree branch, 10.7.2
     file, 2.5     all, 2.6.14
     hits, 9.5.7     amino acid, 2.6.13
     image plot, 10.4.18     duplicates, 6.29
     ligand receptor complex, 9.17     molecule, 2.6.12
     object, 2.1.9     neighbors, 2.6.15
     pdb, 2.5          graphic, 2.6.16
     project icb, 2.1.10     object, 2.6.11
     slide, 5.4     residue, 2.6.13, 2.6.18
     smiles string, 6.4.15          by number, 2.6.18
     table, 10.1.20          number, 2.6.18
          spreadsheet, 9.5.7     tree, 10.7.2
     tree, 10.7.3     atom, 2.1.5, 2.6.3
          sdf, 6.4.14     graphical, 2.1.5, 2.6.3
     image, 1.6.1.15, 2.1.14     object, 2.1.5, 2.6.3
     object, 2.1.9     purple.box, 1.6.3.23
     password, 1.6.1.11     residue, 2.1.5, 2.6.3
     picture, 1.6.1.15     workspace, 2.1.5, 2.6.3
     project, 1.6.1.8, 1.6.1.9, 1.6.1.10, 2.1.10selectall, 1.6.2.3
     table.view, 10.1.7selecting.neighbors, 2.6.16
saving, 1.6.1.8selection, 2.6.4, 2.6.5, 2.6.21, 4.3.4, 6.4.11, 10.4.16, 10.7.2, 10.7.4
     project, 1.6.1.8     clear, 1.6.2.7
scaffold, 6.14     neighbors, 1.6.2.8
scale, 2.7.5     alignment, 2.6.19
     r group, 9.7     all, 1.6.2.3
score, 9.4, 13.6.3, 13.6.5     alter, 2.6.7
screen, 6.35, 13.6.4     atom, 1.6.2.5
screenshot, 4.16, 4.16.2     basic, 2.6.2
     movie, 4.16.2     change, 2.6.7
script, 2.3, 5.6.4, 5.6.5     clear, 1.6.2.7
sdf, 6.2, 6.2.2, 6.2.4, 6.2.5, 6.2.6, 6.3.35, 6.10, 6.10.3, 6.17.1, 9.9, 11.1     column, 10.1.22
search, 6.10, 6.10.4, 11.2     filter, 1.6.2.5, 2.6.8
     chembl, 2.2.3     graphical, 2.6.16
     drugbank, 2.2.8     invert, 1.6.2.6, 10.1.22
     filter, 6.5.2     level, 1.6.3.3
     in workspace, 1.6.2.4     mode, 1.6.3.4
     pdb, 2.2.1     near atoms, 1.6.2.8
          chemical, 2.2.1     neighbors, 1.6.2.5, 1.6.2.8, 2.6.15, 2.6.17
          ligand code, 2.2.7     object, 2.6.11
     pocketome, 2.2.2     other, 2.6.19
     pubchem, 2.2.9     properties, 1.6.2.5
     surechembl, 2.2.4     range, 10.1.22
     tab field, 2.2.1.3     residue, 1.6.2.5
          pdb chemical, 2.2.1.1     row, 10.1.22
               sequence, 2.2.1.2     sphere, 2.6.15
     uniprot, 2.2.6     spherical, 1.6.2.8
     in.workspace, 1.6.2.4     superposition, 3.4.1
secondary aliphatic amines, 6.15     table, 2.6.19, 10.1.22

     tools, 2.6.1, 2.6.2, 2.6.7, 2.6.8smooth, 4.3.9.3
     whole, 2.6.11solid, 4.3.9.3
     workspace, 2.6.9, 2.6.17sort table, 1.6.10.4
selectioninvert, 1.6.2.6sorting compounds, 10.7
selections, 2.6sp3, 6.11.1
selectneighbors workspace, 2.6.17spec, 1.7.2
sequence, 1.6.4, 2.2, 2.2.1.2, 2.2.5, 2.2.6, 2.3, 13.3speed, 4.10.7.2
     pattern, 2.2.1.2split, 6.32.1
set, 6.3.31spreadsheet, 6.17.2
     formal charges, 6.15standard table, 10.1
setup ligand receptor, 9.1standardize, 6.12
shading, 4.3.12     table, 6.12
shadow, 4.10.2start, 6.10.2
share model, 7.1.4stereo, 2.7.6, 4.6, 6.3.28, 6.4.2
shell preferences, 2.7.10     bond, 6.4.2
shift, 4.8.3     hardware, 1.6.3.7
shine, 1.7.2, 2.7.5     side-by-side, 1.6.3.6
shineStyle, 2.7.3stereoisomer, 6.17.5
show, 5.3.1, 10.1.36stereoisomers, 6.22
     hide column, 10.1.36stick, 2.7.5
side, 6.3.29stl, 4.7
     by side, 6.3.29stop, 4.10.7.3
               stereo, 1.6.3.6store, 1.6.3.19, 4.10.7.4
     chain refinement, 9.13     current view, 1.6.3.19
sigmaLevel, 3.3.6, 3.3.7strain, 3.5.11, 6.24, 6.24.2, 9.4
similarity, 6.27structure, 3.3.3, 7, 10.6, 13.3
single, 6.4.10     analysis, 13.3.4
singlet, 6.4.7     representation, 4.1
sites, 3.4.6     smiles, 6.17.4
size, 3.2.3.1structures, 6, 6.1
sketch accents, 4.10.3style, 2.7.5
     markush, 6.31.1substituent, 6.31.2, 9.5.2
     smiles, 6.4.12substructure, 6.10.4, 6.13
     accents, 1.6.3.14, 4.10.3     alerts, 6.13
skin, 1.7.1, 4.1.4superimpose, 1.6.8, 3.4.2, 3.4.6, 13.3.3
slab, 4.3.10, 4.13.1     3D, 3.4.3
slice, 4.13     Calpha, 3.4.3
slide, 4.10.7.4, 5.2, 5.3.1, 5.6.1     arrange.grid, 3.4.5
     effects, 5.5     backbone, 3.4.3
     movie, 4.16.1     flexible, 6.33.3
          file, 5.2     heavy atoms, 3.4.3
     navigation, 5.3.2     multiple, 3.4.4
     show, 5.3     rigid, 6.33.1, 6.33.2
     blend, 5.5     substructure, 6.33.1, 6.33.2, 6.33.3
     edit, 5.4.1superposition, 6.33, 6.34.1, 6.34.2, 13.3.3, 13.6.1
     effect, 5.5surface, 1.7.1, 2.7.5, 3.2.1, 3.2.2, 4.1.6, 4.3, 4.3.3, 4.3.4
     smooth, 5.5     area, 3.5
     transition, 5.5     area, 3.5.5
slides, 4.16.1, 5, 5.1, 5.3surfaces, 3.2, 4.3.1, 4.3.2, 4.10.5
smiles, 6.4.9, 6.11, 6.17, 6.17.3, 6.17.4symmetry, 3.3.1, 3.3.3, 13.3.8, 13.3.9

tab, 10.1.2, 10.1.20     edit, 6.3.17
     pdb, 1.7.4     excel, 6.3.10, 10.1.19
table, 2.3, 6.1.3, 6.3.24, 6.3.25, 6.3.28, 6.3.30, 6.3.31, 6.3.34, 6.3.35, 6.17.2, 6.20, 6.33.1, 9.9, 10, 10.1.32, 10.1.37, 10.1.42, 10.4, 10.4.1, 10.4.4, 10.4.7, 10.4.9, 10.4.11, 10.4.12, 10.4.13, 10.4.14, 10.4.15, 10.4.16, 10.4.17, 10.7.1     filter, 6.3.12, 10.1.40
     alignment, 10.1.11     find-replace, 6.3.13
     clone, 10.1.15          to screen, 10.1.4
     color, 10.1.9     font, 10.1.10
     column format, 10.1.37     grid lines, 10.1.4
     copy, 10.1.33, 10.1.34     hide, 10.1.36
     delete, 10.1.16     hyperlink, 6.3.15
     edit, 10.1.23     insert, 10.1.30
     filter, 10.1.40     join, 1.6.10.5
     find, 10.1.8     label, 6.3.14
          replace, 6.3.32     landscape, 10.1.17
     font, 10.1.10     mark, 6.3.14
     grid, 10.1.5     merge, 1.6.10.5, 6.3.23, 6.28
     histogram, 10.4.1     mouse, 10.1.44
     insert, 10.1.25     name, 10.1.14
     layout, 10.1.5     new, 10.1.1
     learning, 10.6     options, 10.1.13
     mark, 10.1.12     orientation, 10.1.17
          row, 10.1.12     portrait, 10.1.17
     mouse, 10.1.44     print, 6.3.11, 10.1.4, 10.1.18
     navigation, 10.1.4     read, 10.1.2
     new column, 10.1.25     rename, 10.1.14
     plot, 10.4     right click, 10.1.13
     print, 10.1.18     row, 10.1.30
     rename, 10.1.14     rows, 1.6.10.7
     rightclick, 10.1.13     save, 6.3.9, 10.1.3, 10.1.4, 10.1.20
     save, 10.1.3     scale, 10.1.17
          selection, 10.1.3     scroll, 10.1.4
     search, 10.1.8     sdf, 6.3.9
     select, 10.1.22     select, 10.1.22
     setup, 10.1.17     setup, 10.1.17
     sort, 10.1.39     sort, 1.6.10.4, 6.3.5, 10.1.39
     split fragments, 6.3.33     standard, 10.1
     view, 10.1.5     view, 6.3.29
          save, 10.1.7     width, 10.1.4
     zoom translate, 6.3.30tables, 6.27, 10
     action, 10.1.44tag, 2.6.21, 9.5.7, 10.1.43
     alignment, 10.1.11tags, 2.6.21
     append, 10.1.40tautomer, 6.21
     clone, 10.1.15tautomers, 6.21
     color, 10.1.9temperature, 3.5.12
     column, 6.3.4, 10.1.25, 10.1.29, 10.1.36template, 6.4.6, 6.33
     columns, 6.3.8templates, 6.4.6
     compare, 6.3.22terminal, 6.3.28
     copy, 6.3.6tether, 9.11.1, 9.11.2
     cursor, 10.1.44text, 2.7.7, 5.6, 5.6.1, 5.6.6, 6.3.28, 6.10.4, 10.4.20
     delete, 10.1.13, 10.1.16     search, 6.5.4
     double.click, 10.1.44texture, 1.7.6

three, 6.3.24unit, 3.3.3
threshold, 2.7.5unsatisfied hydrogen bonds, 9.3.8
tier, 2.1.13     hyrdrogen bonds, 9.3.8
     racemic, 6.17unusual peptide, 2.3
tools 3D, 1.6.6     activeicm, 5.12
     analysis, 1.6.7user, 6.10.5
     append rows, 1.6.10.7     defined groups, 9.5.3
     extras, 1.6.9     modifiers, 9.5.3
          plot function, 1.6.9.1user-defined groups, 6.4.5
     superimpose, 1.6.8uundisplay-all, 1.6.3.1
     table, 1.6.10van der waal, 4.8.14
          Learn, 1.6.10.1variable, 2.7.7
          clustering, 1.6.10.3verbose, 6.20
          merge, 1.6.10.5     large sdf files, 6.1.2
          predict, 1.6.10.2vicinity, 6.20
tooltip, 10.4.21video, 4.16, 4.16.1, 4.16.2
     balloons, 10.4.21view, 1.6.3.19, 5.3.1, 6.3.28
torsion, 4.12.6, 9.5.4     animate view, 1.6.3.15
     angles, 4.12, 4.12.6     center, 1.6.3.20
toxscore, 6.11.2     color background, 1.6.3.18
trace, 4.1.10     fog, 1.6.3.5
transitions, 5     macroshape, 1.6.3.22
translate, 2.1.3, 4, 4.12, 6.3.30     menu, 1.6.3
translation, 4.12.3, 10.4.15     mesh clip, 4.13.1
transparent, 4.3.9.3     perspective, 1.6.3.9
     background, 4.15.3     selection level, 1.6.3.3
tree, 6.25.7, 10.7.2, 10.7.3, 10.7.4          mode, 1.6.3.4
     distance, 6.25.3     shadow, 1.6.3.13
     edit, 6.25.4     sketch accents, 1.6.3.14
     reorder, 6.25.3     slide show, 5.3.1
triplet, 6.4.7     tools, 1.6.3
tsv, 10.1.20     tree, 10.7.4
tut analyze alternative orientations, 13.3.11     undisplay all, 1.6.3.1
          occupancy, 13.3.10virtual ligand screening, 8
          symmetry, 13.3.9virus, 3.3.3
tut3e, 13.3.12visualize apf fields, 9.3.11
tutorial 2D pharmacophore, 13.4.6     ligand strain, 9.3.10
     3D pharmacophore, 13.4.5volume, 6.4.9
     chemical clustering, 13.4.3wavefront, 1.7.6, 4.3.11
          search, 13.4.2web, 13.2
     molecular documents, 13.2     browser, 1.6.1.12
tutorials, 13weight, 6.11
two, 6.3.24weighted, 10.7.1
unclip, 4.3.10, 4.13.1width, 10.1.21
undisplay, 2.1.4, 4.1.7window, 2.1.13
     origin, 4.8.11windows, 2.1.13.1, 6.10.1
undo, 1.6.2.9, 2.7, 6.4.11, 9.5.5wire, 1.7.1, 2.7.5, 4.1.1
     redo, 9.5.5wireBondSeparation, 2.7.1
uniprot, 2.2.6workspace, 2.1.4, 6.7.2
unique, 6.3.28, 6.29     panel, 2.1.4

     navigation, 2.6.10 
write, 2.1.14, 2.5, 10.4.18 
     excel, 6.2.3 
     image, 1.6.1.15 
     images, 4.15 
     pdb, 2.5 
     image, 1.6.1.15 
     object, 2.1.9 
     picture, 1.6.1.15 
     project, 1.6.1.8, 2.1.10 
     table, 10.1.3 
     ray, 1.6.5 
xi, 4.8.5 
xls, 6.2.3 
xlsx, 6.2.3 
xstick, 4.1.2 
zoom, 2.1.3, 4, 4.12, 4.12.4, 6.3.30, 10.4.15 

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