Sep 13 2018 Feedback.
Contents
 
Help Videos
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, 5.8.8, 7.3.24, 7.3.28, 7.14, 7.17.2, 7.17.4FTP.createFile, 3.7.11
     Interaction Diagram, 10.3.7     keep File, 3.7.11
     bioisostere, 7.9.1     proxy, 3.7.11
     from PDB, 7.1.1Filter.zip, 3.7.2
     screening, 9Force Auto Bond Typing, 3.7.11
     to 3D, 7.17, 7.17.3GIF, 2.6.1.15, 5.16, 5.16.2
     depiction, 7.17.2GRAPHIC.store Display, 3.7.3
3D, 5.6, 5.8.8, 7.1.3, 7.3.24, 7.3.28, 7.3.31, 7.17.2, 14.2     NtoC Rainbow, 3.7.4
     QSAR, 7.36.4, 8.4, 14.8     alignment Rainbow, 3.7.4
     chemical, 7.4.16, 7.17.1     atomLabelShift, 3.7.7
     interactive ligand editor, 2.7.5     ballStickRatio, 3.7.1
     ligand editor, 10.3.4     center Follows Clipping, 3.7.3
     object, 5.3.9     clash Style, 3.7.3
     pharmacophore, 10.3.11     clashWidth, 3.7.3
     print, 5.7     clip Grobs, 3.7.3
     printing, 5.7          Skin, 3.7.3
     screening, 9          Static, 3.7.3
     stereo, 5.6     discrete Rainbow, 3.7.4
3DQsar, 8.4     displayLineLabels, 3.7.7
3Dqsar tutorial, 14.8     displayMapBox, 3.7.3
     bioisostere, 7.9.2     distance Label Drag, 3.7.1
     predict local flexibility, 4.5.12     dnaBallRadius, 3.7.9
          protein health, 4.5.11     dnaRibbonRatio, 3.7.9
          tools identify ligand binding pocket, 4.5.14     dnaRibbonWidth, 3.7.9
               oda, 4.5.13     dnaRibbonWorm, 3.7.9
4D dock, 10.16     dnaStickRadius, 3.7.9
     docking, 3.2.2     dnaWormRadius, 3.7.9
APF, 7.35.3, 7.36.4, 8.4, 9, 9.7, 14.8     font Scale, 3.7.7
     template, 7.35     fontColor, 3.7.7
ActiveICM, 2.6.1.12     fontLineSpacing, 3.7.7
Atom Single Style, 3.7.3     grobLineWidth, 3.7.3
Atomic Property Fields, 8.4, 14.8     hbond Ball Period, 3.7.1
Baell, 7.4.9               Style, 3.7.1
Beep, 3.7.11     hbondAngleSharpness, 3.7.1
BlastDB Directory, 3.7.2     hbondMinStrength, 3.7.1
     alphas, 5.8.3     hbondStyle, 3.7.1
COLLADA, 2.6.1.7     hbondWidth, 3.7.1
CPK, 2.7.1     hetatmZoom, 3.7.1
ChEMBL, 3.2.3, 7.1     hydrogenDisplay, 3.7.1
Chemical Cluster, 14.4.3     light, 3.7.3
     Search, 14.4.2     lightPosition, 3.7.3
Clash Threshold, 3.7.10     mapLineWidth, 3.7.3
DNA, 3.3     occupancy Radius Ratio, 3.7.3
Decomposition, 7.33.2     occupancyDisplay, 3.7.3
Dock Directory, 3.7.2     quality, 3.7.3
Drug Bank, 3.2.8     rainbow Bar Style, 3.7.4
Editor, 3.7.2     resLabelDrag, 3.7.7
FILTER.Z, 3.7.2     resize Keep Scale, 3.7.3
     gz, 3.7.2     ribbonRatio, 3.7.9
     uue, 3.7.2     ribbonWidth, 3.7.9

     rocking, 3.7.4     lineWidth2D, 3.7.6
          Range, 3.7.4     orientation, 3.7.6
          Speed, 3.7.4     paper Size, 3.7.6
     selectionStyle, 3.7.3     previewResolution, 3.7.6
     site Label Drag, 3.7.7     previewer, 3.7.6
               Shift, 3.7.7     print, 3.7.6
     siteArrow, 3.7.7     printerDPI, 3.7.6
     stereoMode, 3.7.3     scale, 3.7.6
     stickRadius, 3.7.1     stereoAngle, 3.7.6
     surfaceDotDensity, 3.7.3     stereoBase, 3.7.6
     surfaceDotSize, 3.7.3     stereoText, 3.7.6
     surfaceProbeRadius, 3.7.3INCHI, 7.17.3
     transparency, 3.7.3Icm Prompt, 3.7.10
     wire Width, 3.7.1InChi, 7.3.20, 7.4.12, 7.17.3
     wormRadius, 3.7.9     key, 7.3.20
     xstick Backbone Ratio, 3.7.1Interaction Diagram 2D, 10.3.7
          Hydrogen Ratio, 3.7.1     Directory, 3.7.2
          Style, 3.7.1JPEG, 2.6.1.15
          Vw Ratio, 3.7.1KMZ, 2.6.1.7
GROB.arrowRadius, 3.7.3Log Directory, 3.7.2
     atomSphereRadius, 3.7.3LogP, 8, 11.6
     contourSigmaIncrement, 3.7.3LogS, 8, 11.6
     relArrow Size, 3.7.3MOL, 7, 7.3.3, 7.3.24, 7.3.25, 7.3.26, 7.3.27, 11.2
     relArrowHead, 3.7.3MOLT, 12.1
GUI.auto Save, 3.7.4MOVIE.frame Grab Mode, 3.7.4
               Interval, 3.7.4MPO, 7.31
     enumberation Memory Limit, 3.7.11Map Atom Margin, 3.7.10
     max Nof Recent Files, 3.7.11     Sigma Level, 3.7.10
          Sequence Length, 3.7.4Markush, 14.4.9
     splash Screen Delay, 3.7.11     create, 14.4.7
               Image, 3.7.11     File Size Mb, 3.7.11
     table Row Mark Colors, 3.7.4Max_Fused_Rings, 7.11
     workspace Folder Style, 3.7.4Mnconf, 3.7.10
     workspaceTabStyle, 3.7.4Model, 8.4
HTTP.proxy, 3.7.11MolPSA, 7.11
     support Cookies, 3.7.11MolScreen, 9
     user Agent, 3.7.11MolVol, 7.11
Hbonds, 10.3.4Molcart, 7.5.3
How To Guide, 2MoldHf, 7.11
Html, 3.2.1.6Movie.fade Nof Frames, 3.7.4
Http Read Style, 3.7.11     quality, 3.7.4
Hydrogen.bond, 3.7.5          Auto, 3.7.4
ICM Browser How To, 2.1Nof_Atoms, 7.11
          Pro How To, 2.2Nof_Chirals, 7.11
IMAGE.bondLength2D, 3.7.6Nof_HBA, 7.11
     color, 3.7.6Nof_HBD, 7.11
     compress, 3.7.6Nof_Rings, 7.11
     gammaCorrection, 3.7.6Nof_RotBonds, 7.11
     generateAlpha, 3.7.6Output Directory, 3.7.2
     lineWidth, 3.7.6PAINS, 7.4.9, 7.11.2

PCA, 8.1, 8.5, 14.4.4SDF, 7, 7.3.24, 7.3.25, 7.3.26, 7.3.27, 11.2
     analysis, 7.26SEQUENCE.site Colors, 3.7.4
PDB, 3.2.1.6, 4.1.2, 4.3.3, 7.1.1, 10.19SITE.label Style, 3.7.7
     Directory, 3.7.2     labelOffset, 3.7.7
          Style, 3.7.2     wrap Comment, 3.7.7
     link, 11.1.39SLIDE.ignore Background Color, 3.7.4
     Search, 2.6.2.12, 2.6.2.13, 2.6.2.14, 2.6.2.15, 2.6.2.16          Fog, 3.7.4
          Field, 2.6.2.13SMILES, 7.1.2, 7.2.4, 7.4.12
          Homology, 2.6.2.15Select Min Grad, 3.7.10
          Identity, 2.6.2.14Show Res Code In Selection, 3.7.7
          Sequence, 2.6.2.16SureChEMBL, 3.2.4
     convert, 4.1.2Swissprot, 2.6.1.7
PFAM, 2.6.1.7     Dat, 3.7.2
PLOT.Yratio, 3.7.8     link, 11.1.39
     color, 3.7.8Temp Directory, 3.7.2
     date, 3.7.8USER.email, 3.7.11
     draw Tics, 3.7.8     friends, 3.7.11
     font, 3.7.8     full Name, 3.7.11
     fontSize, 3.7.8     organization, 3.7.11
     labelFont, 3.7.8     phone, 3.7.11
     lineWidth, 3.7.8Uniprot, 11.1.39
     logo, 3.7.8Van Drie, 7.33.4
     markSize, 3.7.8     Label Style, 3.7.7
     orientation, 3.7.8Water Radius, 3.7.10
     paper Size, 3.7.8Wire Style, 3.7.1
     previewer, 3.7.8XPDB Directory, 3.7.2
     rainbowStyle, 3.7.8Xstick, 2.7.1
     seriesLabels, 3.7.8a-bright, 2.7.2
PLS, 8.1about model, 8.1.1
PNG, 2.6.1.15, 3.1.14, 5.16, 5.16.2acceptor, 7.4.9, 7.36.1
Projects Directory, 3.7.2active, 6.7
Prosite Dat, 3.7.2activeICM, 6.8
     Viewer, 3.7.2activeicm, 6.7, 6.12, 6.14, 6.14.1
Pub Chem, 3.2.9     advanced, 6.14
PubMed, 3.2.1.7     background images, 6.15
     Reference, 11.1.39     control, 6.13
Pubchem, 3.2.9activeicmjs, 6.16
QSAR, 8, 8.1, 11.6, 14.8activity cliff, 7.33.4, 7.33.5, 14.4.11
R, 7.8, 7.33.1          tutorial, 14.4.11
R-Group, 7.33.2activityy, 8, 11.6
R-groups, 10.5.3add database, 7.10.3
RMSD, 4.4.2     new data, 7.3.7
RNA, 3.3     to table, 10.5.7
Ramachandran Plot, 4.5.9adding fragment, 7.4.8
Real Format, 3.7.10          in editor, 7.4.8
     Label Shift, 3.7.7administration, 7.10.5
          Style, 3.7.7album, 5.15.3
SALI, 7.33.4, 14.4.11alias, 7.4.5
SAR, 8, 9.7, 11.4.23, 11.6align, 3.1.11, 7.14
     table, 7.33.2, 14.4.9     color 2D scaffold, 7.14

alpha, 2.7.2atomic energy circles, 10.3.5
     channel, 3.7.6     property field, 7.35.1, 7.35.2, 10.3.11
ambient, 2.7.2               score, 7.36.2
amidinium, 7.15          fields, 4.4.6, 7.36, 7.36.1, 7.36.3, 14.6
amino acid, 3.3attachment, 7.4.3, 7.5.1
     acids, 7.4.6     point, 7.32.4
anaglyph, 5.6author, 3.2.1.3
analysis, 2.6.4     close tree, 7.25.5
angle, 4.5.7, 4.5.8, 5.8.5, 5.9, 5.12.6     play slide, 6.13
animate, 2.6.3.15, 5.10.7ave, 11.7.1
     view, 5.10.7avi, 5.16, 5.16.2
animation, 5.10.7.1, 5.10.7.2, 5.10.7.3, 5.10.7.4axes, 11.4.14
     store, 5.10.7.4axis, 11.4.10
animations, 6     options, 11.4.9
annotate, 3.6.21, 7.13     grid, 11.4.9
     by substructure, 7.13     range, 11.4.9
     plot, 11.4.22     title, 11.4.9
antialias, 2.6.1.15, 2.6.3.10b-factor, 4.5.12, 14.3.10
     lines, 2.6.3.17backbone, 5.1.10
     lines, 2.6.3.17background, 5.4.2, 5.4.3
apf, 4.4.6, 7.35.1, 7.35.2, 7.36, 8, 10.3.11, 10.18, 14.6, 14.6.1, 14.6.2, 14.6.3, 14.6.4, 14.6.5     images activeicm, 6.15
     flexible template, 7.35.2     image, 5.4.3
     pairwise, 7.35.1backup, 2.6.2.11
     super, 7.35bad, 7.11
     template, 10.13     groups, 7.4.9
     tools, 7.36ball, 3.7.5
          3DQSAR, 7.36.4     and stick, 2.7.1
          consensus ph4, 7.36.1balloon, 11.4.24
          pairwise score, 7.36.2bases, 7.4.6
          screen, 7.36.3basicsel, 3.6.2
     tutorial, 14.6bayesian classifier, 8
          cluster, 14.6.5best, 7.3.34
          consensus, 14.6.2bicyclics, 7.4.6
          score, 14.6.3binding properties, 5.3.1
          screen, 14.6.4bioinfo menu, 2.6.4
          superposition, 14.6.1bioisoester, 7.9
     alignment, 7.35.3bioisostere, 7.9, 7.9.1, 7.9.2, 10.8
append, 11.1.43biological, 4.3.3
     table, 11.1.43biomolecule, 2.6.5, 4.3.3, 14.3.8, 14.3.12
     rows, 2.6.10.7blast, 3.2.5
applying prediction models, 8.2     search, 3.2.5
area, 4.5.3, 4.5.13, 14.3.5bond, 4.2.3, 4.2.3.1, 4.2.3.2, 7.4.10
aromatic, 7.3.28, 7.36.1     type, 7.7.1, 7.7.2, 7.7.3
arrange, 3.1.13.1bonding, 5.1.8
     window, 3.1.13.1     preferences, 3.7.1
as2_graph, 3.6.5box, 3.7.7, 5.8.15
assign, 5.1.3     size, 10.9.1
     2D coordinates, 7.17.2browse, 7.3.31
atom, 3.7.5, 7.3.28     mode, 7.3.31
atomLabelStyle, 3.7.7     molt, 12.2

buttons, 6.14     sketch, 14.4.1
bye, 2.6.1.19     space, 7.27
     alpha, 5.1.10     spreadsheet, 3.2.3, 7.1.3, 7.3.1, 7.4.14, 14.4.1
     trace, 5.1.10          compare, 7.3.22
ca-trace, 5.1.10          template, 7.3.2
cache, 6.14.1     spreadsheets, 7.3
calculate, 7.11     substituent, 7.9
     properties, 7.11     substructure, 3.2.1.1
carboxylic acid, 7.15     table, 10.10
cartesian, 7.20          display, 7.3.3
cavities, 4.5     tables, 11.2
     closed, 4.5.4     toxicity, 7.11.2
cell, 4.3.2     2D, 7.7
center, 2.6.3.20, 3.1.3, 5.12, 5.12.5, 10.3.13, 11.1.39     3D, 7.7
     on ligand, 10.3.13     append, 7.4.13
     and representative members, 11.7.2     clustering, 7.25, 7.25.1
change box size, 10.9.1     convert, 7.7, 7.7.1, 7.7.2, 7.7.3
     height of all rows, 11.1.6     draw, 7.4.1
     ligand, 10.5.1     duplicates, 7.3.21
     row height, 11.1.6     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, 7.29
charge, 2.6.3.21, 5.8.2, 7.4.3, 7.5.1, 7.7.1, 7.7.2, 7.7.3, 7.36.1     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
          editor, 7.2.4     search, 7.4.3, 7.5, 7.5.1, 7.5.3
          image, 7.2.6     similarity, 7.4.3, 7.5, 7.5.1, 7.5.3
          table, 7.2.2     spreadsheet, 7.2, 7.2.2, 7.2.4, 7.2.5, 7.2.6, 7.3
     super, 7.34     structure, 7.4.13
     view, 7.3.28     superimpose, 7.34.1, 7.34.2, 7.34.3
chembl, 3.2.3, 3.2.4     superposition, 7.35, 7.35.3
chemical, 7, 7.3.28, 7.3.30, 7.3.31, 7.3.34, 7.3.35, 7.4.10, 7.8, 7.10.4, 7.11.2, 7.17.2, 7.21, 7.32.4, 7.32.5, 7.34, 7.35.1, 7.35.2, 11.7.1, 14.4.4     table, 7.3, 11.2
     clustering, 7.25, 7.25.6cheminformatics, 7, 7.3
     dictionary, 7.4.4, 7.4.5, 7.4.6     tutorials, 14.4
     draw, 14.4.1chemistry, 7.21
          spreadsheet tutorial, 14.4.1     convert, 7.17
     edit buttons, 7.4.11          2dto3d, 7.17.1
     editor, 7.4, 7.4.8     pca, 7.26
     fingerprint, 9     smiles, 7.17.3
     fragments, 7.3.33     duplicates, 7.30
     group, 7.4.5     remove.redundant, 7.30
     groups, 7.4.5, 7.4.8chemspace append, 14.4.4.4
     modifiers, 7.32.2     build visualize, 14.4.4.1
     properties, 14.4.4     compare, 14.4.4.8
     right click, 7.4.3     delete row, 14.4.4.3
     search, 7.5     distinguish, 14.4.4.7
          filter, 7.5.2     export, 14.4.4.5
          text, 7.5.4     project, 14.4.4.6

chi, 5.8.5combine, 2.6.10.5
chiral, 7.22     display style, 3.7.9
chirality, 7.22compact tree, 7.25.5
clash, 3.7.5, 5.8.14compare, 7.3.29, 7.28, 7.29
classes, 7.3.28     table, 7.3.22
classification model, 9.6     tables, 7.28
clear display and planes, 2.6.3.2compatible, 2.6.1.10
     selection, 3.6.6complex, 7.6
     planes, 2.6.3.2compound, 3.2.1.3, 7.21, 11.2
click, 3.1.12, 5.11, 5.12compress, 3.7.6
clip, 5.3.10, 5.13.1conditions, 7.5.2
clipboard, 5.15.3, 11.7.3     gen, 7.20
clipping planes, 5conformation, 7.20
     tool, 5.13conformational entropy, 7.24
     tools, 5.13conformers, 7.20
clone, 2.6.1.2connect, 5.3.9.1, 5.12, 5.12.7
close, 5.3.3, 5.3.4, 10.21     object, 5.12.7
     downstream cluster, 7.25.5connectivity, 7.4.3, 7.5.1
     project, 10.21consensus, 7.36, 14.6.2
     cavities, 4.5.14     pharmacophore, 7.36.1
cluster, 11.7.1construct, 2.6.1.1, 5.10.7.1
     representative.center, 7.25.2     molecule, 2.6.1.1
clustering, 11.7, 14.4.3     object, 2.6.1.1
cns, 7.31contact, 4.5, 4.5.3, 14.3.5
collada, 2.7.6, 5.3.7     surface, 5.3.2
color, 4.5.11, 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, 11.1.44, 11.7.4contacts, 5.3.3, 5.3.4, 7.6, 10.3.12
     background, 5.4.2contour, 4.3.6, 4.3.7
     by, 5.4convert, 4.1.2, 7.17.1, 7.17.5
     chemical, 7.3.35     chemical, 7.3.24
     surface by proximity, 5.3.3          2D 3D, 7.7
               selection, 5.3.4          3D molecular editor, 7.4.16
     table, 7.3.27     local database, 2.6.1.6
     2D sketch, 7.5.5.5     pdb, 14.3.2
     background, 2.6.3.18, 5.4.2          chem, 7.7.1
     distance, 5.8.10     local.database, 2.6.1.6
     mesh, 5.3.9.3     smiles, 7.17, 7.17.3, 7.17.4
     table, 7.3.27converting pdb, 4.1.2
coloring, 5.4.1coordinates, 7.1.3
coloumn, 11.1.24copy, 7.3.25, 7.4.11, 7.4.17, 7.5.5.2, 11.1.34
column, 11, 11.1.21, 11.1.38, 11.1.39, 11.4, 11.4.1     cell, 11.1.35
     annotation, 11.1.40     chemical, 7.3.25
     order, 11.1.28     paste row, 11.1.34
     row width, 11.1.21     row, 11.1.35
     statistics, 11.1.31     rows, 11.1.43
     visibility order, 11.1.27     selection to table, 11.1.36
     color, 11.1.9     chemical, 7.3.16
     hide, 7.3.8covalent, 10.10.1
     show, 7.3.8     docking, 10.17
combinatorial chemistry, 7.32cpk, 5.1.5
     library, 14.4.8crash, 2.6.2.11

create, 11.1.1     angle, 4.5
     markush, 7.32.3directories preferences, 3.7.2
     new objects, 3.3directory, 3.7
cross section, 5.13dislay ligand receptor interaction, 7.6
crystal, 4.3.2display, 3.1.4, 3.1.13.1, 3.7, 4.2.3, 4.2.3.1, 4.2.3.2, 5.8.14, 5.14, 7.22
crystallographic analysis, 4.3     delete distances, 5.9.4
          biomolecule, 4.3.3     dihedral, 5.9.3
          contour map, 4.3.6     distance restraints, 5.8.13
          convert2grid, 4.3.7     distance2, 5.9.1
          crystallographic cell, 4.3.2          angles, 5.9
          load eds, 4.3.4     formal charge, 5.1.9
          maps cell, 4.3.5     gradient, 5.8.16
          symmetry packing, 4.3.1     hbonds, 10.3.4
          tools, 14.3.8     hydrogen, 5.1.7
     cell, 2.6.5          atoms ligand editor, 10.3.3
     neigbor, 4.3.1     mesh, 5.3.5
     neighbors, 2.6.5     meshes, 5.3.8
crystallography, 4.3.4, 4.3.6, 4.3.7     options, 10.3
csv, 7.2.3, 11.1.2, 11.1.3, 11.1.20     planar angle, 5.9.2
current.slide, 6.13     tab, 2.7.1
curves, 11.4.5     tether, 5.8.12
custom, 5.12, 7.3.3, 7.34     toggle, 5.8.15
     actions, 11.1.39     CPK, 5.1.5
     fragments, 7.13     angle, 5.9.2
     label, 5.8.8     chemical, 7.3.3
     rotation, 5.12.2     dihedral.angle, 5.9.3
cut, 11.1.34     distace, 5.8.10
database, 7.10, 7.32.4, 12.1     distance, 5.8.13, 5.9.1
decompose.library, 14.4.9     electrostatic, 2.6.3.21
decomposition, 7.32.4, 7.33.1, 11.4.23     energy.gradient, 5.8.16
default, 3.1.13     hydrogen, 5.1.7
delete, 2.6.2.1, 3.6.6, 6.6.8          polar, 5.1.7
     all, 2.6.2.2     macroshape, 5.3.6
     column row, 11.1.37     meshes, 5.3.5
     label, 5.8.9          and display.macroshape, 2.7.6
     all, 2.6.2.2     molecule, 7.3.24
     angle.label, 5.9.4     origin, 5.8.11
     column, 11.1.37     potential, 2.6.3.21
     distance.label, 5.9.4     representations, 2.7.1
     label, 5.8.9     restraints, 5.8.13
     row, 11.1.37     ribbon, 5.1.3
     selection, 2.6.2.1     skin, 5.1.4
dendrogram, 7.27.1     surface, 5.1.6, 5.3.1
density, 4.3.4, 4.3.6, 4.3.7     surfaces, 2.7.6
depth, 5.3.12, 5.10.5     table, 7.3.3
dfa, 9.1.3     tethers, 5.8.12
dfz, 9.1.2     wire, 5.1.1
dialog, 6.6.5     xstick, 5.1.2
diffuse, 2.7.2distance, 4.5, 4.5.6, 5.8.10, 5.9, 7.28
dihedral, 4.5.8, 5.8.5     label, 3.7.7

diverse set, 11.7electron, 4.3.4, 4.3.6, 4.3.7
dock, 10.10, 10.10.1     denisty map, 4.3.5
     apf, 10.18     densitry map.contour, 2.6.5
     table, 10.10          map, 2.6.1.7, 2.6.5, 4.3.4, 4.3.6
          covalent, 10.10.1electrostatic potential, 2.6.3.21
docking, 4.5.13, 10.10, 10.10.1, 10.11     surface, 5.3
     templates, 10.13electrostatics, 5.3.1
document, 6.6.4, 6.6.5elegant sketch, 5.10.4
     navigation, 6.6.7element, 7.4.10
documents, 5.15.3embed browser, 6.11
donator, 7.4.9     powerpoint03, 6.8
     envelope, 2.7.1     powerpoint07, 6.9
     surface, 3.7.5     powerpoint10, 6.10
dotted line, 5.1.3     activeicm, 6.13
double, 7.4.10          script, 6.13
doublet, 7.4.7     browser, 6.7, 6.11
dpc, 9.1.4     firefox, 6.7, 6.11
drag, 3.1.11, 3.7.7, 5.8.3, 6.6.4     internet.explorer, 6.7, 6.11
     residue label, 2.6.3.16     microsoft, 6.7
draganddrop, 3.1.11     powerpoint, 6.7, 6.8, 6.9, 6.10
draw, 7.4.17, 7.32.5energy, 4.5.11, 5.8.14, 7.24, 7.24.2
     chemical, 7.4.1entropy, 7.24.1
drop, 3.1.11, 6.6.4enumerate formal charge states, 7.16
drug, 7.11     reaction, 14.4.10
     bank, 3.2, 3.2.8, 7.1enumeration, 7.32.4
drugbank, 7.1eps, 7.2.6
druglikeness, 7.4.9eraser, 7.4.11
dsPocket, 3.1.8evaluate score strain, 10.4
easy rotate, 2.6.3.12exact, 7.28
ecfp, 8.3excel, 7.2.3
edit, 4.2.3.1, 10.5.8exclude fragment, 7.5.2
     2D, 10.5.1     volume, 10.3.11
     chemical moledit, 7.3.26exit, 2.6.1.19
     ligand, 10.5, 10.5.1explicit, 7.3.28
          2D, 10.5.1export, 4.5.10
          editor preferences, 10.2     dock project, 10.20
          multiple substituents, 10.5.2extra windows, 5.2
          tools, 2.6.2.17extract, 3.4.2, 7.1.3
     menu, 2.6.2     2D, 7.1.1
     molecular document, 6.6.1     3d coordinates to spreadsheet, 7.1.3
     molecule, 7.4     icb, 2.6.1.5
     molt, 12.3     object icb, 3.4.2
     selection, 2.6.2.5     icb, 2.6.1.5
     slide, 6.4.1     pharmacophore, 7.5.5.4
     table row, 11.1.23file, 2.6.1.3
     molecule, 7.3.26     close, 2.6.1.13
     structure, 7.3.26     compatible, 2.6.1.10
editpdbsearch, 2.6.2.12     export, 2.6.1.12
eds, 4.3.4, 4.3.6, 4.3.7     high quality image, 5.15.1
effort, 7.20, 7.34     load, 2.6.1.7

     password, 2.6.1.11               labels, 14.1.3
     preferences, 2.6.1.16graphics, 3.1
     quick image, 2.6.1.14     controls, 5
     icb, 3.1.10     effects, 5.10
     recent, 2.6.1.17     panel, 5.2
     bak, 2.6.2.11     preferences, 3.7.3
filter, 12.2     shadow, 2.6.3.13, 5.10.2
     selection, 3.6.8grid, 7.3.3, 7.34
find chemical, 7.3.32grob, 3.7.5, 4.3.4, 4.3.6, 4.3.7, 5.3
fingerprint, 8, 8.3, 14.7group, 7.33.1, 10.6
     method, 8.3     column, 11.1.45
fit, 7.3.34groups, 7.8, 7.11, 7.12
fitting, 11.4.15guanidinium, 7.15
flex super, 7.34.3gui, 3.1.1, 3.7.4
flexibility, 4.5.12     menus, 2.6
flexible, 7.34     preferences, 3.7.4
     docking, 10.14     tabs, 2.7
     receptor groups, 10.14h-bond, 4.2.3, 4.2.3.1, 4.2.3.2
fog, 2.6.3.5, 5, 5.10.1halogen, 7.11.1
font, 3.7, 3.7.7, 4.2.3.1, 5.8.2, 5.8.3, 7.3.28, 11.1.39, 11.7.4hardware stereo, 2.6.3.7
     preferences, 3.7.7hbond, 4.2, 14.3.6
form view, 11.1.5header, 3.2.1.6, 11.4.8
formal charge, 5.1.9, 7.15, 7.16health, 4.5.11
format, 11.1.2, 11.1.39heatmap, 11.4.6
formula, 7.4.9, 7.11     example, 11.4.6.1
fragment, 7.3.35, 7.33.1, 10.11help, 1
     linking, 10.11     videos, 1
fragments, 7.8hetero, 7.3.28
free radical, 7.4.7     scan, 10.7
freeze column, 11.1.29hide, 11.1.38
     row, 11.1.30     column, 11.1.27
frequency, 7.3.35high, 2.6.1.15
front, 5.3.10, 5.13.1     quality, 2.6.3.11
full scene antialias, 2.6.3.10highlight new data, 7.3.7.1
     screen, 2.6.3.8histogram, 11.4, 11.4.1, 11.4.8, 11.4.10, 11.4.12, 11.4.13, 11.4.14, 11.4.15, 11.4.16, 11.4.17, 11.4.19, 11.4.21
function, 11.1.25, 11.1.31     bins, 11.4.3
functional.groups, 7.13     options, 11.4.2
general preferences, 3.7.5     bin.size, 11.4.2
generalselecttools, 3.6.1     bins, 11.4.3
generator, 4.3.3, 7.20     color, 11.4.2
getting started, 3     source, 11.4.2
glasses, 5.6     style, 11.4.2
google, 2.6.1.7     title, 11.4.2
     objects, 5.3.7homology, 3.2.1.2, 3.2.5
     3D, 2.7.6, 5.3.7hover, 11.4.24
graphical display, 7.7.2, 7.7.3     3D editor, 14.5
          tutorial, 14.1     add columns, 7.3.4
               2D3D labels, 14.1.4     cluster center, 7.25.2
               annotation, 14.1.2     color 2D by ph4, 7.5.5.5
               color representation, 14.1.1     copy 2D, 7.3.16

     decompose, 14.4.9     atom display, 10.3.3
     duplicate chemicals, 7.3.21     bond, 4.2, 5.1.8, 7.6, 14.3.6
     edit table, 7.3.17          donor, 7.36.1
          tree, 7.25.4          label edit, 4.2.3.1
     excel, 7.3.10               move, 4.2.3.2
     extract 3D ph4, 7.5.5.4     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, 14.4.8hyperlink, 6.6.1, 6.6.2, 11.1.39
          structure, 14.4.7hyrophobic, 7.36.1
     merge tables, 7.3.23iSee, 2.6.1.5, 2.6.1.12, 3.1.10, 5.15.3, 14.2
     properties, 7.3.19icb, 3.4.2, 3.5
     reactions, 14.4.10     chemist howto chemical search, 2.4.3
     reorder, 7.25.3               cluster, 2.4.5
     sdf, 7.3.9               combi library, 2.4.7
     show hide, 7.3.8               ph4, 2.4.4
     sort column, 7.3.5               plots, 2.4.8
     standardize, 7.3.18               sketch, 2.4.1
     table hyperlinks, 7.3.15               spreadsheets, 2.4.2
          print, 7.3.11               stereoisomers tautomers, 2.4.6
          activeicm, 2.3          pro 3D ligand editor, 2.5.1
               create molecular documents, 2.3.3               chem3D, 2.5.2
                    slides, 2.3.2               chemsuper, 2.5.4
               getting started, 2.3.1               energy, 2.5.3
               ppt, 2.3.4               qsar, 2.5.5
               web, 2.3.5               tutorials, 2.5
          chemical clusering, 7.25.1          tutorials, 2.4
          icm browser convert display pocket, 2.1.4     object, 4.1, 14.3.2
                    distances angles, 2.1.9     script, 11.1.39
                    get started, 2.1.1icmPocketFinder, 4.5.14
                    graphical display, 2.1.2icmjs, 6.16
                         effects, 2.1.5icmpocketfinder, 14.3.7
                    images, 2.1.7id, 11.1.26
                    labels annotation, 2.1.6identity, 3.2.1.2
                    pro crystallographic tools, 2.2.6image, 3.1.14, 3.7, 3.7.5, 5.15.3, 6.6.3, 7.2, 7.2.6, 11.4.20
                         get started, 2.2.1     advanced, 5.15.3
                         graphics, 2.2.2     preferences, 3.7.6
                         plots, 2.2.8     multiple, 2.6.1.7
                         sequence analysis, 2.2.7     quality, 2.6.3.11
                         structure analysis, 2.2.3     quick, 2.6.1.14, 5.15.2
                         superimpose, 2.2.5images, 5.15
                         surfaces, 2.2.4improve model, 8.1.3
                    selections, 2.1.3inchi, 7.17.3
                    superimpose, 2.1.8increment, 11.1.26
          search, 3.2     id, 11.1.26
          use gui, 3.1induced fit, 10.14
html, 2.6.1.12, 3.3, 6.6.1, 6.6.7insert, 6.6.4
hybridization, 7.4.3, 7.5.1     column, 11.1.25
hydrogen, 4.2.3, 4.2.3.1, 4.2.3.2, 5.1.8, 7.4.3, 7.5.1, 14.3.6     image, 6.6.3, 11.1.33

     row, 11.1.32     tab, 2.7.3
     script, 6.6.4landscape, 3.7.6
install, 7.10.1large chemical space, 14.4.4
interaction, 4.5.3, 7.6     sdf, 7.1.2
interactions, 10.3.12layer, 5.14
interactive, 14.2layers, 5.14
interrupt, 5.10.7.3learn, 7.18, 7.19, 8, 8.1, 11.6
     animation, 5.10.7.3learning, 8
invert selection, 11.1.22     theory, 8.5
isee, 6.6.5least.squares, 11.4.15
isis, 7.4.17library, 7.32.4
isotope, 7.4.3, 7.5.1     reaction, 14.4.10
iupac, 7.2.7, 7.3.20ligand, 4.2.2, 7.6, 7.24, 7.24.1, 7.24.2, 10.3.12, 10.3.13, 10.5.8, 10.10, 10.11
javascript, 6.16     based screen, 7.36.3
join, 7.29     best replace, 10.6
jpg, 5.15     code, 3.2.1.3, 3.2.7
     means, 11.7.1     editor, 10, 10.10, 10.10.1, 10.17, 10.18
kcc, 9.1.1, 9.6          bioisostere, 10.8
kernel regression, 9.1.1          covalent docking, 10.17
     chemical, 7.4.10          mrc, 10.16
keyboard mouse, 5.11          preferences, 2.6.2.18
keystokes in chem-edit, 7.4.10     energetics, 7.24
kmz, 2.7.6, 5.3.7          conformational entropy, 7.24.1
knime, 13          strain, 7.24.2
label, 3.7.7, 11.7.4     pocket, 4.2.4
     atoms, 5.8.2          surface, 10.3.2
     color, 5.8.7     receptor contacts, 10.3.12
     move, 5.8.4          display, 4.2
     residues, 5.8.3          interaction, 7.6
     sites, 5.8.6     strain, 10.3.10
     variables, 5.8.5     surface, 4.2.2
     2D, 2.7.3     tether, 10.12
     3D, 2.7.3, 5.8.1     editor, 10, 10.1
     atom, 5.8.1          binding.re-dock ligand, 10.9
     atoms, 5.8.2          display, 10.3
     color, 5.8.7          edit, 10.5
     custom, 5.8.8          energy, 10.3
     delete, 5.8.1, 5.8.9          hydrogen.bond, 10.3
     distance, 5.8.10          pocket, 10.3
     drag, 2.6.3.16          preferences, 10.2
     move, 2.6.3.16, 5.8.4          restraint, 10.12
     residue, 5.8.1          surface, 10.3
     residues, 5.8.3          tether, 10.12
     site, 5.8.1     pocket, 3.1.8
     sites, 5.8.6     receptor.contact, 4.5.3
     variable, 5.8.1ligand_pocket_interactions, 4.2.4
     variables, 5.8.5ligedit distance restraint, 10.12.2
labeling, 5.8.1     tab, 2.7.5
labels, 5.8, 7.3.28     tether, 10.12.1
     distances, 5.8.10light, 2.7.2

lighting, 5.3.9.4, 5.5max, 11.7.1
likeness, 7.11maxColorPotential, 3.7.10
line, 3.7.5, 11.7.4maximum common substructure, 7.25.6, 7.27, 7.27.1
lineWidth, 3.7.3               dendrogram, 7.27.1
links, 3.6.20mcs, 7.25.6, 7.27.1
linux, 7.10.1     rgroup decomposition, 7.25.7
lipinski rule, 7.31memory, 7.1.2
list, 3.6.18menu, 6.6.5
load, 2.6.1.3, 2.6.1.17, 4.3.4, 4.3.6, 4.3.7     chemistry, 2.6.14
     nmr model, 3.2.1.4     docking, 2.6.15
     protein structure, 4.1.1     homology, 2.6.13
local databases, 12     molmechanics, 2.6.16
     database.browse, 12.2     tools chemical search, 2.6.11
          edit, 12.3          molecular editor, 2.6.12
          query, 12.4     windows, 2.6.17
          row, 12.3merge, 7.29
lock, 5.3.10, 5.13.1, 7.3.31     two sets, 7.29
log, 11.4.10mesh, 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, 5.13.1
logP, 7.4.9, 7.11     clip, 5.3.10
logS, 7.4.9, 7.11     color lighting, 5.3.9.4
logarithmic, 11.4.10     options, 5.3.9
logout, 2.6.1.19     representation, 5.3.9.3
mac, 7.10.1     save, 5.3.11
machine learning, 14.7     options, 5.3.9
macros, 6.14meshes, 5.3.2, 5.10.5
macroshape, 2.6.3.22, 5.3, 5.3.6     surfaces grobs, 5.3
make, 5.10.7.1, 11.1.1     tab, 2.7.6
     animation, 5.10.7.1metabolic oxidation, 9.8
     apf docking sar model, 9.7min, 11.7.1
     complex, 10.21mmff, 7.4.16
     molecular document, 6.6     type, 5.8.2
     molt, 12.1mmp, 14.4.11
     selection, 3.6mnSolutions, 3.7.10
     molecule, 2.6.1.1model weight, 8.1.2
     object, 2.6.1.1modification history, 10.5.6
making molecular slides, 6.1mol, 7.2, 7.2.2, 7.2.4, 7.2.5, 7.2.6, 7.4.13
     html, 6.6mol2, 7.2, 7.2.2, 7.2.4, 7.2.5, 7.2.6
     color, 11.4.13molcart, 7.10, 7.10.1, 7.10.2, 7.10.3, 7.10.4, 7.10.5, 12
manual change torsion, 10.5.4     add database, 7.10.3
map, 3.7.7, 4.3.4, 4.3.6, 4.3.7     administration, 7.10.5
     cel, 4.3.5     installation, 7.10.1
mark, 11.1.44     search, 7.10.4
     row, 11.1.44     start, 7.10.2
     shape, 11.4.12molecular, 7.3.30, 7.3.31, 7.3.34, 7.3.35, 7.20
     size, 11.4.12     animations slides, 6
markush, 7.25.7, 7.32.1, 7.32.3, 7.33.1     documents, 14.2
     library, 14.4.8     graphics, 5
matched pair, 7.33.5, 14.4.11     matched pairs, 14.4.11
          analysis, 7.33.5     table, 7.17.2
materials, 2.7.6     weight, 7.4.9

moledit, 7.4.8     in.table, 11.3
molscreen, 9occlusion, 5.3.12, 5.10.5
     brief panel, 9.2     shading, 5.3.12
     custom model panel, 9.4          effect, 5.10.5
     full panel, 9.3occupancy, 5.1.3, 14.3.10
     model type, 9.1     display, 3.2.1.5
     results, 9.5oda, 4.5.13
molskin, 5.3.2older version, 2.6.1.10
molt, 12, 12.4omega, 5.8.5
monochrome, 7.3.28open, 2.6.1.3, 3.4, 11.1.2
mouse, 3.1.3, 5.11, 5.12     file, 3.4
mov, 5.16, 5.16.2     password, 3.4.1
move, 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     with password, 2.6.1.4
     column, 11.1.27     movie, 5.16, 5.16.2
     mesh, 5.3.9.2     password, 2.6.1.4, 3.4.1
     slide, 6.4.2optimal, 4.5.13
     structure, 5.12orange, 3.6.5
     tools, 5     selection, 3.6.5
     rotate, 5.11origin, 5.8.11
     slab, 5.11other selection, 3.6.19
     translate, 5.11overlay, 14.3.3
     z-rotation, 5.11package.activeicm, 6.13
     zoom, 5.11packing, 4.3.1
movie, 5.16.1pairwise, 7.35.1, 7.35.2
     making, 5.16, 5.16.2     apf score, 7.36
     open, 5.16, 5.16.2password, 7.10.5
mpa, 14.4.11paste, 7.4.11, 7.4.17, 11.1.34
mpeg, 5.16, 5.16.1, 5.16.2pca, 11.5
mpg, 5.16, 5.16.2pdb, 2.6.1.7, 3.2, 3.2.1.1, 3.2.7, 3.5, 7.7.1, 14.3
mpo, 7.31     chem gl, 7.7.3
multi apf super, 7.35.3          iw, 7.7.2
     panel, 5.2     html, 3.2.1.6
     parameter optimization, 7.31     preparation, 14.3.11
     windows, 5.2     search, 3.2.1, 3.2.1.2, 3.2.1.3, 14.3.1
multiple position group scan, 10.7     recent, 2.6.1.18
     receptor, 3.2.2     search, 2.7.4, 3.1.2
          docking, 10.16pdbsearchfield, 2.6.2.13
navigate workspace, 3.6.10pdbsearchhomology, 2.6.2.15
new icm session, 2.6.1.2pdbsearchidentity, 2.6.2.14
     table, 11.1.1pdbsearcsequence, 2.6.2.16
     table, 11.1.1peptide, 3.3
nmr model, 3.2.1.4perspective, 2.6.3.9, 5.10.6
nof, 7.11.1ph4, 7.5.5
     chemical, 7.11.1     draw 2d, 7.5.5.1
non-contiguous selection, 3.6.18          3d, 7.5.5.2
number of sp3, 7.11.1     search, 7.5.5.3
numbers, 7.3.28pharmacophore, 7.3.35, 7.5.5.5, 14.6.2
object, 3.1.11, 3.5, 14.3     2D, 14.4.6
objects, 4.1.2     3D, 14.4.5
     in table, 11.3     clone, 7.5.5.2

     draw3D, 7.5.5.2     metabolic oxidation, 9.8
     edit, 7.5.5.1, 7.5.5.2predicting bioassays, 8.2
     move, 7.5.5.2     compound properties, 8.2
     new, 7.5.5.2preferences, 3.7
     search, 7.5.5, 7.5.5.3, 14.4.5, 14.4.6presentatio, 6.6.5
phi, 5.8.5presentation, 6.7, 6.12
picking, 5presentations, 6
picture, 2.6.1.14, 3.1.14, 5.15.2, 6.6.3press-and-hold to rotate, 7.4.8
     tips, 3.1.14pretty view, 10.3.6
     chart, 11.4.7primary aliphatic amines, 7.15
pka, 7.15principal component analysis, 11.5
planar, 4.5.7, 5.8.5          regression, 8
     angle, 4.5     components, 8.5
     angle, 5.9.2print, 5.7, 11.4.19, 11.7.3
plane, 5.3.10, 5.13, 5.13.1, 5.14     plot, 11.4.19
plot, 3.7, 3.7.8, 11.4, 11.4.1, 11.4.4, 11.4.8, 11.4.10, 11.4.12, 11.4.13, 11.4.14, 11.4.15, 11.4.16, 11.4.17, 11.4.19, 11.4.20, 11.4.21printer.resolution, 3.7.6
     R group sar, 7.33.3pro-drug, 7.23
     axis, 11.4.10prodrug, 7.23
     color, 11.4.13project, 2.6.1.5, 14.4.4.6
     function, 2.6.9, 2.6.9.1     close, 2.6.1.13
     grid, 11.4.14     rename, 2.6.1.9
     header, 11.4.8properties, 5.8.2, 7.11
     inline, 11.4.21property, 7.4.9
     logarithmic, 11.4.11     monitor, 7.4.9
     mark, 11.4.12protect, 6.6.8
     point label, 11.4.18protein, 4.4.6
     preferences, 3.7.8     health, 4.5.11
          groups, 11.4.23     structure, 4
     regression, 11.4.15          analysis, 4.5
     selection, 11.4.17               closed cavities, 4.5.4
     zoom translate, 11.4.16               contact areas, 4.5.3
     axis, 11.4.14               distance, 4.5.6
     display, 11.4.14               find related chains, 4.5.1
     grid, 11.4.14               finding dihedral angle, 4.5.8
     inline, 11.4.21                    planar angle, 4.5.7
     logarithmic, 11.4.11               rama export, 4.5.10
pls, 7.18, 7.19, 8, 11.6, 14.7               ramachandran plot, 4.5.9
png, 2.6.1.14, 5.15, 5.15.2, 6.6.3, 7.2, 7.2.6               rmsd, 4.5.2
pocket, 3.1.8, 4.2, 4.2.1, 4.2.2, 4.5.14, 14.3.7               surface area, 4.5.5
     surface, 4.2.1          tutorials, 14.3
     peptide, 3.1.8               analysis, 14.3.4
     properties, 3.1.8               contact area, 14.3.5
pocketome, 3.2, 3.2.2               convert, 14.3.2
point label, 11.4.18               hydrogen bond, 14.3.6
portait, 3.7.6               icmpocketfinder, 14.3.7
post edit ligand, 10.5.8               search, 14.3.1
postscript, 3.7.6               superimpose, 14.3.3
powerpoint, 14.2     superposition, 4.4
ppt, 6.12, 6.14          select, 4.4.1
predict, 7.18, 7.19, 8, 8.2, 11.6          sites by apf, 4.4.6

               grid, 4.4.5     table, 11
               multiple proteins, 4.4.4reagent, 7.32.5
protein-protein, 4.5.13rear, 5.3.10, 5.13.1
proximity, 5.3.3, 5.3.4recent files, 2.6.1.17
psa, 7.4.9     pdb codes, 2.6.1.18
psi, 5.8.5receptor, 4.2.1, 4.2.2, 7.6, 10.3.12
pubchem, 7.1     flexibility, 10.16
publication quality images, 5.3.2     pocket, 10.3.1
pubmed, 3.2.1.7          surface, 10.3.1, 10.3.2
purple box, 2.6.3.23, 10.9.1recover, 2.6.2.11
qs hydrogen bond, 4.2.3redo, 2.6.2.10, 7.4.11, 10.5.5
qsar, 7.18, 7.19, 8.1, 14.7regresion, 11.4.15
     learn predict, 7.18regression, 8.1, 8.5, 14.7
     predict, 7.19relationship, 8, 11.6
quality, 2.6.1.15, 3.7.5relaxed ligand, 10.3.9
query molt, 12.4remove.explixit.hydrogens, 7.12
     processing, 7.5.3     salt, 7.12
     setup, 7.5.1rename, 11.1.24
quick, 3.1.14     colunn, 11.1.24
     image, 5.15.2     project, 2.6.1.9
     start move structure, 3.1.3reorder column, 11.1.28
          read pdb, 3.1.2replace chemical, 7.3.32
          representation, 3.1.6replacement, 10.6
          selection, 3.1.5     group, 10.8
               level, 3.6.3representation, 2.6.3.19
          what is selected, 3.6.4residue, 3.7.7
     dispalay.distance, 5.9.1     alternative orientaiton, 14.3.11
     start color, 3.1.7     range, 3.6.18
quit, 2.6.1.19     content, 2.6.4
     group, 7.25.7, 7.32.4residues, 4.2.1, 4.2.2
          table, 7.32.2resize, 5.3.9.1, 5.15.3
     groups, 7.32.2     mesh, 5.3.9.1
r-group, 7.25.7, 7.32.2resolution, 3.2.1.3
     decomposition, 7.25.7restore, 2.6.2.11, 5.3.10, 5.13.1
     enumeration, 7.25.7     recent backup, 2.6.2.11
r-groups, 11.4.23restraing, 10.12.1, 10.12.2
racemic, 7.3.28, 7.17.5rgroup, 7.32.4
rainbow, 3.7.5, 5.8.15, 7.3.35ribbon, 2.7.1, 3.7.9, 5.1.3
ramachandran plot, 4.5, 4.5.10     preferences, 3.7.9
random forest, 8, 14.7     style, 3.7.9
range, 5.10.7.2     breaks, 5.1.3
ratio.selection, 3.7.5     cylinders, 5.1.3
     dock ligand, 10.9     smooth, 5.1.3
reactions, 7.8, 7.32.5     worm, 5.1.3
reactivity, 7.11.2ribbonColorStyle, 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, 7.34
     table, 11.1.2     super, 7.34.2
     pdb, 3.1.2          table, 7.34.1

rings, 7.3.28, 7.20, 7.34     project, 2.6.1.8, 2.6.1.9, 2.6.1.10, 3.1.10
rmsd, 4.5, 4.5.2     table.view, 11.1.7
rock, 2.6.3.15, 5.10.7, 5.10.7.1, 6saving, 2.6.1.8
     speed, 5.10.7.2     project, 2.6.1.8
root mean square deviation, 4.5.2scaffold, 7.14
rotate, 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     hopping, 10.8
     chemical, 7.3.34scale, 3.7.5
     when pasting, 7.4.8     r group, 10.7
     easy, 2.6.3.12score, 10.4, 14.6.3, 14.6.5
     speed, 5.10.7.2screen, 7.36, 14.6.4
rotating fragment in editor, 7.4.8screenshot, 5.16, 5.16.2
rotation, 5.12.1     movie, 5.16.2
row, 11, 11.1.21, 11.1.34, 11.1.44script, 3.3, 6.6.4, 6.6.5
     flag, 11.1.12sdf, 7.2, 7.2.2, 7.2.4, 7.2.5, 7.2.6, 7.3.35, 7.10, 7.10.3, 7.17.1, 10.10, 12.1
     height, 11.1.6search, 7.10, 7.10.4, 12.2
     mark, 11.1.12     chembl, 3.2.3
     hide, 7.3.8     drugbank, 3.2.8
     show, 7.3.8     filter, 7.5.2
ruler, 5.8.15     in workspace, 2.6.2.4
rxn, 7.4.13     pdb, 3.2.1
sali, 7.33.4          chemical, 3.2.1
     bridge, 14.3.6          ligand code, 3.2.7
salts, 7.3.18     pocketome, 3.2.2
sample, 7.34     pubchem, 3.2.9
sar, 7.25.7, 7.33, 11.4.23     surechembl, 3.2.4
     analysis, 7.33     tab field, 3.2.1.3
     table, 7.33.2          pdb chemical, 3.2.1.1
save, 3.5, 5.3.11, 5.10.7.4, 7.2.3, 11.4.20, 11.7.3               sequence, 3.2.1.2
     SMILES, 7.4.15     tautomer, 7.5.3
     chemical mol, 7.4.13     uniprot, 3.2.6
          spreadsheet workspace, 7.2.1     in.workspace, 2.6.2.4
          to chemical spreadsheet, 7.4.14secondary aliphatic amines, 7.15
     docked ligand, 10.19     structure, 2.6.4, 5.1.3
     file, 3.5select, 3.6.12, 3.6.13, 11, 11.1.44
     hits, 10.5.7     a tree branch, 11.7.2
     image plot, 11.4.20     all, 3.6.14
     ligand receptor complex, 10.19     amino acid, 3.6.13
     object, 3.1.9     duplicates, 7.30
     pdb, 3.5     molecule, 3.6.12
     project icb, 3.1.10     neighbors, 3.6.15
     slide, 6.4          graphic, 3.6.16
     smiles string, 7.4.15     object, 3.6.11
     table, 11.1.20     residue, 3.6.13, 3.6.18
          spreadsheet, 10.5.7          by number, 3.6.18
     tree, 11.7.3          number, 3.6.18
          sdf, 7.4.14     tree, 11.7.2
     image, 2.6.1.15, 3.1.14     atom, 3.1.5, 3.6.3
     object, 3.1.9     graphical, 3.1.5, 3.6.3
     password, 2.6.1.11     object, 3.1.5, 3.6.3
     picture, 2.6.1.15     purple.box, 2.6.3.23

     workspace, 3.1.5, 3.6.3shineStyle, 3.7.3
selectall, 2.6.2.3show, 6.3.1, 11.1.38
selecting.neighbors, 3.6.16     hide column, 11.1.38
selection, 3.6.4, 3.6.5, 3.6.21, 5.3.4, 7.4.11, 11.4.17, 11.7.2, 11.7.4side, 7.3.29
     clear, 2.6.2.7     by side, 7.3.29
     neighbors, 2.6.2.8               stereo, 2.6.3.6
     alignment, 3.6.19     chain refinement, 10.15
     all, 2.6.2.3sigmaLevel, 4.3.6, 4.3.7
     alter, 3.6.7similarity, 7.28
     atom, 2.6.2.5single, 7.4.10
     basic, 3.6.2singlet, 7.4.7
     change, 3.6.7sites, 4.4.6
     clear, 2.6.2.7size, 4.2.3.1
     column, 11.1.22sketch accents, 5.10.3
     filter, 2.6.2.5, 3.6.8     markush, 7.32.1
     graphical, 3.6.16     smiles, 7.4.12
     invert, 2.6.2.6, 11.1.22     accents, 2.6.3.14, 5.10.3
     level, 2.6.3.3skin, 2.7.1, 5.1.4
     mode, 2.6.3.4slab, 5.3.10, 5.13.1
     near atoms, 2.6.2.8slice, 5.13
     neighbors, 2.6.2.5, 2.6.2.8, 3.6.15, 3.6.17slide, 5.10.7.4, 6.2, 6.3.1, 6.6.1
     object, 3.6.11     effects, 6.5
     other, 3.6.19     movie, 5.16.1
     properties, 2.6.2.5          file, 6.2
     range, 11.1.22     navigation, 6.3.2
     residue, 2.6.2.5     show, 6.3
     row, 11.1.22     blend, 6.5
     sphere, 3.6.15     edit, 6.4.1
     spherical, 2.6.2.8     effect, 6.5
     superposition, 4.4.1     smooth, 6.5
     table, 3.6.19, 11.1.22     transition, 6.5
          elements, 11.1.22slides, 5.16.1, 6, 6.1, 6.3
     tools, 3.6.1, 3.6.2, 3.6.7, 3.6.8smiles, 7.4.9, 7.11, 7.17, 7.17.3, 7.17.4
     whole, 3.6.11smooth, 5.3.9.3
     workspace, 3.6.9, 3.6.17solid, 5.3.9.3
selectioninvert, 2.6.2.6sort table, 2.6.10.4
selections, 3.6sorting compounds, 11.7
selectneighbors workspace, 3.6.17sp3, 7.11.1
     organized network, 7.27spec, 2.7.2
sequence, 2.6.4, 3.2, 3.2.1.2, 3.2.5, 3.2.6, 3.3, 14.3speed, 5.10.7.2
     pattern, 3.2.1.2split, 7.33.1
set, 7.3.31spreadsheet, 7.17.2
     formal charges, 7.15standard table, 11.1
setup ligand receptor, 10.1standardize, 7.12
shading, 5.3.12     table, 7.12
shadow, 5.10.2start, 7.10.2
share model, 8.1.4stereo, 3.7.6, 5.6, 7.3.28, 7.4.2
shell preferences, 3.7.10     bond, 7.4.2
shift, 5.8.3     hardware, 2.6.3.7
shine, 2.7.2, 3.7.5     side-by-side, 2.6.3.6

stereoisomers, 7.22     insert, 11.1.25
stick, 3.7.5     layout, 11.1.5
stl, 5.7     learning, 11.6
stop, 5.10.7.3     mark, 11.1.12
store, 2.6.3.19, 5.10.7.4          row, 11.1.12
     current view, 2.6.3.19     mouse, 11.1.46
strain, 4.5.11, 7.24, 7.24.2, 10.4     navigation, 11.1.4
structure, 4.3.3, 8, 11.6, 14.3     new column, 11.1.25
     analysis, 14.3.4     plot, 11.4
     representation, 5.1     print, 11.1.18
     smiles, 7.17.4     rename, 11.1.14
structures, 7, 7.1     rightclick, 11.1.13
style, 3.7.5     save, 11.1.3
substituent, 7.9.1, 7.9.2, 7.32.2, 10.5.2          selection, 11.1.3
substructure, 7.10.4, 7.13     search, 11.1.8
     template, 10.13     select, 11.1.22
     alerts, 7.13     setup, 11.1.17
superimpose, 2.6.8, 4.4.2, 4.4.6, 14.3.3     sort, 11.1.41
     3D, 4.4.3     split fragments, 7.3.33
     Calpha, 4.4.3     view, 11.1.5
     arrange.grid, 4.4.5          save, 11.1.7
     backbone, 4.4.3     zoom translate, 7.3.30
     flexible, 7.34.3     action, 11.1.46
     heavy atoms, 4.4.3     alignment, 11.1.11
     multiple, 4.4.4     append, 11.1.42
     rigid, 7.34.1, 7.34.2     clone, 11.1.15
     substructure, 7.34.1, 7.34.2, 7.34.3     color, 11.1.9
superposition, 7.34, 7.35.1, 7.35.2, 14.3.3, 14.6.1     column, 7.3.4, 11.1.25, 11.1.31, 11.1.38
surface, 2.7.1, 3.7.5, 4.2.1, 4.2.2, 5.1.6, 5.3, 5.3.3, 5.3.4     columns, 7.3.8
     area, 4.5     compare, 7.3.22
     area, 4.5.5     copy, 7.3.6
surfaces, 4.2, 5.3.1, 5.3.2, 5.10.5     cursor, 11.1.46
symmetry, 4.3.1, 4.3.3, 14.3.8, 14.3.9     delete, 11.1.13, 11.1.16
system preferences, 3.7.11     double.click, 11.1.46
tab, 11.1.2, 11.1.20     edit, 7.3.17
     pdb, 2.7.4     excel, 7.3.10, 11.1.19
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, 7.17.2, 7.20, 7.34.1, 10.10, 11, 11.1.34, 11.1.39, 11.1.44, 11.4, 11.4.1, 11.4.4, 11.4.8, 11.4.10, 11.4.12, 11.4.13, 11.4.14, 11.4.15, 11.4.16, 11.4.17, 11.4.19, 11.7.1     filter, 7.3.12, 11.1.42
     alignment, 11.1.11     find-replace, 7.3.13
     clone, 11.1.15          to screen, 11.1.4
     color, 11.1.9     font, 11.1.10
     column format, 11.1.39     grid lines, 11.1.4
     copy, 11.1.35, 11.1.36     hide, 11.1.38
     delete, 11.1.16     hyperlink, 7.3.15
     edit, 11.1.23     insert, 11.1.32
     filter, 11.1.42     join, 2.6.10.5
     find, 11.1.8     label, 7.3.14
          replace, 7.3.32     landscape, 11.1.17
     font, 11.1.10     mark, 7.3.14
     grid, 11.1.5     merge, 2.6.10.5, 7.3.23, 7.29
     histogram, 11.4.1     mouse, 11.1.46

     new, 11.1.1     balloons, 11.4.24
     options, 11.1.13torsion, 5.12.6, 10.5.4
     orientation, 11.1.17     angles, 5.12, 5.12.6
     portrait, 11.1.17toxscore, 7.11.2
     print, 7.3.11, 11.1.4, 11.1.18trace, 5.1.10
     read, 11.1.2transitions, 6
     rename, 11.1.14translate, 3.1.3, 5, 5.12, 7.3.30
     right click, 11.1.13translation, 5.12.3, 11.4.16
     row, 11.1.32transparent, 5.3.9.3
     rows, 2.6.10.7     background, 5.15.3
     save, 7.3.9, 11.1.3, 11.1.4, 11.1.20tree, 7.25.7, 11.7.2, 11.7.3, 11.7.4
     scale, 11.1.17     distance, 7.25.3
     scroll, 11.1.4     edit, 7.25.4
     sdf, 7.3.9     reorder, 7.25.3
     select, 11.1.22triplet, 7.4.7
     setup, 11.1.17tsv, 11.1.20
     sort, 2.6.10.4, 7.3.5, 11.1.41tut analyze alternative orientations, 14.3.11
     standard, 11.1          occupancy, 14.3.10
     view, 7.3.29          symmetry, 14.3.9
     width, 11.1.4tut3e, 14.3.12
tables, 7.28, 11tutorial 2D pharmacophore, 14.4.6
tag, 3.6.21, 10.5.7, 11.1.45     3D pharmacophore, 14.4.5
tags, 3.6.21     chemical clustering, 14.4.3
tautomer, 7.21          search, 14.4.2
tautomers, 7.21     molecular documents, 14.2
temperature, 4.5.12tutorials, 14
template, 7.4.6, 7.34two, 7.3.24
templates, 7.4.6unclip, 5.3.10, 5.13.1
terminal, 7.3.28undisplay, 3.1.4, 5.1.7
tether, 10.12.1, 10.12.2     origin, 5.8.11
text, 3.7.7, 6.6, 6.6.1, 6.6.7, 7.3.28, 7.10.4, 11.4.22undo, 2.6.2.9, 3.7, 7.4.11, 10.5.5
     search, 7.5.4     redo, 10.5.5
texture, 2.7.6uniprot, 3.2.6
thoroughness, 7.20, 7.34unique, 7.3.28, 7.30
three, 7.3.24unit, 4.3.3
threshold, 3.7.5unsatisfied hydrogen bonds, 10.3.8
tier, 3.1.13     hyrdrogen bonds, 10.3.8
     racemic, 7.17unusual peptide, 3.3
tools 3D, 2.6.6     activeicm, 6.12
     analysis, 2.6.7user, 7.10.5
     append rows, 2.6.10.7     defined groups, 10.5.3
     extras, 2.6.9     modifiers, 10.5.3
          plot function, 2.6.9.1user-defined groups, 7.4.5
     superimpose, 2.6.8uundisplay-all, 2.6.3.1
     table, 2.6.10van der waal, 5.8.14
          Learn, 2.6.10.1variable, 3.7.7
          clustering, 2.6.10.3verbose, 7.20
          merge, 2.6.10.5     large sdf files, 7.1.2
          predict, 2.6.10.2vicinity, 7.20
tooltip, 11.4.24video, 1, 5.16, 5.16.1, 5.16.2

     animate view, 2.6.3.15xlsx, 7.2.3
     center, 2.6.3.20xstick, 5.1.2
     color background, 2.6.3.18youtube, 1
     fog, 2.6.3.5zoom, 3.1.3, 5, 5.12, 5.12.4, 7.3.30, 11.4.16
     macroshape, 2.6.3.22 
     menu, 2.6.3 
     mesh clip, 5.13.1 
     perspective, 2.6.3.9 
     selection level, 2.6.3.3 
          mode, 2.6.3.4 
     shadow, 2.6.3.13 
     sketch accents, 2.6.3.14 
     slide show, 6.3.1 
     tools, 2.6.3 
     tree, 11.7.4 
     undisplay all, 2.6.3.1 
virtual ligand screening, 9 
virus, 4.3.3 
visualize, 7.27 
     apf fields, 10.3.11 
     chemical space, 7.27 
     ligand strain, 10.3.10 
volume, 7.4.9 
wavefront, 2.7.6, 5.3.11 
web, 14.2 
     browser, 2.6.1.12 
weight, 7.11 
weighted, 11.7.1 
width, 11.1.21 
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, 11.4.20 
     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, 11.1.3 
     ray, 2.6.5 
xi, 5.8.5 
xls, 7.2.3 

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