Jan 4 2018 Feedback.
Contents
 
Introduction
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Sequences & Alignments
Protein Modeling
Cheminformatics
Learn and Predict
Docking
Virtual Screening
MolScreen
3D Ligand Editor
Tables and Plots
Local Databases
ICM-Scarab
KNIME
Tutorials
FAQs
 
Index

Index

2D, 5.8.8, 9.3.24, 9.3.28, 9.14, 9.17.2, 9.17.4DNA, 3.3, 7, 7.3.3
     Interaction Diagram, 14.3.7Decomposition, 9.33.2
     bioisostere, 9.9.1Display, 20.2.26
     from PDB, 9.1.1Distance, 12.1.10.6
     screening, 13Dock Directory, 3.7.2
     to 3D, 9.17, 9.17.3Docking, 20.2.26
     depiction, 9.17.2Drug Bank, 3.2.8
3D, 5.6, 5.8.8, 9.1.3, 9.3.24, 9.3.28, 9.3.31, 9.17.2, 19.2Editor, 3.7.2
     QSAR, 9.36.4, 10.4, 19.14Error in saving configuation settings: You are not a license administrator, 20.1.10
     chemical, 9.4.16, 9.17.1FILTER.Z, 3.7.2
     interactive ligand editor, 2.7.5     gz, 3.7.2
     ligand editor, 14.3.4     uue, 3.7.2
     object, 5.3.9FTP.createFile, 3.7.11
     pharmacophore, 12.3, 14.3.11     keep File, 3.7.11
     print, 5.7     proxy, 3.7.11
     printing, 5.7Filter.zip, 3.7.2
     screening, 13Force Auto Bond Typing, 3.7.11
     stereo, 5.6Formula, 20.8.7, 20.8.10
3DQsar, 10.4Frequently Asked Questions, 20
3Dqsar tutorial, 19.14GAMESS, 8.20.16
     bioisostere, 9.9.2GIF, 2.6.1.15, 5.16, 5.16.2
     predict, 4.6GPCR Modeling Example, 19.5.1
          helices strands, 4.6.1GRAPHIC.store Display, 3.7.3
          local flexibility, 4.6.3     NtoC Rainbow, 3.7.4
          protein health, 4.6.2     alignment Rainbow, 3.7.4
          tools identify ligand binding pocket, 4.6.5     atomLabelShift, 3.7.7
               oda, 4.6.4     ballStickRatio, 3.7.1
4D, 11.2.2, 19.12.1     center Follows Clipping, 3.7.3
     dock, 14.15     clash Style, 3.7.3
     docking, 3.2.2     clashWidth, 3.7.3
64, 20.1.3     clip Grobs, 3.7.3
APF, 9.35.3, 9.36.4, 10.4, 13, 13.7, 19.14          Skin, 3.7.3
     template, 9.35          Static, 3.7.3
ActiveICM, 2.6.1.12     discrete Rainbow, 3.7.4
Area, 20.2.26     displayLineLabels, 3.7.7
Atom Single Style, 3.7.3     displayMapBox, 3.7.3
Atomic Property Fields, 10.4, 19.14     distance Label Drag, 3.7.1
Bad Groups, 20.8.7, 20.8.10     dnaBallRadius, 3.7.9
Baell, 9.4.9     dnaRibbonRatio, 3.7.9
Beep, 3.7.11     dnaRibbonWidth, 3.7.9
Blast, 20.2.25     dnaRibbonWorm, 3.7.9
BlastDB Directory, 3.7.2     dnaStickRadius, 3.7.9
     alphas, 5.8.3     dnaWormRadius, 3.7.9
COLLADA, 2.6.1.7     font Scale, 3.7.7
CPK, 2.7.1     fontColor, 3.7.7
ChEMBL, 3.2.3, 9.1     fontLineSpacing, 3.7.7
Chemical Cluster, 19.6.3     grobLineWidth, 3.7.3
     Search, 19.6.2     hbond Ball Period, 3.7.1
CisTransAmide Angle, 12.1.10.6               Style, 3.7.1
Clash Threshold, 3.7.10     hbondAngleSharpness, 3.7.1

     hbondStyle, 3.7.1     workspace Folder Style, 3.7.4
     hbondWidth, 3.7.1     workspaceTabStyle, 3.7.4
     hetatmZoom, 3.7.1HBA, 20.8.7, 20.8.10
     hydrogenDisplay, 3.7.1HBD, 20.8.7, 20.8.10
     light, 3.7.3HTTP.proxy, 3.7.11
     lightPosition, 3.7.3     support Cookies, 3.7.11
     mapLineWidth, 3.7.3     user Agent, 3.7.11
     occupancy Radius Ratio, 3.7.3Hbond to selection, 12.1.10.6
     occupancyDisplay, 3.7.3Hbonds, 14.3.4
     quality, 3.7.3How To Guide, 2
     rainbow Bar Style, 3.7.4Html, 3.2.1.6
     resLabelDrag, 3.7.7Http Read Style, 3.7.11
     resize Keep Scale, 3.7.3Hydrogen.bond, 3.7.5
     ribbonRatio, 3.7.9ICM Browser How To, 2.1
     ribbonWidth, 3.7.9          Pro How To, 2.2
     ribbonWorm, 3.7.9     graphics crash, 20.1.11
     rocking, 3.7.4     start, 1
          Range, 3.7.4IMAGE.bondLength2D, 3.7.6
          Speed, 3.7.4     color, 3.7.6
     selectionStyle, 3.7.3     compress, 3.7.6
     site Label Drag, 3.7.7     gammaCorrection, 3.7.6
               Shift, 3.7.7     generateAlpha, 3.7.6
     siteArrow, 3.7.7     lineWidth, 3.7.6
     stereoMode, 3.7.3     lineWidth2D, 3.7.6
     stickRadius, 3.7.1     orientation, 3.7.6
     surfaceDotDensity, 3.7.3     paper Size, 3.7.6
     surfaceDotSize, 3.7.3     previewResolution, 3.7.6
     surfaceProbeRadius, 3.7.3     previewer, 3.7.6
     transparency, 3.7.3     print, 3.7.6
     wire Width, 3.7.1     printerDPI, 3.7.6
     wormRadius, 3.7.9     scale, 3.7.6
     xstick Backbone Ratio, 3.7.1     stereoAngle, 3.7.6
          Hydrogen Ratio, 3.7.1     stereoBase, 3.7.6
          Style, 3.7.1     stereoText, 3.7.6
          Vw Ratio, 3.7.1INCHI, 9.17.3
GROB.arrowRadius, 3.7.3ISIS, 20.8.3
     atomSphereRadius, 3.7.3Icm Prompt, 3.7.10
     contourSigmaIncrement, 3.7.3InChi, 9.3.20, 9.4.12, 9.17.3
     relArrow Size, 3.7.3     key, 9.3.20
     relArrowHead, 3.7.3Interaction Diagram 2D, 14.3.7
GUI.auto Save, 3.7.4Internal Coordinates Table, 8.20.13
               Interval, 3.7.4     Directory, 3.7.2
     autoSave, 20.2.33JPEG, 2.6.1.15
     autoSaveInterval, 20.2.33KMZ, 2.6.1.7
     enumberation Memory Limit, 3.7.11Log Directory, 3.7.2
     max Nof Recent Files, 3.7.11LogP, 10, 15.6
          Sequence Length, 3.7.4LogS, 10, 15.6
     splash Screen Delay, 3.7.11MOL, 9, 9.3.3, 9.3.24, 9.3.25, 9.3.26, 9.3.27, 12.1.3, 15.2
               Image, 3.7.11MOL2, 12.1.3
     table Row Mark Colors, 3.7.4MOLT, 16.1

MPO, 9.31PFAM, 2.6.1.7
Mac, 20.1.15PLOT.Yratio, 3.7.8
     Atom Margin, 3.7.10     color, 3.7.8
     Sigma Level, 3.7.10     date, 3.7.8
Markush, 19.6.9     draw Tics, 3.7.8
     create, 19.6.7     font, 3.7.8
     File Size Mb, 3.7.11     fontSize, 3.7.8
Max_Fused_Rings, 9.11     labelFont, 3.7.8
Mnconf, 3.7.10     lineWidth, 3.7.8
Model, 10.4     logo, 3.7.8
MolCart, 20.9     markSize, 3.7.8
MolIPSA, 20.8.7, 20.8.10     orientation, 3.7.8
MolLogP, 20.8.7, 20.8.10     paper Size, 3.7.8
MolLogS, 20.8.7, 20.8.10     previewer, 3.7.8
MolPSA, 9.11     rainbowStyle, 3.7.8
MolScreen, 13     seriesLabels, 3.7.8
MolVol, 9.11PLS, 10.1
Molcart, 9.5.3PNG, 2.6.1.15, 3.1.14, 5.16, 5.16.2
MoldHf, 9.11, 20.8.7, 20.8.10Pharmacophore RMSD, 12.1.10.6
Movie.fade Nof Frames, 3.7.4Projects Directory, 3.7.2
     quality, 3.7.4Prosite Dat, 3.7.2
          Auto, 3.7.4Protein, 20.2.26
NCBI, 20.2.25     Viewer, 3.7.2
NVIDIA, 20.1Pub Chem, 3.2.9
Nof_Atoms, 9.11PubMed, 3.2.1.7
Nof_Chirals, 9.11     Reference, 15.1.39
Nof_HBA, 9.11Pubchem, 3.2.9
Nof_HBD, 9.11QSAR, 10, 10.1, 15.6, 19.14
Nof_Rings, 9.11R, 9.8, 9.33.1
Nof_RotBonds, 9.11     and S, 20.5.21
Non-overlap, 12.1.10.6R-Group, 9.33.2
Nvidia GL failutre, 20.1.11R-groups, 14.5.3
ODA, 20.2.26RMSD, 4.4.2
Optimal, 20.2.26RNA, 3.3
Output Directory, 3.7.2Ramachandran Plot, 4.5.9
PAINS, 9.4.9, 9.11.2Real Format, 3.7.10
     chemica, 9.4.9     Label Shift, 3.7.7
PBS, 12.1.7          Style, 3.7.7
PCA, 10.1, 10.5, 19.6.4RotB, 20.8.7, 20.8.10
     analysis, 9.26SALI, 9.33.4, 19.6.11
PDB, 3.2.1.6, 4.1.2, 4.3.3, 7.1, 9.1.1, 14.18SAR, 10, 13.7, 15.4.23, 15.6
     Directory, 3.7.2     table, 9.33.2, 19.6.9
          Style, 3.7.2SCARE, 11.2.4
     link, 15.1.39SCORE, 20.5.6, 20.5.17
     Search, 2.6.2.12, 2.6.2.13, 2.6.2.14, 2.6.2.15, 2.6.2.16SDF, 9, 9.3.24, 9.3.25, 9.3.26, 9.3.27, 12.1.3, 15.2
          Field, 2.6.2.13SEQUENCE.site Colors, 3.7.4
          Homology, 2.6.2.15SITE.label Style, 3.7.7
          Identity, 2.6.2.14     labelOffset, 3.7.7
          Sequence, 2.6.2.16     wrap Comment, 3.7.7
     convert, 4.1.2SLIDE.ignore Background Color, 3.7.4

SMILES, 9.1.2, 9.2.4, 9.4.12align, 3.1.11, 9.14
Select Min Grad, 3.7.10     color 2D scaffold, 9.14
Show Res Code In Selection, 3.7.7     dna protein, 7.6.4
Smiles, 20.8.7, 20.8.10, 20.8.11     multiple, 7.6.5
SureChEMBL, 3.2.4     sequence structure, 7.6.3
Swissprot, 2.6.1.7     two sequences, 7.6.2
     Dat, 3.7.2     DNA to protein, 7.6.4
     link, 15.1.39     sequence, 7.6, 7.6.6
Temp Directory, 3.7.2     two sequences, 7.3.5, 7.6.2
UNIX, 12.1.7alignment, 7.3.8, 7.6.1, 7.7.7, 7.7.7.1, 7.7.16, 7.8, 9.35.1, 9.35.2, 19.4.4, 20.4.12, 20.6, 20.6.2
USER.email, 3.7.11     annotation tutorial, 19.4.4
     friends, 3.7.11     box shade font, 7.7.7
     full Name, 3.7.11     editing, 7.7.1
     organization, 3.7.11     editor, 7.7
     phone, 3.7.11     example, 7.3.14
Uniprot, 15.1.39     font size, 20.2.1
VLS, 12.1, 12.1.1, 12.1.2, 12.1.7, 12.1.10.2     format, 7.7.11
     preferences, 12.1.4     gaps, 7.7.11
Van Drie, 9.33.4     image, 7.7.2
     Label Style, 3.7.7     profile, 19.4.4
Volume, 20.8.7, 20.8.10     reorder, 7.3.12
     Change, 12.1.10.6     search, 7.7.12
Water Radius, 3.7.10     secondary, 19.4.4
Wire Style, 3.7.1          structure, 7.7.16, 20.6.2
XPDB Directory, 3.7.2     selection, 7.7.13
Xstick, 2.7.1     strength, 7.3.8
a-bright, 2.7.2          profile, 7.3.8
about model, 10.1.1     view options, 7.7.10
acceptor, 9.4.9, 9.36.1     color, 7.7.9
active, 6.7, 20.3.3     comment, 7.7.6
activeICM, 6.8     consensus, 7.7.9, 7.7.14
activeicm, 6.7, 6.12, 6.14, 6.14.1, 20.3     cut, 7.3.11
     advanced, 6.14     display title, 7.7.10
     background images, 6.15     editor, 7.7
     control, 6.13     extract, 7.3.10
activeicmjs, 6.16     gaps, 7.7.11
activity cliff, 9.33.4, 9.33.5, 19.6.11     horizontal scroll, 7.7.10
          tutorial, 19.6.11     image, 7.7.2
activityy, 10, 15.6     multiple, 7.3.7, 7.6.5
add database, 9.10.3     options, 7.7.10
     new data, 9.3.7     rename, 7.7.10
     to table, 14.5.7     reorder, 7.3.12
adding fragment, 9.4.8     ruler, 7.7.10
          in editor, 9.4.8     save, 7.7.2
adjust row height, 20.2.39     search, 7.7.12
administration, 9.10.5     selection, 7.7.13, 7.7.14
advanced alignment selection, 7.7.14     sequence offset, 7.7.10
alanine, 11.2.4     table, 7.7.10
album, 5.15.3     view, 7.7.10
alias, 9.4.5alignments, 7.6, 19.4

     channel, 3.7.6as2_graph, 3.6.5
ambient, 2.7.2as_graph, 20.2.8
amidinium, 9.15asparagine, 8.20.2
amino acid, 3.3assign, 5.1.3
     acids, 9.4.6     2D coordinates, 9.17.2
anaglyph, 5.6, 20.1, 20.1.8     helices, 4.6.1
     stereo faq, 20.1.8     strands, 4.6.1
analysis, 2.6.4, 7.3atom, 3.7.5, 9.3.28, 20.2.4, 20.2.5, 20.2.8, 20.2.16, 20.2.17, 20.4.10
angle, 4.5.7, 4.5.8, 5.8.5, 5.9, 5.12.6, 20.2.18, 20.4.16     charge, 20.4.21
angstrom, 20.4.7atomLabelStyle, 3.7.7
animate, 2.6.3.15, 5.10.7atomic energy circles, 14.3.5
     view, 5.10.7     property field, 9.35.1, 9.35.2, 14.3.11
animation, 5.10.7.1, 5.10.7.2, 5.10.7.3, 5.10.7.4               score, 9.36.2
     store, 5.10.7.4          fields, 4.4.6, 9.36, 9.36.1, 9.36.3, 12, 19.8
animations, 6attachment, 9.4.3, 9.5.1
annotate, 3.6.21, 9.13     point, 9.32.4
     alignment, 7.7.6author, 3.2.1.3
     by substructure, 9.13     close tree, 9.25.5
     plot, 15.4.22     play slide, 6.13
annotation, 7.7.6autofit, 11.5
antialias, 2.6.1.15, 2.6.3.10autosave, 20.2.33
     lines, 2.6.3.17ave, 15.7.1
     lines, 2.6.3.17avi, 5.16, 5.16.2
apf, 4.4.6, 9.35.1, 9.35.2, 9.36, 10, 11.3, 12, 12.1.10.7, 12.3, 14.3.11, 14.17, 19.8, 19.8.1, 19.8.2, 19.8.3, 19.8.4, 19.8.5, 20.8.12axes, 15.4.14
     flexible template, 9.35.2axis, 15.4.10
     pairwise, 9.35.1     options, 15.4.9
     super, 9.35     grid, 15.4.9
     template, 14.12     range, 15.4.9
     tools, 9.36     title, 15.4.9
          3DQSAR, 9.36.4b-factor, 4.6.3, 19.3.10
          consensus ph4, 9.36.1     coloring scale, 20.2.38
          pairwise score, 9.36.2backbone, 5.1.10, 20.2.13
          screen, 9.36.3background, 5.4.2, 5.4.3
     tutorial, 19.8     color shortcut, 20.2.2
          cluster, 19.8.5     images activeicm, 6.15
          consensus, 19.8.2     image, 5.4.3
          score, 19.8.3backup, 2.6.2.11
          screen, 19.8.4bad, 9.11
          superposition, 19.8.1     groups, 9.4.9
     alignment, 9.35.3ball, 3.7.5
apf3Dqsa, 20.8.12     and stick, 2.7.1
append, 15.1.43balloon, 15.4.24
     table, 15.1.43bases, 9.4.6
     rows, 2.6.10.7basicsel, 3.6.2
applying prediction models, 10.2batch, 11.1.10, 11.6.9, 12.1.7
area, 4.5.3, 4.6.4, 11.6, 11.6.2, 11.6.3, 19.3.5     file, 11.1.10.2
aromatic, 9.3.28, 9.36.1     index, 11.1.10.4
arrange, 3.1.13.1     loaded icm object, 11.1.10.1
     window, 3.1.13.1     mol mol2, 11.1.10.3
     graph, 20.2.8     molcart, 11.1.10.5

bayesian classifier, 10cartesian, 9.20
beep, 20.2.35cavities, 4.5
begin docking simulation, 11.1.8     closed, 4.5.4
best, 9.3.34ccp4, 20.2.27, 20.2.28
bicyclics, 9.4.6cell, 4.3.2
binding, 19.5.3, 20.2.14, 20.5.2, 20.5.10center, 2.6.3.20, 3.1.3, 5.12, 5.12.5, 14.3.13, 15.1.39, 20.4.22
     properties, 5.3.1     on ligand, 14.3.13
bioinfo align multiple, 7.3.7     and representative members, 15.7.2
          two sequences, 7.3.5chain.breaks, 20.2.34
     links, 7.3.9chair, 20.5.20
     menu, 2.6.4change box size, 14.8.1
     secondary structure, 7.3.2     height of all rows, 15.1.6
     translation, 7.3.3     ligand, 14.5.1
bioisoester, 9.9     row height, 15.1.6
bioisostere, 9.9, 9.9.1, 9.9.2     selection, 3.6.7
biological, 4.3.3     speed range, 5.10.7.2
biomolecule, 2.6.5, 4.3.3, 19.3.8, 19.3.12changing font in alignment editor, 7.7
bit, 20.1.3charge, 2.6.3.21, 4.1.3, 4.1.3.1, 4.1.3.2, 5.8.2, 9.4.3, 9.5.1, 9.7.1, 9.7.2, 9.7.3, 9.36.1, 12.1.10.6, 20.4.1
blast, 3.2.5, 7.4     groups, 11.1.6, 20.5.22
     search, 3.2.5check box, 6.6.6
blue lines, 7.2     convert, 20.8.5
boat, 20.5.20     export excel, 9.2.3
bond, 4.1.3, 4.2.3, 4.2.3.1, 4.2.3.2, 8.9, 9.4.10, 20.4.1, 20.8.7, 20.8.10     save, 9.2
     covalent, 20.4.2          3D, 9.2.5
     type, 4.1.3.1, 4.1.3.2, 9.7.1, 9.7.2, 9.7.3          editor, 9.2.4
bonding, 5.1.8          image, 9.2.6
     preferences, 3.7.1          table, 9.2.2
box, 3.7.7, 5.8.15, 7.7.7, 7.7.7.1, 20.5.9     super, 9.34
     alignment, 19.4.4     view, 9.3.28
     size, 14.8.1chembl, 3.2.3, 3.2.4
browse, 9.3.31, 11.1.12.1, 17.4chemical, 9, 9.3.28, 9.3.30, 9.3.31, 9.3.34, 9.3.35, 9.4.10, 9.8, 9.10.4, 9.11.2, 9.17.2, 9.21, 9.32.4, 9.32.5, 9.34, 9.35.1, 9.35.2, 15.7.1, 19.6.4, 20.8.4, 20.8.5, 20.8.7, 20.8.8, 20.8.9, 20.8.10
     mode, 9.3.31     clustering, 9.25, 9.25.6
     molt, 16.2     descriptors, 20.8.15
     stack, 8.20.15     dictionary, 9.4.4, 9.4.5, 9.4.6
build, 5.10.7.1     draw, 19.6.1
     homology model, 8.1.2          spreadsheet tutorial, 19.6.1
     hydrogens, 8.20.5     edit buttons, 9.4.11
buried molSurface, 12.1.10.6     editor, 9.4, 9.4.8
buttons, 6.14          not starting, 20.1.13
bye, 2.6.1.19     fingerprint, 13
     alpha, 5.1.10     fingerprints, 20.8.15
     trace, 5.1.10     fragments, 9.3.33
ca-trace, 5.1.10     group, 9.4.5
cache, 6.14.1     groups, 9.4.5, 9.4.8
calculate, 9.11, 20.5.2     modifiers, 9.32.2
     properties, 9.11     properties, 19.6.4
     sequence similarity, 7.7.15     right click, 9.4.3
     startup, 20.10.2     search, 9.5
carbon, 20.2.4, 20.2.5          filter, 9.5.2
carboxylic acid, 9.15          text, 9.5.4

     spreadsheet, 3.2.3, 9.1.3, 9.3.1, 9.4.14, 19.6.1, 20.8.13     select, 19.6.4.2
          compare, 9.3.22chi, 5.8.5, 20.2.18
          template, 9.3.2chiral, 9.22, 11.1.1.3
     spreadsheets, 9.3chirality, 9.22, 11.1.1.3
     substituent, 9.9     considerations, 11.1.1.3
     substructure, 3.2.1.1chrome, 20.3
     table, 14.9, 20.8.11cis trans proline, 19.5.2
          display, 9.3.3clash, 3.7.5, 5.8.14
     tables, 15.2     volumes, 12.1.11
     toxicity, 9.11.2classes, 9.3.28
     2D, 9.7classification model, 13.6
     3D, 9.7clear display and planes, 2.6.3.2
     append, 9.4.13     selection, 3.6.6
     clustering, 9.25, 9.25.1     planes, 2.6.3.2
     convert, 4.1.3, 4.1.3.1, 4.1.3.2, 8.20.1, 9.7, 9.7.1, 9.7.2, 9.7.3, 20.4.1click, 3.1.12, 5.11, 5.12
     display.fit, 20.8.13clip, 5.3.10, 5.13.1, 20.2.11
     draw, 9.4.1clipboard, 5.15.3, 15.7.3
     duplicates, 9.3.21clipping, 20.2.19
     editor, 9.2, 9.2.2, 9.2.4, 9.2.5, 9.2.6     planes, 5
     load, 9.1     tool, 5.13
     merge, 9.29     tools, 5.13
     new, 9.4.1clone, 2.6.1.2
     properties, 9.3.19close, 5.3.3, 5.3.4, 14.20
     query, 9.4.3, 9.5.1, 9.5.3     downstream cluster, 9.25.5
     read, 9.1     project, 14.20
     save, 9.2, 9.2.2, 9.2.4, 9.2.5, 9.2.6, 9.4.13     cavities, 4.6.5
     search, 9.4.3, 9.5, 9.5.1, 9.5.3cluster, 12.1.7, 12.1.10.7, 15.7.1
     similarity, 9.4.3, 9.5, 9.5.1, 9.5.3     representative.center, 9.25.2
     spreadsheet, 9.2, 9.2.2, 9.2.4, 9.2.5, 9.2.6, 9.3clustering, 15.7, 19.6.3
     structure, 9.4.13cns, 9.31
     superimpose, 9.34.1, 9.34.2, 9.34.3collada, 2.7.6, 5.3.7
     superposition, 9.35, 9.35.3color, 4.6.2, 5.3.2, 5.3.3, 5.3.4, 5.3.9.4, 5.4, 5.4.1, 5.8.2, 5.8.3, 7.8, 9.3.35, 9.14, 15.1.44, 15.7.4, 20.2.4, 20.2.5, 20.2.16, 20.2.20
     table, 9.3, 15.2     alignment, 7.7.9
cheminformatics, 9, 9.3, 20.8     background, 5.4.2
     tutorials, 19.6     by, 5.4
chemistry, 9.21, 20.8          alignment, 7.8
     convert, 9.17     chemical, 9.3.35
          2dto3d, 9.17.1     faq, 20.2.20
     pca, 9.26     key, 20.2.38
     smiles, 9.17.3     scale, 20.2.38
     duplicates, 9.30     surface by proximity, 5.3.3
     remove.redundant, 9.30               selection, 5.3.4
chemlib.so, 20.1.3     table, 9.3.27
chemspace append, 19.6.4.4     2D sketch, 9.5.5.5
     build visualize, 19.6.4.1     background, 2.6.3.18, 5.4.2
     compare, 19.6.4.8     distance, 5.8.10
     delete row, 19.6.4.3     mesh, 5.3.9.3
     distinguish, 19.6.4.7     table, 9.3.27
     export, 19.6.4.5coloring, 5.4.1
     project, 19.6.4.6coloumn, 15.1.24

     annotation, 15.1.40          chem, 9.7.1
     order, 15.1.28     smiles to 2D, 20.8.11
     row width, 15.1.21     local.database, 2.6.1.6
     statistics, 15.1.31     smiles, 9.17, 9.17.3, 9.17.4
     visibility order, 15.1.27converting pdb, 4.1.2
     color, 15.1.9coordinates, 9.1.3
     hide, 9.3.8copy, 9.3.25, 9.4.11, 9.4.17, 9.5.5.2, 15.1.34
     show, 9.3.8     cell, 15.1.35
combinatorial chemistry, 9.32     chemical, 9.3.25
     library, 19.6.8     loop, 8.4
combine, 2.6.10.5     paste row, 15.1.34
     display style, 3.7.9     row, 15.1.35
command, 20.5.16     rows, 15.1.43
     line, 20.2.32     selection to table, 15.1.36
commands, 20.10.1     chemical, 9.3.16
compact tree, 9.25.5covalent, 14.9.1
compare, 9.3.29, 9.28, 9.29     bond, 19.9.3
     table, 9.3.22     docking, 11.4, 11.4.1, 14.16, 19.9.3
     tables, 9.28          tutorial, 19.9.3
compatible, 2.6.1.10cpk, 5.1.5, 20.2.21
complex, 9.6, 12.1.10.5crash, 2.6.2.11
compound, 3.2.1.3, 9.21, 15.2creat, 6.6.1
compounds, 20.9.3create, 15.1.1
compress, 3.7.6     markush, 9.32.3
conditions, 9.5.2     new objects, 3.3
     gen, 9.20cross, 20.2.10
configuration error, 20.1.19     section, 5.13
conformation, 9.20, 11.2.2crystal, 4.3.2
conformational entropy, 9.24crystallographic analysis, 4.3
conformations, 20.9.8          biomolecule, 4.3.3
conformers, 9.20          contour map, 4.3.6
connect, 5.3.9.1, 5.12, 5.12.7          convert2grid, 4.3.7
     object, 5.12.7          crystallographic cell, 4.3.2
connectivity, 9.4.3, 9.5.1          load eds, 4.3.4
consensus, 9.36, 19.8.2          maps cell, 4.3.5
     pharmacophore, 9.36.1          symmetry packing, 4.3.1
construct, 2.6.1.1, 5.10.7.1          tools, 19.3.8
     molecule, 2.6.1.1     cell, 2.6.5
     object, 2.6.1.1     neigbor, 4.3.1
contact, 4.5, 4.5.3, 19.3.5     neighbors, 2.6.5
     surface, 5.3.2crystallography, 4.3.4, 4.3.6, 4.3.7, 20.2.27, 20.2.28
contacts, 5.3.3, 5.3.4, 9.6, 12.1.10.8, 14.3.12csv, 9.2.3, 15.1.2, 15.1.3, 15.1.20, 17.2
contour, 4.3.6, 4.3.7current, 20.2.22
convert, 4.1.2, 9.17.1, 9.17.5, 20.8.5     slide, 6.13
     chemical, 9.3.24curves, 15.4.5
          2D 3D, 9.7custom, 5.12, 9.3.3, 9.34
          3D molecular editor, 9.4.16     actions, 15.1.39
          from pdb, 4.1.3     fragments, 9.13
     local database, 2.6.1.6     label, 5.8.8
     pdb, 19.3.2     rotation, 5.12.2

     vertical alignment block, 7.3.11     hbond, 12.1.10.5
cyclic peptide, 8.19     hbonds, 12.1.10.6, 14.3.4
damaged skin, 20.1.12     hydrogen, 5.1.7
dash, 20.2.12          atoms ligand editor, 14.3.3
database, 7.4, 9.10, 9.32.4, 12.1.3, 12.1.6, 16.1, 17     mesh, 5.3.5
     file format, 12.1.3     meshes, 5.3.8
     seach and alignment, 7.4     options, 14.3
databases, 20.9.3     planar angle, 5.9.2
decompose.library, 19.6.9     tab, 2.7.1, 20.2.16
decomposition, 9.32.4, 9.33.1, 15.4.23     tether, 5.8.12
default, 3.1.13     toggle, 5.8.15
delete, 2.6.2.1, 3.6.6, 6.6.8, 20.4.9     CPK, 5.1.5
     alignment, 7.7.5     angle, 5.9.2
     all, 2.6.2.2     chemical, 9.3.3
     column row, 15.1.37     dihedral.angle, 5.9.3
     label, 5.8.9     distace, 5.8.10
     alignment, 7.7.5     distance, 5.8.13, 5.9.1
     all, 2.6.2.2     electrostatic, 2.6.3.21
     angle.label, 5.9.4     energy.gradient, 5.8.16
     column, 15.1.37     hydrogen, 5.1.7
     distance.label, 5.9.4          polar, 5.1.7
     label, 5.8.9     macroshape, 5.3.6
     row, 15.1.37     meshes, 5.3.5
     selection, 2.6.2.1          and display.macroshape, 2.7.6
     tether, 8.20.5     molecule, 9.3.24
dendrogram, 9.27     origin, 5.8.11
density, 4.3.4, 4.3.6, 4.3.7, 20.2.27, 20.2.28     potential, 2.6.3.21
depth, 5.3.12, 5.10.5     representations, 2.7.1
deselect, 20.2.7     restraints, 5.8.13
design loop, 8.3, 8.20.10     ribbon, 5.1.3
deviation, 20.4.7     skin, 5.1.4
dfa, 13.1.3     status, 20.2.32
dfz, 13.1.2     surface, 5.1.6, 5.3.1
dialog, 6.6.5     surfaces, 2.7.6
diffuse, 2.7.2     table, 9.3.3
dihedral, 4.5.8, 5.8.5, 20.2.18     tethers, 5.8.12
     angle, 4.5     wire, 5.1.1
dimensional, 20.8.6     xstick, 5.1.2
directories preferences, 3.7.2distance, 4.5, 4.5.6, 5.8.10, 5.9, 9.28, 20.2.12, 20.4.8, 20.4.10
directory, 3.7     faq, 20.4.10
disappearing labels, 20.1.12     restraint, 11.1.7
dislay ligand receptor interaction, 9.6     label, 3.7.7
display, 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, 9.22, 11.1.6.3, 20.2.4, 20.2.5, 20.2.8, 20.2.10, 20.2.11, 20.2.17, 20.2.21, 20.2.30, 20.2.32, 20.4.10, 20.4.11, 20.4.20, 20.8.4distances, 2.7.3
     delete distances, 5.9.4disulfide, 8.9, 8.16
     dihedral, 5.9.3     bonds, 8.16
     distance restraints, 5.8.13diverse set, 15.7
     distance2, 5.9.1dock, 11, 11.1, 11.5, 14.9, 14.9.1, 19.9.3, 19.11.1, 19.11.2, 19.12.1, 20.5.3, 20.5.4, 20.5.5, 20.5.7, 20.5.8, 20.5.10, 20.5.11, 20.5.12, 20.5.13, 20.5.14, 20.5.15, 20.5.16, 20.5.21
          angles, 5.9     apf, 14.17
     formal charge, 5.1.9     chemical table, 11.1.15
     gradient, 5.8.16     command, 20.5.16

     table, 14.9dpc, 13.1.4
          covalent, 14.9.1drag, 3.1.11, 3.7.7, 5.8.3, 6.6.4, 7.6.6, 20.4.5
docking, 4.6.4, 11, 11.1.1, 11.1.2, 11.1.3, 11.1.16, 11.2, 11.2.1, 11.2.2, 11.2.3, 11.6, 11.6.1, 11.6.2, 11.6.3, 11.6.4, 11.6.5, 11.6.6, 11.6.8, 11.6.9, 11.6.10, 12.1, 12.1.1, 12.1.2, 12.1.6, 12.2, 14.9, 14.9.1, 14.10, 19.9, 19.9.1, 19.9.2, 19.11.3, 19.12, 19.12.2, 20.5, 20.5.1, 20.5.9, 20.5.17, 20.5.18     and drop sequences, 7.6.6
     batch index, 11.1.10.4     residue label, 2.6.3.16
     covalent, 11.4draganddrop, 3.1.11
     display, 11.1.17draw, 9.4.17, 9.32.5, 20.8.2
     explicit group, 19.12.2     chemical, 9.4.1
     from table, 11.1.9.1, 11.1.9.2drop, 3.1.11, 6.6.4, 7.6.6, 20.4.5
     introduction, 11.1.1drug, 9.11, 20.8.7, 20.8.9
     macrocycles, 11.1.6     bank, 3.2, 3.2.8, 9.1
     maps, 11.1.4, 11.1.5drugbank, 9.1
     preferences, 11.1.6druglikeness, 9.4.9
          database scan, 11.1.6.2dsPocket, 3.1.8
          display, 11.1.6.3dual alanine scanning, 11.2.4
          general, 11.1.6.1easy rotate, 2.6.3.12
     project, 12.1.5ecfp, 10.3
          table, 12.1.5edit, 4.2.3.1, 14.5.8, 20.8.3
     results display, 11.1.17     2D, 14.5.1
     setup, 20.5.13     alignment, 7.7.1
     start, 11.1.3     chemical moledit, 9.3.26
     steps, 11.1.2     ligand, 14.5, 14.5.1
     template, 11.3          2D, 14.5.1
     templates, 14.12          editor preferences, 14.2
     tutorials, 19.9          multiple substituents, 14.5.2
     background, 20.5.19          tools, 2.6.2.17
     batch, 11.1.10     menu, 2.6.2
     conformations, 20.5.20     molecular document, 6.6.1
     flexible.rings, 20.5.20     molecule, 9.4
     hitlist, 11.1.13     molt, 16.3
     interactive, 11.1.9     selection, 2.6.2.5
     preparation, 11.1.3     slide, 6.4.1
     procedure, 11.1.8     table row, 15.1.23
     rank, 11.1.13     molecule, 9.3.26
     results, 11.1.12, 11.1.12.1, 11.1.12.2, 11.1.13     structure, 9.3.26
     sampling, 20.5.20editor, 20.4.12
     score, 11.1.13editpdbsearch, 2.6.2.12
     stack, 11.1.12.2eds, 4.3.4, 4.3.6, 4.3.7
     template, 11.3effect of mutation, 8.14, 8.15
document, 6.6.4, 6.6.5               on binding tutorial, 19.5.3
     navigation, 6.6.7                              example2, 19.5.3.1
documents, 5.15.3                    stability tutorial, 19.5.4
dollar, 20.10.3effort, 9.20, 9.34, 20.5.12
donator, 9.4.9electron, 4.3.4, 4.3.6, 4.3.7, 20.2.27, 20.2.28
     envelope, 2.7.1     denisty map, 4.3.5
     surface, 3.7.5     densitry map.contour, 2.6.5
dotted line, 5.1.3          map, 2.6.1.7, 2.6.5, 4.3.4, 4.3.6, 11.5
     lines, 20.2.34electrostatic coloring scale, 20.2.38
double, 9.4.10     potential, 2.6.3.21
doublet, 9.4.7     surface, 5.3
download, 20.1.1, 20.9.3electrostatics, 5.3.1, 11.6.8

element, 9.4.10     icb, 2.6.1.5
eln, 17.7     pharmacophore, 9.5.5.4
embed browser, 6.11faq, 20, 20.2, 20.2.13, 20.4, 20.5, 20.7, 20.10, 20.10.2
     powerpoint03, 6.8     ISISdraw, 20.8.3
     powerpoint07, 6.9     MolCart, 20.9
     powerpoint10, 6.10     activeicm, 20.3
     activeicm, 6.13          path, 20.3.3
          script, 6.13     alignment secondary structure, 20.6.2
     browser, 6.7, 6.11     apf model, 20.8.12
     firefox, 6.7, 6.11     atom charge, 20.4.21
     internet.explorer, 6.7, 6.11          display, 20.2.17
     microsoft, 6.7     autosave, 20.2.33
     powerpoint, 6.7, 6.8, 6.9, 6.10     backbone, 20.2.13
empty hostid, 20.1.18     background color, 20.2.2
enantiomer, 20.5.21          job, 20.5.19
enantiomers, 11.1.1.3     beep, 20.2.35
energy, 4.6.2, 5.8.14, 9.24, 9.24.2, 11.1.12.2, 20.5.1, 20.5.2, 20.9.8     binding energy, 20.5.2
     circles, 12.1.11     blend transition, 20.2.31
     maps, 11.1.4, 11.1.5     breaks, 20.2.34
     terms, 8.20.18     change torsion, 20.4.16
ensemble, 11.2.2     chem table display, 20.8.4
entropy, 9.24.1     chemical monitor, 20.8.10
enumerate formal charge states, 9.16          query2, 20.8.1
     reaction, 19.6.10     cheminformatics, 20.8
enumeration, 9.32.4     clipping plane, 20.2.11
eps, 9.2.6     closest, 20.4.22
epsilon, 20.4.15     color carbon, 20.2.4
eraser, 9.4.11          skin, 20.2.16
errno, 20.1.3     command line display, 20.2.32
error, 20.1.3, 20.1.19, 20.2.35     convert chemical from pdb, 20.4.1
evaluate score strain, 14.4     covalent bond, 20.4.2
exact, 9.28     delete, 20.4.9
excel, 9.2.3     descriptors, 20.8.15
exclude fragment, 9.5.2     deselect, 20.2.7
     volume, 14.3.11     dihedral, 20.2.18
exit, 2.6.1.19     dock charge groups, 20.5.22
explicit, 9.3.28, 11.2.1          probe, 20.5.13
     flex, 11.2.1          racemic, 20.5.21
     group, 11.2.3          repeat, 20.5.5
          docking, 11.2.3          working directory, 20.5.23
     groups, 19.12.2     docking, 20.5
export, 4.5.10, 17.4     docktime, 20.5.11
     dock project, 14.19     dollar, 20.10.3
extra windows, 5.2     download install, 20.1.1
extract, 3.4.2, 7.1, 9.1.3, 20.4.12, 20.8.8     druglikeness, 20.8.9
     2D, 9.1.1     energy, 20.5.1
     3d coordinates to spreadsheet, 9.1.3     error admin, 20.1.10
     icb, 2.6.1.5     extract ligand, 20.8.8
     object icb, 3.4.2     flexible dock, 20.5.15
     sub alignment, 7.3.10          ring docking, 20.5.20

     foreground table, 20.10.4     solvent accessible surface table, 20.4.19
     gl failure, 20.1.11     ss, 20.4.17
     gui, 20.2     structure, 20.4
     guided dock, 20.5.3     superimpose, 20.4.6
     hitlist, 20.5.7     surface display, 20.2.37
     hydrogen bond acceptors, 20.8.17     thoroughness, 20.5.12
     iSee, 20.2.30     transparent ribbon, 20.2.3
     icmPocketFinder, 20.5.10     truncate mesh, 20.2.15
     insert column, 20.8.7     view stack, 20.9.8
     installation, 20.1     weak hydrogen bonds, 20.4.20
     interactions, 20.2.12     write pdb, 20.4.3
     ligandbox, 20.5.9faqcontour, 20.2.28
     measure distance ring, 20.8.16faqhbondstrength, 20.2.29
     merge, 20.4.5faqmaps, 20.2.27
     modeling, 20.7faqoda, 20.2.26
     molcart 64bit, 20.1.3faqstereo, 20.1.14
          query, 20.9.5fasta, 7.1.5
          sdf, 20.9.4fbdd, 12.2
          text search, 20.9.6fft, 11.6.1
     molecule c, 20.2.5     protein protein docking, 11.6.1
     moledit, 20.8.2file, 2.6.1.3
     movie planes, 20.2.19     close, 2.6.1.13
     newscript, 20.10.1     compatible, 2.6.1.10
     nmr, 20.4.18     export, 2.6.1.12
     nvidia error, 20.1.2     high quality image, 5.15.1
     origin, 20.2.10     load, 2.6.1.7
     plist, 20.1.9     menu, 2.6.1
     pmf score, 20.5.6     password, 2.6.1.11
     pockets, 20.2.14     preferences, 2.6.1.16
     preserve coordinates, 20.8.6     quick image, 2.6.1.14
     quad buffer, 20.1.7     icb, 3.1.10
     receptor selection, 20.5.14     recent, 2.6.1.17
     reload dock, 20.5.4     bak, 2.6.2.11
     remove salt, 20.8.14filter, 16.2, 20.2.4
          select, 20.2.6     selection, 3.6.8
     renumber, 20.4.4filters, 12.1.5
     residue number selection, 20.2.36find chemical, 9.3.32
     rmsd, 20.4.7fingerprint, 10, 10.3, 19.13, 20.8.1, 20.9.5
     rmsdtips, 20.4.8     method, 10.3
     rocking active ppt, 20.3.1fingerprints, 20.8.15
          speed, 20.3.2firefox, 20.3
     rotate chemical, 20.8.13fit, 9.3.34, 11.5, 20.5.15
     scale display, 20.2.38fitting, 11.5, 15.4.15
     scanScoreExternal, 20.5.17flex super, 9.34.3
     scanScoreExternal2, 20.5.18flexibility, 4.6.3, 11.2.3, 19.12
     score, 20.5.8flexible, 9.34, 11.2, 11.2.1, 11.2.2, 19.12.1, 20.5.15
     script, 20.10     docking, 14.13
     sequence secondary structure, 20.6.1     receptor groups, 14.13
          alignments, 20.6     ring sampling level, 11.1.6
     smiles, 20.8.11flood, 8.20.17

font, 3.7, 3.7.7, 4.2.3.1, 5.8.2, 5.8.3, 7.7.7, 7.7.7.1, 9.3.28, 15.1.39, 15.7.4     controls, 5
     preferences, 3.7.7     defects, 20.1.12
     size, 7.7, 20.1.16, 20.2.1     effects, 5.10
form view, 15.1.5     panel, 5.2
formal, 4.1.3, 20.4.21     preferences, 3.7.3
     charge, 5.1.9, 9.15, 9.16     shadow, 2.6.3.13, 5.10.2
format, 15.1.2, 15.1.39green arrows, 7.7.16, 20.6.2
formula, 9.4.9, 9.11     lines, 7.2, 20.6.1
fragment, 9.3.35, 9.33.1, 12, 12.2, 14.10grid, 9.3.3, 9.34, 19.12.1, 20.8.4
     linking, 14.10grob, 3.7.5, 4.3.4, 4.3.6, 4.3.7, 5.3
     screening, 12.2group, 9.33.1, 14.6
fragments, 9.8     column, 15.1.45
frame, 7.3.3groups, 9.8, 9.11, 9.12
free energy, 8.12, 8.13guanidinium, 9.15
     radical, 9.4.7gui, 3.1.1, 3.7.4
freeze column, 15.1.29     menus, 2.6
     row, 15.1.30     preferences, 3.7.4
frequency, 9.3.35     tabs, 2.7
front, 5.3.10, 5.13.1guided docking, 11.1.7, 20.5.3
full model, 8.1.3h-bond, 4.2.3, 4.2.3.1, 4.2.3.2, 20.2.12
          builder, 8.1.3halogen, 9.11.1
          multiple chain, 8.1.3.1hardware stereo, 2.6.3.7, 20.1
     refinement, 8.1.3hbond, 4.2, 19.3.6, 20.2.29
     scene antialias, 2.6.3.10     strength, 20.2.29
     screen, 2.6.3.8header, 3.2.1.6, 15.4.8
function, 15.1.25, 15.1.31health, 4.6.2
functional.groups, 9.13heatmap, 15.4.6
fuzzy, 11.3     example, 15.4.6.1
gap, 8.3helix, 20.2.20
general preferences, 3.7.5hetero, 9.3.28
generalselecttools, 3.6.1     scan, 14.7
generator, 4.3.3, 9.20hidden block format, 7.7.11
getting started, 3          width, 7.7.11
glasses, 5.6, 20.1.6, 20.1.14hide, 15.1.38
glutamine proline, 8.20.2     column, 15.1.27
google, 2.6.1.7high, 2.6.1.15
     objects, 5.3.7     quality, 2.6.3.11
     3D, 2.7.6, 5.3.7highlight new data, 9.3.7.1
gpcr_model, 19.5.1his, 20.4.15
graft loop, 8.4histidine, 8.20.2, 20.4.15
graphical, 20.2.4     tautomer, 20.4.15
     display, 4.1.3.1, 4.1.3.2, 9.7.2, 9.7.3histogram, 12.1.10.2, 12.1.10.3, 15.4, 15.4.1, 15.4.8, 15.4.10, 15.4.12, 15.4.13, 15.4.14, 15.4.15, 15.4.16, 15.4.17, 15.4.19, 15.4.21
          tutorial, 19.1     bins, 15.4.3
               2D3D labels, 19.1.4     options, 15.4.2
               annotation, 19.1.2     bin.size, 15.4.2
               color representation, 19.1.1     bins, 15.4.3
               labels, 19.1.3     color, 15.4.2
     user interface, 20.2     source, 15.4.2
graphics, 3.1     style, 15.4.2
     card, 20.1.2     title, 15.4.2

     cluster apf, 12.1.10.7                         graphics, 2.2.2
     export, 11.1.14                         plots, 2.2.8
homology, 3.2.1.2, 3.2.5, 8, 8.1, 8.1.1, 8.1.1.1, 8.1.2.1, 8.1.2.2, 8.1.3.1, 8.2, 8.7, 19.5                         sequence analysis, 2.2.7
     model, 8.1, 8.1.1.2                         structure analysis, 2.2.3
          introduction, 8.1.1                         superimpose, 2.2.5
     older versions, 8.1.1.3                         surfaces, 2.2.4
hover, 15.4.24                    selections, 2.1.3
     3D editor, 19.7                    superimpose, 2.1.8
     add columns, 9.3.4          search, 3.2
     cluster center, 9.25.2          use gui, 3.1
     color 2D by ph4, 9.5.5.5hrydrogen.bond, 20.2.29
     copy 2D, 9.3.16html, 2.6.1.12, 3.3, 6.6.1, 6.6.7, 20.3
          paste, 9.3.6html-doc font size, 20.2.1
     decompose, 19.6.9hybridization, 9.4.3, 9.5.1
     duplicate chemicals, 9.3.21hydrogen, 4.2.3, 4.2.3.1, 4.2.3.2, 5.1.8, 9.4.3, 9.5.1, 19.3.6, 20.2.12, 20.8.7, 20.8.10
     edit table, 9.3.17     atom display, 14.3.3
          tree, 9.25.4     bond, 4.2, 5.1.8, 9.6, 12.1.10.5, 19.3.6
     excel, 9.3.10          acceptors, 20.8.17
     extract 3D ph4, 9.5.5.4          donor, 9.36.1
     filter, 9.3.12          label edit, 4.2.3.1
     find replace, 9.3.13               move, 4.2.3.2
     mark row, 9.3.14     bonds, 4.2.4
     markush, 19.6.8     bond, 9.4.9, 20.4.20
          structure, 19.6.7hydrogens, 9.3.28
     merge tables, 9.3.23     remove, 9.3.18
     properties, 9.3.19hyperlink, 6.6.1, 6.6.2, 15.1.39
     reactions, 19.6.10hyrophobic, 9.36.1
     reorder, 9.25.3iSee, 2.6.1.5, 2.6.1.12, 3.1.10, 5.15.3, 19.2, 20.2.30, 20.2.31, 20.3.3
     sdf, 9.3.9icb, 3.4.2, 3.5, 20.2.30, 20.3.3
     show hide, 9.3.8icm, 20.3.3
     sort column, 9.3.5     chemist howto chemical search, 2.4.3
     standardize, 9.3.18               cluster, 2.4.5
     table hyperlinks, 9.3.15               combi library, 2.4.7
          print, 9.3.11               ph4, 2.4.4
          activeicm, 2.3               plots, 2.4.8
               create molecular documents, 2.3.3               sketch, 2.4.1
                    slides, 2.3.2               spreadsheets, 2.4.2
               getting started, 2.3.1               stereoisomers tautomers, 2.4.6
               ppt, 2.3.4          pro 3D ligand editor, 2.5.1
               web, 2.3.5               chem3D, 2.5.2
          chemical clusering, 9.25.1               chemsuper, 2.5.4
          icm browser convert display pocket, 2.1.4               energy, 2.5.3
                    distances angles, 2.1.9               qsar, 2.5.5
                    get started, 2.1.1               tutorials, 2.5
                    graphical display, 2.1.2          tutorials, 2.4
                         effects, 2.1.5     hanging, 20.1.13
                    images, 2.1.7     object, 4.1, 19.3.2
                    labels annotation, 2.1.6     script, 15.1.39
                    pro crystallographic tools, 2.2.6icm-crash, 20.1.13
                         get started, 2.2.1icmFastAlignment, 7.4

icmdb, 17invisible residue label, 20.1.12
icmjs, 6.16isee, 6.6.5
icmpocketfinder, 19.3.7isis, 9.4.17
id, 15.1.26isotope, 9.4.3, 9.5.1
identity, 3.2.1.2iupac, 9.2.7, 9.3.20
image, 3.1.14, 3.7, 3.7.5, 5.15.3, 6.6.3, 9.2, 9.2.6, 15.4.20, 20.1.20javascript, 6.16
     advanced, 5.15.3job, 20.5.19
     distortion, 20.1.20jobs, 12.1.7
     preferences, 3.7.6join, 9.29
     problem, 20.1.20jpg, 5.15
     multiple, 2.6.1.7     means, 15.7.1
     quality, 2.6.3.11kcc, 13.1.1, 13.6
     quick, 2.6.1.14, 5.15.2keep carboxyls neutral, 11.1.6
images, 5.15kernel regression, 13.1.1
impose, 11.2.2     chemical, 9.4.10
improve model, 10.1.3keyboard mouse, 5.11
in-a-window, 20.1.7keystokes in chem-edit, 9.4.10
inchi, 9.17.3kmz, 2.7.6, 5.3.7
increment, 15.1.26knime, 18
     id, 15.1.26label, 3.7.7, 15.7.4, 20.2.17
index, 20.9.6     atoms, 5.8.2
induced, 20.5.15     color, 5.8.7
     fit, 11.2, 11.2.1, 11.2.3, 14.13, 19.12, 19.12.1     move, 5.8.4
insert, 6.6.4     residues, 5.8.3
     column, 15.1.25     sites, 5.8.6
     image, 6.6.3, 15.1.33     variables, 5.8.5
          table, 15.1.33     2D, 2.7.3
     row, 15.1.32     3D, 2.7.3, 5.8.1
     script, 6.6.4     atom, 5.8.1
install, 1, 9.10.1, 17.1, 20.1.3, 20.1.4     atoms, 5.8.2
installation, 20.1     color, 5.8.7
interactio, 20.5.2     custom, 5.8.8
interaction, 4.5.3, 9.6, 20.2.12     delete, 5.8.1, 5.8.9
     fingerprint, 12.1.10.8     distance, 5.8.10
     fingerprints, 12.1.10.8     drag, 2.6.3.16
     restraint, 11.1.7     move, 2.6.3.16, 5.8.4
     restraints, 11.1.7     residue, 5.8.1
interactions, 14.3.12     residues, 5.8.3
interactive, 11.1.9, 19.2     site, 5.8.1
     loaded ligand, 11.1.9.2     sites, 5.8.6
     loop, 8.1.4.2     variable, 5.8.1
     modeling, 8.1.4     variables, 5.8.5, 20.2.18
          table ligand, 11.1.9.1labeling, 5.8.1
     modeling, 8.1.4labels, 5.8, 9.3.28
interface prediction, 19.10     distances, 5.8.10
internet explorer, 20.3     tab, 2.7.3
interrupt, 5.10.7.3landscape, 3.7.6
     animation, 5.10.7.3large chemical space, 19.6.4
introduction, 1     font, 20.1.16
invert selection, 15.1.22          size, 20.1.9

layer, 5.14light, 2.7.2
layers, 5.14     tab, 2.7.2
learn, 9.18, 9.19, 10, 10.1, 15.6, 20.8.12lighting, 5.3.9.4, 5.5
learning, 10likeness, 9.11, 20.8.9
     theory, 10.5line, 3.7.5, 15.7.4, 20.2.12
least.squares, 15.4.15lineWidth, 3.7.3
library, 9.32.4link, 7.3.9
     reaction, 19.6.10     structure to alignment, 19.4
license, 20.1.4links, 3.6.20
ligand, 4.2.2, 9.6, 9.24, 9.24.1, 9.24.2, 11.1.1, 11.2, 11.6.6, 11.6.7, 14.3.12, 14.3.13, 14.5.8, 14.9, 14.10, 20.4.5, 20.4.11, 20.5.2, 20.5.9, 20.8.8linux, 9.10.1
     based screen, 9.36.3, 12.3lipinski rule, 9.31
     best replace, 14.6list, 3.6.18
     binding, 8.15lmhostid, 20.1.18
     code, 3.2.1.3, 3.2.7load, 2.6.1.3, 2.6.1.17, 4.3.4, 4.3.6, 4.3.7, 7.1
     considerations, 11.1.1.2     example alignment, 7.3.14
     editor, 14, 14.9, 14.9.1, 14.16, 14.17     nmr model, 3.2.1.4
          covalent docking, 14.16     protein structure, 4.1.1
          mrc, 14.15     sequence, 7.1
          preferences, 2.6.2.18          extract pdb, 7.1.3
     energetics, 9.24          from file, 7.1.4
          conformational entropy, 9.24.1          paste, 7.1.2
          strain, 9.24.2          swissprot, 7.1.1
     pocket, 4.2.4, 20.4.11     libraries, 8.20.6
          surface, 14.3.2local, 20.2.24, 20.2.25
     receptor contacts, 14.3.12     databases, 16
          display, 4.2     database.browse, 16.2
          interaction, 9.6          edit, 16.3
     strain, 14.3.10          query, 16.4
     surface, 4.2.2          row, 16.3
     tether, 14.11localpdb, 20.2.24
ligand-based, 12, 12.3localseq, 20.2.25
     convert, 8.20.1lock, 5.3.10, 5.13.1, 9.3.31
     editor, 14, 14.1log, 15.4.10
          binding.re-dock ligand, 14.8logP, 9.4.9, 9.11
          display, 14.3logS, 9.4.9, 9.11
          edit, 14.5logarithmic, 15.4.10
          energy, 14.3logout, 2.6.1.19
          hydrogen.bond, 14.3loop, 8.2, 8.4, 20.2.20
          pocket, 14.3     analysis, 8.6
          preferences, 14.2     design, 8.3
          restraint, 14.11     find pdb segments, 8.6
          surface, 14.3     model, 8.2, 8.3, 19.5.2
          tether, 14.11          tutorial, 19.5.2
     optimization, 19.11.3     modeling, 8.1.4.2, 8.5, 8.6, 8.20.10
     pocket, 3.1.8     preferred residues, 8.5
     receptor.contact, 4.5.3     model, 8.20.9
ligand_pocket_interactions, 4.2.4     sample, 8.20.9
ligedit distance restraint, 14.11.2     energy water, 8.20.17
     tab, 2.7.5mac, 9.10.1, 20.1.9, 20.1.16
     tether, 14.11.1     font, 20.1.16

machine learning, 19.13     molmechanics, 2.6.16
macrocycles, 8.19     tools chemical search, 2.6.11
macros, 6.14          molecular editor, 2.6.12
macroshape, 2.6.3.22, 5.3, 5.3.6     windows, 2.6.17
make, 5.10.7.1, 15.1.1merge, 9.29, 20.4.5
     alignment, 7.6.1     two sets, 9.29
     animation, 5.10.7.1mesh, 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
     apf docking sar model, 13.7     clip, 5.3.10
     complex, 12.1.10.6, 14.20     color lighting, 5.3.9.4
     flat, 20.8.13     options, 5.3.9
     molecular document, 6.6     representation, 5.3.9.3
     molt, 16.1     save, 5.3.11
     receptor maps, 11.1.5     options, 5.3.9
     selection, 3.6meshes, 5.3.2, 5.10.5
     bond, 20.4.2     surfaces grobs, 5.3
     disulfide, 8.9, 20.4.17     tab, 2.7.6
     molecule, 2.6.1.1metabolic oxidation, 13.8
     object, 2.6.1.1min, 15.7.1
making molecular slides, 6.1minimization, 8.17
     html, 6.6     cartesian, 8.20.8
     color, 15.4.13     global, 8.20.8
manual change torsion, 14.5.4     local, 8.20.8
map, 3.7.7, 4.3.4, 4.3.6, 4.3.7minimum specifications, 1
     cel, 4.3.5mmff, 8.20.6, 9.4.16, 20.2.17, 20.8.5
maps, 11.1.4, 11.1.5, 11.6.8, 19.12.1, 20.2.27, 20.2.28, 20.5.9     type, 5.8.2
mark, 15.1.44mmp, 19.6.11
     row, 15.1.44mnSolutions, 3.7.10
     shape, 15.4.12model, 8, 8.1, 8.1.1, 8.1.1.1, 8.1.2, 8.1.2.1, 8.1.2.2, 8.1.3.1, 8.2, 8.7, 8.17, 19.5
     size, 15.4.12     domain interaction, 8.17
markush, 9.25.7, 9.32.1, 9.32.3, 9.33.1, 19.11.3     start, 8.1.1.2
     docking, 19.11.3     weight, 10.1.2
     library, 19.6.8modelers view, 8.1.4.1
mass, 20.4.22     view, 8.1.4.1
matched pair, 9.33.5, 19.6.11modeling, 8.20.3
          analysis, 9.33.5     options, 8.1.1.1
materials, 2.7.6modeller view, 8.1.4
max, 15.7.1modification history, 14.5.6
maxColorPotential, 3.7.10modify, 8.11
maximum common substructure, 9.25.6, 9.27     amino acid, 8.11
               dendrogram, 9.27     group, 8.10
mcs, 9.25.6, 9.27mol, 9.2, 9.2.2, 9.2.4, 9.2.5, 9.2.6, 9.4.13, 19.11.2
     rgroup decomposition, 9.25.7mol2, 9.2, 9.2.2, 9.2.4, 9.2.5, 9.2.6
mean, 20.4.7molcart, 9.10, 9.10.1, 9.10.2, 9.10.3, 9.10.4, 9.10.5, 16, 17, 20.1.3, 20.8, 20.8.1, 20.9.3, 20.9.4, 20.9.5, 20.9.6
measure distance, 20.8.16     add database, 9.10.3
          to ring, 20.8.16     administration, 9.10.5
memory, 9.1.2     connect, 20.9.2
menu, 6.6.5     download dbs, 20.9.3
     chemistry, 2.6.14     hostid, 20.9.1
     docking, 2.6.15     installation, 9.10.1
     homology, 2.6.13     license, 20.1.4

     start, 9.10.2move, 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, 8.17, 20.4.5
     connect, 20.9.2     column, 15.1.27
     hostid, 20.9.1     mesh, 5.3.9.2
     license, 20.9.1     slide, 6.4.2
molclart, 20.1.4     structure, 5.12
molecular, 9.3.30, 9.3.31, 9.3.34, 9.3.35, 9.20, 20.8.7, 20.8.10     tools, 5
     animations slides, 6     rotate, 5.11
     documents, 19.2     slab, 5.11
     editor, 20.8.2     translate, 5.11
     graphics, 5     z-rotation, 5.11
     matched pairs, 19.6.11     zoom, 5.11
     mechanics, 8.20movie, 5.16.1, 20.2.19, 20.9.7
          convert, 8.20.1     montecarlo, 20.9.7
          design loop, 8.20.10     making, 5.16, 5.16.2
          edit structure, 8.20.5     open, 5.16, 5.16.2
          gamess, 8.20.16mpa, 19.6.11
          generate normal mode stack, 8.20.14mpeg, 5.16, 5.16.1, 5.16.2
          his asn, 8.20.2mpg, 5.16, 5.16.2
          ic table, 8.20.13mpo, 9.31
          impose conformation, 8.20.4multi apf super, 9.35.3
          minimize, 8.20.8     panel, 5.2
          mmff, 8.20.6     parameter optimization, 9.31
          regularization, 8.20.3     template, 8.1.4.3
          sample loop, 8.20.9     windows, 5.2
               peptide, 8.20.12multiple, 11.2.2, 19.12.1
               protein, 8.20.11     chain, 8.1.2.2, 8.1.3.1
          terms, 8.20.18     position group scan, 14.7
          view stack, 8.20.15     rec, 11.2.2
     modeling, 8     receptor, 3.2.2, 19.12
     table, 9.17.2          docking, 14.15
     weight, 9.4.9     protein, 20.2.5
molecule, 20.2.8, 20.8.3mutant, 8.10, 20.4.13, 20.4.14
     editor, 9.4mutate, 8.12, 8.13, 20.4.15
moledit, 9.4.8     residue, 20.4.13
molmechanics, 20.9.8          N C, 20.4.14
     minimize, 8.20.8mutation, 8.10, 8.12, 8.13, 8.15, 19.5.3, 19.5.4, 20.4.13, 20.4.14
     mmff, 8.20.6     protein binding, 8.12
molscreen, 12, 13          ligand, 8.15
     brief panel, 13.2          peptide, 8.14
     custom model panel, 13.4          stability, 8.13
     full panel, 13.3mysql, 17
     model type, 13.1navigate workspace, 3.6.10
     results, 13.5nearest, 20.4.22
molskin, 5.3.2new, 7.1
molt, 16, 16.4     icm session, 2.6.1.2
monitor, 20.8.10     table, 15.1.1
monochrome, 9.3.28     table, 15.1.1
montecarlo, 20.9.7nmr, 20.4.18
mouse, 3.1.3, 5.11, 5.12     model, 3.2.1.4
mov, 5.16, 5.16.2nof, 9.11.1

non-contiguous selection, 3.6.18     recent, 2.6.1.18
normal modes, 8.20.14     search, 2.7.4, 3.1.2
number of sp3, 9.11.1pdbsearchfield, 2.6.2.13
numbers, 9.3.28pdbsearchhomology, 2.6.2.15
nvidia, 20.1.2pdbsearchidentity, 2.6.2.14
object, 3.1.11, 3.5, 19.3, 20.2.8pdbsearcsequence, 2.6.2.16
objects, 4.1.2peptide, 3.3, 8.14, 8.19
     in table, 15.3     modeling, 8.19
     in.table, 15.3percentage similarity, 7.7.15, 19.4.4
occlusion, 5.3.12, 5.10.5perspective, 2.6.3.9, 5.10.6
     shading, 5.3.12ph4, 9.5.5
          effect, 5.10.5     draw 2d, 9.5.5.1
occupancy, 5.1.3, 19.3.10          3d, 9.5.5.2
     display, 3.2.1.5     search, 9.5.5.3
oda, 4.6.4, 11.6, 11.6.2, 11.6.3pharmacophore, 9.3.35, 9.5.5.5, 19.8.2
older version, 2.6.1.10     2D, 19.6.6
omega, 5.8.5, 20.2.18     3D, 19.6.5
open, 2.6.1.3, 3.4, 15.1.2     clone, 9.5.5.2
     file, 3.4     draw2D, 9.5.5.1
     password, 3.4.1     draw3D, 9.5.5.2
     with password, 2.6.1.4     edit, 9.5.5.1, 9.5.5.2
     movie, 5.16, 5.16.2     move, 9.5.5.2
     password, 2.6.1.4, 3.4.1     new, 9.5.5.2
optimal, 4.6.4, 11.6, 11.6.2, 11.6.3     search, 9.5.5, 9.5.5.3, 19.6.5, 19.6.6
optimize, 8.20.2phi, 5.8.5, 20.2.18
oracle, 17phylogenetic, 7.7.8
orange, 3.6.5phylogeny, 7.7.8
     selection, 3.6.5picking, 5
origin, 5.8.11, 20.2.10picture, 2.6.1.14, 3.1.14, 5.15.2, 6.6.3
other selection, 3.6.19     tips, 3.1.14
outside, 20.5.9     chart, 15.4.7
overlay, 19.3.3, 20.2.5, 20.4.6pka, 9.15
package.activeicm, 6.13planar, 4.5.7, 5.8.5, 20.2.18
packing, 4.3.1     angle, 4.5
pages, 17.7     angle, 5.9.2
pairwise, 9.35.1, 9.35.2plane, 5.3.10, 5.13, 5.13.1, 5.14, 20.2.11, 20.2.19, 20.2.21
     apf score, 9.36     faq, 20.2.21
parallelization, 12.1.8plot, 3.7, 3.7.8, 12.1.10.2, 15.4, 15.4.1, 15.4.4, 15.4.8, 15.4.10, 15.4.12, 15.4.13, 15.4.14, 15.4.15, 15.4.16, 15.4.17, 15.4.19, 15.4.20, 15.4.21
password, 9.10.5     R group sar, 9.33.3
paste, 9.4.11, 9.4.17, 15.1.34     axis, 15.4.10
pbs, 12.1.7     color, 15.4.13
pca, 15.5     function, 2.6.9, 2.6.9.1
pdb, 2.6.1.7, 3.2, 3.2.1.1, 3.2.7, 3.5, 4.1.3, 9.7.1, 19.3, 20.2.24, 20.2.25, 20.4.4     grid, 15.4.14
     chem gl, 9.7.3     header, 15.4.8
          iw, 9.7.2     inline, 15.4.21
     file, 20.4.3     logarithmic, 15.4.11
     html, 3.2.1.6     mark, 15.4.12
     preparation, 19.3.11     point label, 15.4.18
     search, 3.2.1, 3.2.1.2, 3.2.1.3, 19.3.1     preferences, 3.7.8
     convert, 8.20.1          groups, 15.4.23

     selection, 15.4.17     components, 10.5
     zoom translate, 15.4.16print, 5.7, 15.4.19, 15.7.3
     axis, 15.4.14     alignment, 7.7.4
     display, 15.4.14     plot, 15.4.19
     grid, 15.4.14     alignment, 7.7.4
     inline, 15.4.21printer.resolution, 3.7.6
     logarithmic, 15.4.11pro-drug, 9.23
pls, 9.18, 9.19, 10, 15.6, 19.13probe, 11.1.4, 20.5.13
pmf, 20.5.6problem, 20.1.14
png, 2.6.1.14, 5.15, 5.15.2, 6.6.3, 9.2, 9.2.6     with selection, 20.1.12
pocket, 3.1.8, 4.2, 4.2.1, 4.2.2, 4.6.5, 11.1, 19.3.7, 20.2.14, 20.4.11, 20.5.10prodrug, 9.23
     conservation, 20.4.12profile, 7.3.8
     surface, 4.2.1, 12.1.11project, 2.6.1.5, 11.6.4, 17.6, 19.6.4.6
     peptide, 3.1.8     close, 2.6.1.13
     properties, 3.1.8     rename, 2.6.1.9
pocketome, 3.2, 3.2.2properties, 5.8.2, 9.11, 20.8.7
point label, 15.4.18property, 9.4.9, 20.8.7, 20.8.8, 20.8.9, 20.8.10
portait, 3.7.6     expression, 12.1.10.6
post edit ligand, 14.5.8     monitor, 9.4.9
     screen, 12.1.10protect, 6.6.8
postscript, 3.7.6protein, 4.4.6, 7, 8.14, 20.4.5
potential mean force, 12.1.4     chain, 8.3
powerpoint, 19.2, 20.3     health, 4.6.2
ppbatch, 11.6.9     model, 8.18
ppepitope, 11.6.7     protein docking, 19.10
ppmaps, 11.6.8               tutorial, 19.10
pprefine, 11.6.11     sculpting, 8.17
ppresults, 11.6.10     structure, 4
pproc, 11.6.3          analysis, 4.5
ppsetligand, 11.6.6               closed cavities, 4.5.4
ppsetproject, 11.6.4               contact areas, 4.5.3
ppsetreceptor, 11.6.5               distance, 4.5.6
ppt, 6.12, 6.14, 20.3.3               find related chains, 4.5.1
predict, 7.3.2, 9.18, 9.19, 10, 10.2, 15.6, 20.8.9, 20.8.12               finding dihedral angle, 4.5.8
     disulfide, 8.16                    planar angle, 4.5.7
     metabolic oxidation, 13.8               rama export, 4.5.10
predicting bioassays, 10.2               ramachandran plot, 4.5.9
     compound properties, 10.2               rmsd, 4.5.2
prediction binding, 8.12               surface area, 4.5.5
preferences, 3.7, 12.1.5, 20.2.24, 20.2.25          tutorials, 19.3
preferred residues, 8.5               analysis, 19.3.4
presentatio, 6.6.5               contact area, 19.3.5
presentation, 6.7, 6.12               convert, 19.3.2
presentations, 6               hydrogen bond, 19.3.6
preserve, 20.8.6               icmpocketfinder, 19.3.7
press-and-hold to rotate, 9.4.8               search, 19.3.1
pretty view, 14.3.6               superimpose, 19.3.3
primary aliphatic amines, 9.15     superposition, 4.4
principal component analysis, 15.5          select, 4.4.1
          regression, 10          sites by apf, 4.4.6

               grid, 4.4.5r-groups, 15.4.23
               multiple proteins, 4.4.4racemic, 9.3.28, 9.17.5, 20.5.21
protein-protein, 4.6.4, 11.6, 11.6.1, 11.6.2, 11.6.3, 11.6.4, 11.6.5, 11.6.6, 11.6.8, 11.6.9, 11.6.10rainbow, 3.7.5, 5.8.15, 9.3.35, 20.2.38
     docking refinement, 11.6.11ramachandran plot, 4.5, 4.5.10
protein-proteindocking, 11.6.7random forest, 10, 19.13
protein-protin, 19.10range, 5.10.7.2
     convert, 8.20.1ratio.selection, 3.7.5
protonated, 20.4.15     dock ligand, 14.8
protonation, 11.1.1.4reactions, 9.8, 9.32.5
     state, 11.1.1.4reactivity, 9.11.2
protprot, 11.6read, 2.6.1.3, 2.6.1.17, 3.4, 7.1, 9.3.1
proximity, 5.3.3, 5.3.4     chemical, 9.1
psa, 9.4.9          spreadsheet, 9.3.1
psi, 5.8.5, 20.2.18     table, 15.1.2
pubchem, 9.1     pdb, 3.1.2
publication quality images, 5.3.2     table, 15
pubmed, 3.2.1.7reagent, 9.32.5
purple box, 2.6.3.23, 11.1.4, 14.8.1rear, 5.3.10, 5.13.1
qs hydrogen bond, 4.2.3recent files, 2.6.1.17
     pdb chem gl, 4.1.3.2     pdb codes, 2.6.1.18
               iw, 4.1.3.1receptor, 4.2.1, 4.2.2, 9.6, 11.1.1, 11.2.2, 11.6.5, 11.6.7, 14.3.12, 19.12.1, 20.5.2, 20.5.14, 20.5.15
qsar, 9.18, 9.19, 10.1, 19.13     considertations, 11.1.1.1
     learn predict, 9.18     flexibility, 14.15
     predict, 9.19     pocket, 14.3.1
quad buffer stereo, 20.1          surface, 14.3.1, 14.3.2
     buffer, 20.1.7     flexibility, 19.12.2
quality, 2.6.1.15, 3.7.5recover, 2.6.2.11
query, 8.1.2, 17, 17.3, 20.8.1, 20.9.5, 20.9.6     cylinders, 7.7.16, 20.6.2
     molt, 16.4     lines, 7.2, 20.6.1
     processing, 9.5.3redo, 2.6.2.10, 9.4.11, 14.5.5
     setup, 9.5.1refine, 8.7, 8.8
quick, 3.1.14     loops, 8.1.3
     image, 5.15.2     side chain, 8.8
     model multiple chain, 8.1.2.2     sidechains, 8.1.3
          single chain, 8.1.2.1refinement, 11.2.4
     start move structure, 3.1.3region, 11.6.7
          read pdb, 3.1.2regresion, 15.4.15
          representation, 3.1.6regression, 10.1, 10.5, 19.13
          selection, 3.1.5regul, 8.7
               level, 3.6.3regularization, 8.7, 8.20.3
          what is selected, 3.6.4relationship, 10, 15.6
     dispalay.distance, 5.9.1     covalent geometry, 11.1.6
     start color, 3.1.7relaxed ligand, 14.3.9
quit, 2.6.1.19reload, 11.1.16, 20.5.4
     group, 9.25.7, 9.32.4     dock results, 11.1.16
          table, 9.32.2remove, 20.2.6, 20.2.7, 20.2.10
     groups, 9.32.2     salt, 20.8.14
r-group, 9.25.7, 9.32.2     explixit.hydrogens, 9.12
     decomposition, 9.25.7     salt, 9.12
     enumeration, 9.25.7rename, 15.1.24

     project, 2.6.1.9     mean square deviation, 4.5.2
renumber, 20.4.4rotate, 2.6.3.15, 3.1.3, 5, 5.10.7, 5.10.7.1, 5.12, 5.12.1, 5.12.2, 6, 9.3.34, 20.8.13
reorder column, 15.1.28     chemical, 9.3.34
replace chemical, 9.3.32     when pasting, 9.4.8
replacement, 14.6     easy, 2.6.3.12
report, 17.3     speed, 5.10.7.2
representation, 2.6.3.19rotating fragment in editor, 9.4.8
residue, 3.7.7, 20.2.8, 20.4.15, 20.4.22rotation, 5.12.1
     alternative orientaiton, 19.3.11rough surface, 20.2.37
     content, 7.3.1row, 15, 15.1.21, 15.1.34, 15.1.44
     number selection, 20.2.36     flag, 15.1.12
     range, 3.6.18     height, 15.1.6, 20.2.39
     content, 2.6.4, 7.3, 7.3.1     mark, 15.1.12
     mutate, 20.4.13, 20.4.14     hide, 9.3.8
residues, 4.2.1, 4.2.2, 20.2.14     show, 9.3.8
resize, 5.3.9.1, 5.15.3ruler, 5.8.15
     mesh, 5.3.9.1rundock, 20.5.16
resolution, 3.2.1.3rxn, 9.4.13
restore, 2.6.2.11, 5.3.10, 5.13.1safari, 20.3
     default, 20.1.9sali, 9.33.4
     recent backup, 2.6.2.11     bridge, 19.3.6
restrained docking, 11.1.7salts, 9.3.18
restraing, 14.11.1, 14.11.2sample, 8.18, 9.34
results, 11.6.10     double bond cis trans, 11.1.6
     stack, 11.1.12.2     peptide, 8.19, 8.20.12
retrieve columns, 20.5.24     protein, 8.18, 8.20.11
          from original database, 20.5.24     racemic centers, 11.1.6
review and adjust binding site, 11.1.4sar, 9.25.7, 9.33, 15.4.23
rgroup, 9.32.4     analysis, 9.33
ribbon, 2.7.1, 3.7.9, 5.1.3, 20.2.23, 20.2.34     table, 9.33.2
     as a mesh object, 20.2.3save, 3.5, 5.3.11, 5.10.7.4, 7.1.5, 9.2.3, 15.4.20, 15.7.3, 20.2.33
     faq, 20.2.23     SMILES, 9.4.15
     preferences, 3.7.9     alignment, 7.7.3
     style, 3.7.9     chemical mol, 9.4.13
     breaks, 5.1.3          spreadsheet workspace, 9.2.1
     cylinders, 5.1.3          to chemical spreadsheet, 9.4.14
     smooth, 5.1.3     docked ligand, 14.18
     worm, 5.1.3     file, 3.5
ribbonColorStyle, 3.7.9     hits, 14.5.7
right, 3.1.12     image plot, 15.4.20
     click, 3.1.12     ligand receptor complex, 14.18
rigid, 9.34     object, 3.1.9
     super, 9.34.2     pdb, 3.5
          table, 9.34.1     project icb, 3.1.10
ring, 9.4.3, 9.4.6, 9.5.1     sequence, 7.1.5
rings, 9.3.28, 9.20, 9.34     slide, 6.4
rmsd, 4.5, 4.5.2, 20.4.7, 20.4.8     smiles string, 9.4.15
rock, 2.6.3.15, 5.10.7, 5.10.7.1, 6     table, 15.1.20
     speed, 5.10.7.2          spreadsheet, 14.5.7
root, 20.4.7     tree, 15.7.3

     image, 2.6.1.15, 3.1.14     structure, 4.6.1, 20.2.20
     object, 3.1.9     sctructure, 7.3.2
     password, 2.6.1.11     structure, 2.6.4, 5.1.3, 7.3
     picture, 2.6.1.15select, 3.6.12, 3.6.13, 15, 15.1.44, 20.4.22
     project, 2.6.1.8, 2.6.1.9, 2.6.1.10, 3.1.10     a tree branch, 15.7.2
     table.view, 15.1.7     all, 3.6.14
saving, 2.6.1.8     amino acid, 3.6.13
     project, 2.6.1.8     duplicates, 9.30
scaffold, 9.14     molecule, 3.6.12
scale, 3.7.5, 20.2.38     neighbors, 3.6.15
scan, 8.20.7, 11.1.12.1          graphic, 3.6.16
     hits, 11.1.12.1     object, 3.6.11
          group, 14.7     residue, 3.6.13, 3.6.18
scarab, 17          by number, 3.6.18
     add user, 17.5          number, 3.6.18
     browse export data, 17.4     tree, 15.7.2
     installation, 17.1     atom, 3.1.5, 3.6.3
     new project, 17.6     graphical, 3.1.5, 3.6.3
     pages, 17.7     object, 3.1.5, 3.6.3
     query, 17.3     purple.box, 2.6.3.23
     upload data, 17.2     residue, 3.1.5, 3.6.3
scare, 11.2.4     workspace, 3.1.5, 3.6.3
scatter, 12.1.10.2selectall, 2.6.2.3
scatterplot, 12.1.10.4selecting.neighbors, 3.6.16
score, 12.1.9, 14.4, 19.8.3, 19.8.5, 20.5.7, 20.5.8, 20.5.18selection, 3.6.4, 3.6.5, 3.6.21, 5.3.4, 9.4.11, 15.4.17, 15.7.2, 15.7.4, 20.2.4, 20.2.6, 20.2.7, 20.2.8, 20.2.13, 20.2.32, 20.4.9, 20.4.10, 20.4.22, 20.5.14
     threshold, 12.1.4     clear, 2.6.2.7
screen, 9.36, 19.8.4, 19.9, 19.11.1     neighbors, 2.6.2.8
screening, 12.1, 12.1.1, 12.1.2, 19.12     alignment, 3.6.19
screenshot, 5.16, 5.16.2     all, 2.6.2.3
     movie, 5.16.2     alter, 3.6.7
script, 3.3, 6.6.4, 6.6.5, 20.4.19, 20.10, 20.10.1, 20.10.2, 20.10.3     atom, 2.6.2.5
sculpting, 8.17     basic, 3.6.2
sdf, 9.2, 9.2.2, 9.2.4, 9.2.5, 9.2.6, 9.3.35, 9.10, 9.10.3, 9.17.1, 14.9, 16.1, 17.2, 19.11.2, 20.9.3, 20.9.4     change, 3.6.7
search, 9.10, 9.10.4, 16.2, 17.3, 20.9.6     clear, 2.6.2.7
     chembl, 3.2.3     column, 15.1.22
     drugbank, 3.2.8     filter, 2.6.2.5, 3.6.8
     filter, 9.5.2     graphical, 3.6.16
     in workspace, 2.6.2.4     invert, 2.6.2.6, 15.1.22
     pdb, 3.2.1     level, 2.6.3.3
          chemical, 3.2.1     mode, 2.6.3.4
          ligand code, 3.2.7     near atoms, 2.6.2.8
     pocketome, 3.2.2     neighbors, 2.6.2.5, 2.6.2.8, 3.6.15, 3.6.17
     pubchem, 3.2.9     object, 3.6.11
     surechembl, 3.2.4     other, 3.6.19
     tab field, 3.2.1.3     properties, 2.6.2.5
          pdb chemical, 3.2.1.1     range, 15.1.22
               sequence, 3.2.1.2     residue, 2.6.2.5
     uniprot, 3.2.6     row, 15.1.22
     in.workspace, 2.6.2.4     sphere, 3.6.15
secondary aliphatic amines, 9.15     spherical, 2.6.2.8

     table, 3.6.19, 15.1.22sheet, 20.2.20
          elements, 15.1.22shell preferences, 3.7.10
     tools, 3.6.1, 3.6.2, 3.6.7, 3.6.8shift, 5.8.3
     whole, 3.6.11shine, 2.7.2, 3.7.5
     workspace, 3.6.9, 3.6.17shineStyle, 3.7.3
selectioninvert, 2.6.2.6show, 6.3.1, 15.1.38
selections, 3.6     hide column, 15.1.38
     links, 7.3.9side, 9.3.29
selectneighbors workspace, 3.6.17     by side, 9.3.29
sequence, 2.6.4, 3.2, 3.2.1.2, 3.2.5, 3.2.6, 3.3, 7, 7.1, 7.1.5, 7.2, 7.3, 7.3.7, 7.6.1, 7.6.5, 8.1.2, 19.3, 19.4, 19.4.4, 20.4.12, 20.6, 20.6.1               error, 20.1.19
     analysis, 7.3               stereo, 2.6.3.6
     editor, 7.5     chain refinement, 14.14
     identity, 7.7.15     chains, 8.8
     pattern, 3.2.1.2side-by-side, 20.1.19
     reordering, 7.7.8side-chain sampling, 11.6.11
     secondary structure, 7.2, 20.6.1side-chains, 11.2.1
     similarity, 7.7.15sigmaLevel, 4.3.6, 4.3.7
     sites, 7.5similarity, 9.28
     structure, 7.3.6simulation, 20.9.8
     type, 7.3.4     length, 20.5.12
     DNA, 7.3.4simulations, 20.7
     alignment, 7.3.5, 7.6.2, 7.6.6single, 9.4.10
     nucleotide, 7.3.4     chain, 8.1.2.1
     protein, 7.3.4singlet, 9.4.7
     search, 7.4sites, 4.4.6
     structure.alignment, 7.3.6, 7.6.3size, 4.2.3.1
sequences, 7, 20.2.25sketch accents, 5.10.3
     unique, 7.3.13     markush, 9.32.1
     extract, 7.3.13     reaction, 11.4.1
     unique, 7.3.13     smiles, 9.4.12
server error, 20.1.17     accents, 2.6.3.14, 5.10.3
set, 9.3.31, 20.4.21skin, 2.7.1, 5.1.4, 20.2.16
     formal charges, 9.15slab, 5.3.10, 5.13.1
     server, 20.1.17slice, 5.13
     bond type, 8.20.5slide, 5.10.7.4, 6.2, 6.3.1, 6.6.1, 20.2.31
     charges, 8.20.6     effects, 6.5
     chirality, 8.20.5     movie, 5.16.1
     disulfide, 8.9, 20.4.17          file, 6.2
          bond, 8.20.5     navigation, 6.3.2
     formal charge, 8.20.5     show, 6.3
     tether, 8.20.5     blend, 6.5
     types, 8.20.6     edit, 6.4.1
setAPFparams, 20.8.12     effect, 6.5
setup, 11.6.6     smooth, 6.5
     ligand receptor, 14.1     transition, 6.5
shade, 7.7.7, 7.7.7.1slides, 5.16.1, 6, 6.1, 6.3, 20.2.30
     alignment, 19.4.4smiles, 9.4.9, 9.11, 9.17, 9.17.3, 9.17.4
shading, 5.3.12smooth, 5.3.9.3
shadow, 5.10.2     surface, 20.2.37
share model, 10.1.4solid, 5.3.9.3

sort hitlist, 12.1.10.1substructure, 9.10.4, 9.13, 11.3, 20.8.1, 20.9.5
     table, 2.6.10.4     template, 14.12
sorting, 12.1.10.1     alerts, 9.13
     compounds, 15.7suface, 20.4.19
sp3, 9.11.1sulfur, 8.9
spec, 2.7.2superimpose, 2.6.8, 4.4.2, 4.4.6, 19.3.3, 20.2.5, 20.4.6, 20.4.7, 20.4.8
specifications, 20.1.5     3D, 4.4.3
specs, 1     Calpha, 4.4.3
     faq, 20.1.5     arrange.grid, 4.4.5
speed, 5.10.7.2     backbone, 4.4.3
sphere, 20.4.11     flexible, 9.34.3
spherical, 20.4.9, 20.4.12     heavy atoms, 4.4.3
split, 9.33.1     multiple, 4.4.4
spreadsheet, 9.17.2     rigid, 9.34.1, 9.34.2
square, 20.4.7     substructure, 9.34.1, 9.34.2, 9.34.3
squence.amino acid, 7.3.4superposition, 9.34, 9.35.1, 9.35.2, 19.3.3, 19.8.1
stability, 8.13, 19.5.3, 19.5.4surface, 2.7.1, 3.7.5, 4.2.1, 4.2.2, 5.1.6, 5.3, 5.3.3, 5.3.4, 20.2.16, 20.2.37
stack, 8.18, 11.1.12, 11.6.10, 20.9.8     area, 4.5
standalone hitlist, 11.1.14     area, 4.5.5
standard table, 15.1surfaces, 4.2, 5.3.1, 5.3.2, 5.10.5
standardize, 9.12surrounding, 20.4.11
     table, 9.12swissprot, 7.1, 7.5
start, 9.10.2sxstrace, 20.1.19
     dock, 11.1symmetric oligomer, 8.1.3
startup, 20.10.2symmetry, 4.3.1, 4.3.3, 19.3.8, 19.3.9
static, 20.4.8system preferences, 3.7.11
stereo, 3.7.6, 5.6, 9.3.28, 9.4.2, 20.1, 20.1.6, 20.1.7, 20.1.14tab, 15.1.2, 15.1.20
     bond, 9.4.2     pdb, 2.7.4
     hardware, 2.6.3.7table, 3.3, 9.1.3, 9.3.24, 9.3.25, 9.3.28, 9.3.30, 9.3.31, 9.3.34, 9.3.35, 9.17.2, 9.20, 9.34.1, 14.9, 15, 15.1.34, 15.1.39, 15.1.44, 15.4, 15.4.1, 15.4.4, 15.4.8, 15.4.10, 15.4.12, 15.4.13, 15.4.14, 15.4.15, 15.4.16, 15.4.17, 15.4.19, 15.7.1, 20.4.19, 20.8.4, 20.8.5, 20.8.7, 20.8.8
     side-by-side, 2.6.3.6     alignment, 15.1.11
stereohard faq, 20.1.6     clone, 15.1.15
stereoisomer, 9.17.5     color, 15.1.9
stereoisomers, 9.22     column format, 15.1.39
stick, 3.7.5     copy, 15.1.35, 15.1.36
stl, 5.7     delete, 15.1.16
stop, 5.10.7.3     edit, 15.1.23
store, 2.6.3.19, 5.10.7.4, 20.2.22     filter, 15.1.42
     current view, 2.6.3.19     find, 15.1.8
               faq, 20.2.22          replace, 9.3.32
strain, 4.6.2, 9.24, 9.24.2, 14.4     font, 15.1.10
strip, 20.4.9          size, 20.2.1
structure, 4.3.3, 10, 15.6, 19.3, 20.4     grid, 15.1.5
     analysis, 19.3.4     histogram, 15.4.1
     ensemble, 8.20.14     insert, 15.1.25
     representation, 5.1     layout, 15.1.5
     smiles, 9.17.4     learning, 15.6
structure-based, 12     mark, 15.1.12
structures, 9, 9.1          row, 15.1.12
style, 3.7.5     mouse, 15.1.46
substituent, 9.9.1, 9.9.2, 9.32.2, 14.5.2     navigation, 15.1.4

     plot, 15.4     print, 9.3.11, 15.1.4, 15.1.18
     print, 15.1.18     read, 15.1.2
     rename, 15.1.14     rename, 15.1.14
     rightclick, 15.1.13     right click, 15.1.13
     row height, 20.2.39     row, 15.1.32
     save, 15.1.3     rows, 2.6.10.7
          selection, 15.1.3     save, 9.3.9, 15.1.3, 15.1.4, 15.1.20
     search, 15.1.8     scale, 15.1.17
     select, 15.1.22     scroll, 15.1.4
     setup, 15.1.17     sdf, 9.3.9
     sort, 15.1.41     select, 15.1.22
     split fragments, 9.3.33     setup, 15.1.17
     view, 15.1.5     sort, 2.6.10.4, 9.3.5, 15.1.41
          save, 15.1.7     standard, 15.1
     zoom translate, 9.3.30     view, 9.3.29
     action, 15.1.46     width, 15.1.4
     alignment, 15.1.11tables, 9.28, 15
     append, 15.1.42tag, 3.6.21, 14.5.7, 15.1.45
     clone, 15.1.15tags, 3.6.21
     color, 15.1.9tautomer, 9.21, 20.4.15
     column, 9.3.4, 15.1.25, 15.1.31, 15.1.38tautomers, 9.21
     columns, 9.3.8temperature, 4.6.3
     compare, 9.3.22template, 8.1.2, 9.4.6, 9.34
     copy, 9.3.6     docking, 20.5.3
     cursor, 15.1.46templates, 9.4.6
     delete, 15.1.13, 15.1.16terminal, 9.3.28
     display, 20.10.4     font size, 20.2.1
     double.click, 15.1.46tether, 11.1.7, 14.11.1, 14.11.2
     edit, 9.3.17text, 3.7.7, 6.6, 6.6.1, 6.6.7, 9.3.28, 9.10.4, 15.4.22, 20.9.6
     excel, 9.3.10, 15.1.19     search, 9.5.4
     filter, 9.3.12, 15.1.42texture, 2.7.6
     find-replace, 9.3.13thoroughness, 9.20, 9.34, 20.5.12
          to screen, 15.1.4three, 9.3.24, 20.8.6
     font, 15.1.10threshold, 3.7.5
     foreground, 20.10.4tier, 3.1.13
     grid lines, 15.1.4time, 20.5.11
     hide, 15.1.38     machine, 20.1.15
     hyperlink, 9.3.15     racemic, 9.17
     insert, 15.1.32tools 3D, 2.6.6
     join, 2.6.10.5     analysis, 2.6.7
     label, 9.3.14     append rows, 2.6.10.7
     landscape, 15.1.17     extras, 2.6.9
     mark, 9.3.14          plot function, 2.6.9.1
     merge, 2.6.10.5, 9.3.23, 9.29     superimpose, 2.6.8
     mouse, 15.1.46     table, 2.6.10
     name, 15.1.14          Learn, 2.6.10.1
     new, 15.1.1          clustering, 2.6.10.3
     options, 15.1.13          merge, 2.6.10.5
     orientation, 15.1.17          predict, 2.6.10.2
     portrait, 15.1.17tooltip, 15.4.24

torsion, 5.12.6, 8.20.7, 14.5.4, 20.4.16undo, 2.6.2.9, 3.7, 9.4.11, 14.5.5
     angles, 5.12, 5.12.6     redo, 14.5.5
     scan, 8.20.7uniprot, 3.2.6, 7.5
toxscore, 9.11.2unique, 9.3.28, 9.30
trace, 5.1.10unit, 4.3.3
transition.blend, 20.2.31units, 20.5.1
transitions, 6, 20.2.30unix, 20.10.2
translate, 3.1.3, 5, 5.12, 9.3.30unsatisfied hydrogen bonds, 14.3.8
translation, 5.12.3, 7.3.3, 15.4.16     hyrdrogen bonds, 14.3.8
transparent, 5.3.9.3unusual peptide, 3.3
     background, 5.15.3upload, 17.2
     ribbon, 20.2.3use activeicm, 6.12
     surface, 20.2.37user, 9.10.5, 17.5
tree, 7.7.8, 9.25.7, 15.7.2, 15.7.3, 15.7.4     defined groups, 14.5.3
     branch swapping, 7.7.8     modifiers, 14.5.3
     distance, 9.25.3user-defined groups, 9.4.5
     edit, 9.25.4uundisplay-all, 2.6.3.1
     reorder, 9.25.3van der waal, 5.8.14
triplet, 9.4.7variable, 3.7.7, 20.2.8
trouble shooting, 20.1.11verbose, 9.20
trouble-shooting, 20.1.12     large sdf files, 9.1.2
truncating a mesh object, 20.2.15vicinity, 9.20
     crash qlock, 20.1.13video, 5.16, 5.16.1, 5.16.2
tsv, 15.1.20view, 2.6.3.19, 6.3.1, 9.3.28, 20.2.22, 20.9.8
tut analyze alternative orientations, 19.3.11     animate view, 2.6.3.15
          occupancy, 19.3.10     center, 2.6.3.20
          symmetry, 19.3.9     color background, 2.6.3.18
     multiple receptor, 19.12.1     dock results, 11.1.12
tut3, 19.5     fog, 2.6.3.5
tut3e, 19.3.12     macroshape, 2.6.3.22
tut5a, 19.9.1     menu, 2.6.3
tut5b, 19.9.2     mesh clip, 5.13.1
tut5c, 19.11.1     perspective, 2.6.3.9
tut5e, 19.11.2     selection level, 2.6.3.3
tutorial 2D pharmacophore, 19.6.6          mode, 2.6.3.4
     3D pharmacophore, 19.6.5     shadow, 2.6.3.13
     chemical clustering, 19.6.3     sketch accents, 2.6.3.14
          search, 19.6.2     slide show, 6.3.1
     molecular documents, 19.2     tools, 2.6.3
     sequence alignment, 19.4     tree, 15.7.4
               link, 19.4.2     undisplay all, 2.6.3.1
               load sequence, 19.4.1     stach, 8.20.15
               sequence conservation, 19.4.3virtual, 12.1, 12.1.1, 12.1.2, 19.9, 19.11.1
tutorials, 19     ligand screening, 13
two, 9.3.24, 20.8.6     screen, 12.3
ubuntu, 20.1.18     screening, 12, 12.2
unclip, 5.3.10, 5.13.1          examples, 19.11
undisplay, 3.1.4, 5.1.7, 20.2.10, 20.2.32virus, 4.3.3
     box shade font, 7.7.7.1visualize apf fields, 14.3.11
     origin, 5.8.11     ligand strain, 14.3.10

     analysis, 12.1.10.6zoom, 3.1.3, 5, 5.12, 5.12.4, 9.3.30, 15.4.16
          display, 12.1.10.5 
     getting started, 12.1.2 
     histogram, 12.1.10.3 
          scatter plot, 12.1.10.2 
     introduction, 12.1.1 
     preferences, 12.1.4 
     results, 12.1.9 
     run, 12.1.6 
     scatterplot, 12.1.10.4 
     visualization, 12.1.11 
     results, 12.1.9 
volume, 9.4.9 
water, 8.20.17 
waters, 8.20.17 
wavefront, 2.7.6, 5.3.11 
weak, 20.4.20 
web, 19.2 
     browser, 2.6.1.12 
weight, 9.11, 20.8.7, 20.8.10 
weighted, 15.7.1 
width, 15.1.21 
window, 3.1.13 
windows, 3.1.13.1, 9.10.1 
wire, 2.7.1, 3.7.5, 5.1.1, 20.2.4, 20.2.21 
wireBondSeparation, 3.7.1 
working directory, 20.5.23 
workspace, 3.1.4, 4.1.3.1, 9.7.2 
     panel, 3.1.4 
     selection, 3.6.9 
     navigation, 3.6.10 
write, 3.1.14, 3.5, 15.4.20, 20.9.4, 20.9.7 
     alignment, 7.7.3 
     excel, 9.2.3 
     image, 2.6.1.15, 20.1.20 
     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, 15.1.3 
writing a pdb file, 20.4.3 
     ray, 2.6.5 
xi, 5.8.5, 20.2.18 
xls, 9.2.3 
xlsx, 9.2.3 
xml, 17.2 
xstick, 5.1.2, 20.2.21 
xyz, 20.2.10 

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