Sep 4 2023 Feedback.
Contents
 
Introduction
Help Videos
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Sequences & Alignments
Protein Modeling
Cheminformatics
Learn and Predict
Docking
Virtual Screening
Molecular Dynamics
MolScreen
3D Ligand Editor
Tables and Plots
Local Databases
ICM-Scarab
KNIME
Tutorials
FAQs
 
Index

Index

2D, 6.8.8, 10.3.24, 10.3.28, 10.14, 10.18.2, 10.18.4Clash Threshold, 4.7.10
     Interaction Diagram, 16.3.7DNA, 4.3, 8, 8.3.3
     bioisostere, 10.9.1Decomposition, 10.34.3
     from PDB, 10.1.1Display, 22.2.26
     screening, 15Distance, 13.1.9.6
     to 3D, 10.18, 10.18.3Dock Directory, 4.7.2
     depiction, 10.18.2Docking, 22.2.26
3D, 6.6, 6.8.8, 10.1.3, 10.3.24, 10.3.28, 10.3.31, 10.18.2, 21.2Drug Bank, 4.2.8
     QSAR, 10.37.4, 11.4, 21.14Editor, 4.7.2
     chemical, 10.4.16, 10.18.1Eintl, 12.1.1.8
     interactive ligand editor, 3.7.5Error in saving configuration settings: You are not a license administrator, 22.1.10
     ligand editor, 16.3.4FILTER.Z, 4.7.2
     object, 6.3.9     gz, 4.7.2
     pharmacophore, 13.3, 16.3.11     uue, 4.7.2
     print, 6.7FTP.createFile, 4.7.11
     printing, 6.7     keep File, 4.7.11
     screening, 15     proxy, 4.7.11
     stereo, 6.6Filter.zip, 4.7.2
3DQsar, 11.4Force Auto Bond Typing, 4.7.11
3D_Similarity_PDB_Search, 5.7Formula, 22.8.7, 22.8.10
3Dqsar tutorial, 21.14Free Wilson, 10.34.2
     bioisostere, 10.9.2Frequently Asked Questions, 22
     predict, 5.6GAMESS, 9.20.16
          helices strands, 5.6.1GIF, 3.6.1.15, 6.16, 6.16.2
          local flexibility, 5.6.4GPCR Modeling Example, 21.5.1
          protein health, 5.6.3GRAPHIC.store Display, 4.7.3
          tools identify ligand binding pocket, 5.6.6     NtoC Rainbow, 4.7.4
               oda, 5.6.5     alignment Rainbow, 4.7.4
4D, 12.2.2, 21.12.1     atomLabelShift, 4.7.7
     dock, 16.15     ballStickRatio, 4.7.1
     docking, 4.2.2     center Follows Clipping, 4.7.3
64, 22.1.3     clash Style, 4.7.3
APF, 10.36.3, 10.37.4, 11.4, 15, 15.6, 21.14     clashWidth, 4.7.3
     template, 10.36     clip Grobs, 4.7.3
ActiveICM, 3.6.1.12          Skin, 4.7.3
Area, 22.2.26          Static, 4.7.3
Atom Single Style, 4.7.3     discrete Rainbow, 4.7.4
Atomic Property Fields, 11.4, 21.14     displayLineLabels, 4.7.7
Bad Groups, 22.8.7, 22.8.10     displayMapBox, 4.7.3
Baell, 10.4.9     distance Label Drag, 4.7.1
Beep, 4.7.11     dnaBallRadius, 4.7.9
Blast, 22.2.25     dnaRibbonRatio, 4.7.9
BlastDB Directory, 4.7.2     dnaRibbonWidth, 4.7.9
     alphas, 6.8.3     dnaRibbonWorm, 4.7.9
COLLADA, 3.6.1.7     dnaStickRadius, 4.7.9
CPK, 3.7.1     dnaWormRadius, 4.7.9
ChEMBL, 4.2.3, 10.1     font Scale, 4.7.7
Chemical Cluster, 21.6.3     fontColor, 4.7.7
     Search, 21.6.2     fontLineSpacing, 4.7.7
CisTransAmide Angle, 13.1.9.6     grobLineWidth, 4.7.3

               Style, 4.7.1     splash Screen Delay, 4.7.11
     hbondAngleSharpness, 4.7.1               Image, 4.7.11
     hbondMinStrength, 4.7.1     table Row Mark Colors, 4.7.4
     hbondStyle, 4.7.1     workspace Folder Style, 4.7.4
     hbondWidth, 4.7.1     workspaceTabStyle, 4.7.4
     hetatmZoom, 4.7.1HBA, 22.8.7, 22.8.10
     hydrogenDisplay, 4.7.1HBD, 22.8.7, 22.8.10
     light, 4.7.3HTTP.proxy, 4.7.11
     lightPosition, 4.7.3     support Cookies, 4.7.11
     mapLineWidth, 4.7.3     user Agent, 4.7.11
     occupancy Radius Ratio, 4.7.3Hbond to selection, 13.1.9.6
     occupancyDisplay, 4.7.3Hbonds, 16.3.4
     quality, 4.7.3How To Guide, 3
     rainbow Bar Style, 4.7.4Html, 4.2.1.6
     resLabelDrag, 4.7.7Http Read Style, 4.7.11
     resize Keep Scale, 4.7.3Hydrogen.bond, 4.7.5
     ribbonRatio, 4.7.9ICM Browser How To, 3.1
     ribbonWidth, 4.7.9          Pro How To, 3.2
     ribbonWorm, 4.7.9     graphics crash, 22.1.11
     rocking, 4.7.4     start, 1
          Range, 4.7.4IMAGE.bondLength2D, 4.7.6
          Speed, 4.7.4     color, 4.7.6
     selectionStyle, 4.7.3     compress, 4.7.6
     site Label Drag, 4.7.7     gammaCorrection, 4.7.6
               Shift, 4.7.7     generateAlpha, 4.7.6
     siteArrow, 4.7.7     lineWidth, 4.7.6
     stereoMode, 4.7.3     lineWidth2D, 4.7.6
     stickRadius, 4.7.1     orientation, 4.7.6
     surfaceDotDensity, 4.7.3     paper Size, 4.7.6
     surfaceDotSize, 4.7.3     previewResolution, 4.7.6
     surfaceProbeRadius, 4.7.3     previewer, 4.7.6
     transparency, 4.7.3     print, 4.7.6
     wire Width, 4.7.1     printerDPI, 4.7.6
     wormRadius, 4.7.9     scale, 4.7.6
     xstick Backbone Ratio, 4.7.1     stereoAngle, 4.7.6
          Hydrogen Ratio, 4.7.1     stereoBase, 4.7.6
          Style, 4.7.1     stereoText, 4.7.6
          Vw Ratio, 4.7.1INCHI, 10.18.3
GROB.arrowRadius, 4.7.3IQR, 17.4.6
     atomSphereRadius, 4.7.3ISIS, 22.8.3
     contourSigmaIncrement, 4.7.3Icm Prompt, 4.7.10
     relArrow Size, 4.7.3InChi, 10.3.20, 10.4.12, 10.18.3
     relArrowHead, 4.7.3     key, 10.3.20
GUI.auto Save, 4.7.4Interaction Diagram 2D, 16.3.7
               Interval, 4.7.4Internal Coordinates Table, 9.20.13
     autoSave, 22.2.33     Directory, 4.7.2
     autoSaveInterval, 22.2.33JPEG, 3.6.1.15
     enumeration Memory Limit, 4.7.11KMZ, 3.6.1.7
     max Nof Recent Files, 4.7.11Log Directory, 4.7.2
          Sequence Length, 4.7.4LogP, 11, 17.6

MD, 14          Homology, 3.6.2.15
MOL, 10, 10.3.3, 10.3.24, 10.3.25, 10.3.26, 10.3.27, 13.1.3, 17.2          Identity, 3.6.2.14
MOL2, 13.1.3          Sequence, 3.6.2.16
MOLT, 18.1     convert, 5.1.2
MOVIE.frame Grab Mode, 4.7.4PFAM, 3.6.1.7
MPO, 10.32PLOT.Yratio, 4.7.8
Mac, 22.1.15     color, 4.7.8
     Atom Margin, 4.7.10     date, 4.7.8
     Sigma Level, 4.7.10     draw Tics, 4.7.8
Markush, 21.6.9     font, 4.7.8
     create, 21.6.7     fontSize, 4.7.8
     File Size Mb, 4.7.11     labelFont, 4.7.8
Max_Fused_Rings, 10.11     lineWidth, 4.7.8
Mnconf, 4.7.10     logo, 4.7.8
Model, 11.4     markSize, 4.7.8
MolCart, 22.9     orientation, 4.7.8
MolIPSA, 22.8.7, 22.8.10     paper Size, 4.7.8
MolLogP, 22.8.7, 22.8.10     previewer, 4.7.8
MolLogS, 22.8.7, 22.8.10     rainbowStyle, 4.7.8
MolPSA, 10.11     seriesLabels, 4.7.8
MolScreen, 15PLS, 11.1
MolVol, 10.11PNG, 3.6.1.15, 4.1.14, 6.16, 6.16.2
Molcart, 10.5.3PROTAC, 12.8
MoldHf, 10.11, 22.8.7, 22.8.10Pharmacophore RMSD, 13.1.9.6
Movie.fade Nof Frames, 4.7.4PowerPoint, 21.2, 22.3
     quality, 4.7.4Projects Directory, 4.7.2
          Auto, 4.7.4Prosite Dat, 4.7.2
NCBI, 22.2.25Protein, 22.2.26
NVIDIA, 22.1     Viewer, 4.7.2
Nof_Atoms, 10.11Pub Chem, 4.2.9
Nof_Chirals, 10.11PubMed, 4.2.1.7
Nof_HBA, 10.11     Reference, 17.1.40
Nof_HBD, 10.11Pubchem, 4.2.9
Nof_Rings, 10.11QSAR, 11, 11.1, 17.6, 21.14
Nof_RotBonds, 10.11R, 10.8, 10.34.1
Non-overlap, 13.1.9.6     and S, 22.5.21
Nvidia GL failutre, 22.1.11R-Group, 10.34.3
ODA, 22.2.26R-groups, 16.5.3
Optimal, 22.2.26REAL, 10.5.5
Output Directory, 4.7.2RMSD, 5.4.2
PAINS, 10.4.9, 10.11.3RNA, 4.3
     chemicals, 10.4.9RTCNN, 12.1.1.4, 12.1.13.1
PCA, 11.1, 11.5, 21.6.4Ramachandran Plot, 5.5.9
     analysis, 10.27Real Format, 4.7.10
PDB, 4.2.1.6, 5.1.2, 5.3.3, 5.7, 8.1, 10.1.1, 16.18     Label Shift, 4.7.7
     Directory, 4.7.2          Style, 4.7.7
          Style, 4.7.2RotB, 22.8.7, 22.8.10
     link, 17.1.40SALI, 10.34.5, 21.6.11
     Search, 3.6.2.12, 3.6.2.13, 3.6.2.14, 3.6.2.15, 3.6.2.16SAR, 11, 15.6, 17.4.25, 17.6
          Field, 3.6.2.13     table, 10.34.3, 21.6.9

SCORE, 22.5.6, 22.5.17     new data, 10.3.7
SDF, 10, 10.3.24, 10.3.25, 10.3.26, 10.3.27, 13.1.3, 17.2     to table, 16.5.7
SEQUENCE.site Colors, 4.7.4adding fragment, 10.4.8
SITE.label Style, 4.7.7          in editor, 10.4.8
     labelOffset, 4.7.7adjust row height, 22.2.39
     wrap Comment, 4.7.7administration, 10.10.5
SLIDE.ignore Background Color, 4.7.4advanced alignment selection, 8.7.14
          Fog, 4.7.4alanine, 12.2.4
SMILES, 10.1.2, 10.2.4, 10.4.12album, 6.15.3
Score, 12.1.1.4alias, 10.4.5
Select Min Grad, 4.7.10align, 4.1.11, 10.14
Show Res Code In Selection, 4.7.7     color 2D scaffold, 10.14
Smiles, 22.8.7, 22.8.10, 22.8.11     dna protein, 8.6.4
SureChEMBL, 4.2.4     multiple, 8.6.5
Swissprot, 3.6.1.7     sequence structure, 8.6.3
     Dat, 4.7.2     two sequences, 8.6.2
     link, 17.1.40     DNA to protein, 8.6.4
Temp Directory, 4.7.2     sequence, 8.6, 8.6.6
USER.email, 4.7.11     two sequences, 8.3.5, 8.6.2
     friends, 4.7.11alignment, 8.3.8, 8.6.1, 8.7.7, 8.7.7.1, 8.7.16, 8.8, 10.36.1, 10.36.2, 21.4.4, 22.4.12, 22.6, 22.6.2
     full Name, 4.7.11     annotation tutorial, 21.4.4
     organization, 4.7.11     box shade font, 8.7.7
     phone, 4.7.11     editing, 8.7.1
Uniprot, 17.1.40     editor, 8.7
VHL, 12.8     example, 8.3.14
VLS, 13.1, 13.1.1, 13.1.2, 13.1.9.2     font size, 22.2.1
     preferences, 13.1.4     format, 8.7.11
Van Drie, 10.34.5     gaps, 8.7.11
     Label Style, 4.7.7     image, 8.7.2
Volume, 22.8.7, 22.8.10     profile, 21.4.4
     Change, 13.1.9.6     reorder, 8.3.12
Water Radius, 4.7.10     search, 8.7.12
Wilson, 10.34.2     secondary, 21.4.4
Wire Style, 4.7.1          structure, 8.7.16, 22.6.2
XPDB Directory, 4.7.2     selection, 8.7.13
Xstick, 3.7.1     strength, 8.3.8
a-bright, 3.7.2          profile, 8.3.8
about model, 11.1.1     view options, 8.7.10
acceptor, 10.4.9, 10.37.1     color, 8.7.9
active, 7.7, 22.3.3     comment, 8.7.6
activeICM, 7.8     consensus, 8.7.9, 8.7.14
activeicm, 7.7, 7.12, 7.14, 7.14.1, 22.3     cut, 8.3.11
     advanced, 7.14     display title, 8.7.10
     background images, 7.15     editor, 8.7
     control, 7.13     extract, 8.3.10
activeicmjs, 7.16     gaps, 8.7.11
activity, 11, 17.6     horizontal scroll, 8.7.10
     cliff, 10.34.5, 10.34.6, 21.6.11     image, 8.7.2
          tutorial, 21.6.11     multiple, 8.3.7, 8.6.5
add database, 10.10.3     options, 8.7.10

     reorder, 8.3.12     alignment, 10.36.3
     ruler, 8.7.10apf3Dqsa, 22.8.12
     save, 8.7.2append, 17.1.44
     search, 8.7.12     table, 17.1.44
     selection, 8.7.13, 8.7.14     rows, 3.6.10.7
     sequence offset, 8.7.10applying prediction models, 11.2
     table, 8.7.10area, 5.5.3, 5.6.5, 12.7, 12.7.2, 12.7.3, 21.3.5
     view, 8.7.10aromatic, 10.3.28, 10.37.1
alignments, 8.6, 21.4arrange, 4.1.13.1
allosteric, 5.6.6     window, 4.1.13.1
alpha, 3.7.2     graph, 22.2.8
     channel, 4.7.6as2_graph, 4.6.5
ambient, 3.7.2as_graph, 22.2.8
amidinium, 10.15asparagine, 9.20.2
amino acid, 4.3assign, 6.1.3
     acids, 10.4.6     2D coordinates, 10.18.2
anaglyph, 6.6, 22.1, 22.1.8     helices, 5.6.1
     stereo faq, 22.1.8     strands, 5.6.1
analysis, 3.6.4, 8.3atom, 4.7.5, 10.3.28, 22.2.4, 22.2.5, 22.2.8, 22.2.16, 22.2.17, 22.4.10
angle, 5.5.7, 5.5.8, 6.8.5, 6.9, 6.12.6, 22.2.18, 22.4.16     charge, 22.4.21
angstrom, 22.4.7atomLabelStyle, 4.7.7
animate, 3.6.3.15, 6.10.7atomic energy circles, 16.3.5
     view, 6.10.7     property field, 10.36.1, 10.36.2, 16.3.11
animation, 6.10.7.1, 6.10.7.2, 6.10.7.3, 6.10.7.4               score, 10.37.2
     store, 6.10.7.4          fields, 5.4.6, 10.37, 10.37.1, 10.37.3, 13, 21.8
animations, 7attachment, 10.4.3, 10.5.1
annotate, 4.6.21, 10.13     point, 10.33.4
     alignment, 8.7.6author, 4.2.1.3
     by substructure, 10.13     close tree, 10.26.5
     plot, 17.4.24     play slide, 7.13
annotation, 8.7.6autofit, 12.5
antialias, 3.6.1.15, 3.6.3.10autosave, 22.2.33
     lines, 3.6.3.17available properties, 10.11.1
     lines, 3.6.3.17ave, 17.7.1
apf, 5.4.6, 10.36.1, 10.36.2, 10.37, 11, 12.3, 13, 13.1.9.7, 13.3, 13.4, 16.3.11, 16.17, 21.8, 21.8.1, 21.8.2, 21.8.3, 21.8.4, 21.8.5, 22.8.12avi, 6.16, 6.16.2
     flexible template, 10.36.2axes, 17.4.15
     pairwise, 10.36.1axis, 17.4.11
     super, 10.36     options, 17.4.10
     template, 16.12.3     grid, 17.4.10
     tools, 10.37     range, 17.4.10
          3DQSAR, 10.37.4     title, 17.4.10
          consensus ph4, 10.37.1b-factor, 5.6.4, 21.3.10
          pairwise score, 10.37.2     coloring scale, 22.2.38
          screen, 10.37.3backbone, 6.1.10, 22.2.13
     tutorial, 21.8background, 6.4.2, 6.4.3
          cluster, 21.8.5     color shortcut, 22.2.2
          consensus, 21.8.2     images activeicm, 7.15
          score, 21.8.3     image, 6.4.3
          screen, 21.8.4backup, 3.6.2.11
          superposition, 21.8.1bad, 10.11

ball, 4.7.5     hydrogens, 9.20.5
     and stick, 3.7.1buried molSurface, 13.1.9.6
balloon, 17.4.26buttons, 7.14
bases, 10.4.6bye, 3.6.1.19
basicsel, 4.6.2     alpha, 6.1.10
batch, 12.1.10, 12.7.9     trace, 6.1.10
     file, 12.1.10.2ca-trace, 6.1.10
     index, 12.1.10.4cache, 7.14.1
     loaded icm object, 12.1.10.1calculate, 10.11, 22.5.2
     mol mol2, 12.1.10.3     properties, 10.11
     molcart, 12.1.10.5     sequence similarity, 8.7.15
     run, 12.1.11     startup, 22.10.2
bayesian classifier, 11carbon, 22.2.4, 22.2.5
bbb, 10.11.4carboxylic acid, 10.15
beep, 22.2.35cartesian, 10.21
begin docking simulation, 12.1.8cavities, 5.5
best, 10.3.34     closed, 5.5.4
bicyclics, 10.4.6ccp4, 22.2.27, 22.2.28
binding, 21.5.3, 22.2.14, 22.5.2, 22.5.10cell, 5.3.2
     properties, 6.3.1center, 3.6.3.20, 4.1.3, 6.12, 6.12.5, 16.3.13, 17.1.40, 22.4.22
bioinfo align multiple, 8.3.7     on ligand, 16.3.13
          two sequences, 8.3.5     and representative members, 17.7.2
     links, 8.3.9cereblon, 12.8
     menu, 3.6.4chain.breaks, 22.2.34
     secondary structure, 8.3.2chair, 22.5.20
     translation, 8.3.3change box size, 16.9.1
bioisoester, 10.9     height of all rows, 17.1.7
bioisostere, 10.9, 10.9.1, 10.9.2, 16.8     ligand, 16.5.1
biological, 5.3.3     row height, 17.1.7
biomolecule, 3.6.5, 5.3.3, 21.3.8, 21.3.12     selection, 4.6.7
bit, 22.1.3     speed range, 6.10.7.2
blast, 4.2.5, 8.4changing font in alignment editor, 8.7
     search, 4.2.5charge, 3.6.3.21, 5.1.3, 5.1.3.1, 5.1.3.2, 6.8.2, 10.4.3, 10.5.1, 10.7.1, 10.7.2, 10.7.3, 10.37.1, 13.1.9.6, 22.4.1
blood brain barrier, 10.11.4     groups, 12.1.6, 22.5.22
blue lines, 8.2check box, 7.6.6
boat, 22.5.20     convert, 22.8.5
bond, 5.1.3, 5.2.3, 5.2.3.1, 5.2.3.2, 9.9, 10.4.10, 22.4.1, 22.8.7, 22.8.10     export excel, 10.2.3
     covalent, 22.4.2     save, 10.2
     type, 5.1.3.1, 5.1.3.2, 10.7.1, 10.7.2, 10.7.3          3D, 10.2.5
bonding, 6.1.8          editor, 10.2.4
     preferences, 4.7.1          image, 10.2.6
box, 4.7.7, 6.8.15, 8.7.7, 8.7.7.1, 22.5.9          table, 10.2.2
     alignment, 21.4.4     super, 10.35
     size, 16.9.1     view, 10.3.28
browse, 10.3.31, 12.1.12.1, 19.4chembl, 4.2.3, 4.2.4
     mode, 10.3.31chemical, 10, 10.3.28, 10.3.30, 10.3.31, 10.3.34, 10.3.35, 10.4.10, 10.8, 10.10.4, 10.11.3, 10.18.2, 10.22, 10.33.4, 10.33.5, 10.35, 10.36.1, 10.36.2, 17.7.1, 21.6.4, 22.8.4, 22.8.5, 22.8.7, 22.8.8, 22.8.9, 22.8.10
     molt, 18.2     clustering, 10.26, 10.26.6
     stack, 9.20.15     descriptors, 22.8.15
build, 6.10.7.1     dictionary, 10.4.4, 10.4.5, 10.4.6
     homology model, 9.1.2     draw, 21.6.1

     edit buttons, 10.4.11     tutorials, 21.6
     editor, 10.4, 10.4.8chemistry, 10.22, 22.8
          not starting, 22.1.13     convert, 10.18
     fingerprint, 15          2dto3d, 10.18.1
     fingerprints, 22.8.15     pca, 10.27
     fragments, 10.3.33     smiles, 10.18.3
     group, 10.4.5     duplicates, 10.31
     groups, 10.4.5, 10.4.8     remove.redundant, 10.31
     modifiers, 10.33.2chemlib.so, 22.1.3
     properties, 21.6.4chemspace append, 21.6.4.4
     right click, 10.4.3     build visualize, 21.6.4.1
     search, 10.5, 13.4     compare, 21.6.4.8
          filter, 10.5.2     delete row, 21.6.4.3
          text, 10.5.4     distinguish, 21.6.4.7
     sketch, 21.6.1     export, 21.6.4.5
     space, 10.28     project, 21.6.4.6
     spreadsheet, 4.2.3, 10.1.3, 10.3.1, 10.4.14, 21.6.1, 22.8.13     select, 21.6.4.2
          compare, 10.3.22chi, 6.8.5, 22.2.18
          template, 10.3.2chiral, 10.23, 12.1.1.5
     spreadsheets, 10.3chirality, 10.23, 12.1.1.5
     substituent, 10.9     considerations, 12.1.1.5
     substructure, 4.2.1.1chrome, 22.3
     table, 16.10, 22.8.11cis trans proline, 21.5.2
          display, 10.3.3clash, 4.7.5, 6.8.14
     tables, 17.2     volumes, 13.1.10
     toxicity, 10.11.3classes, 10.3.28
     2D, 10.7classification model, 15.5
     3D, 10.7clear display and planes, 3.6.3.2
     append, 10.4.13     selection, 4.6.6
     clustering, 10.26, 10.26.1     planes, 3.6.3.2
     convert, 5.1.3, 5.1.3.1, 5.1.3.2, 9.20.1, 10.7, 10.7.1, 10.7.2, 10.7.3, 22.4.1click, 4.1.12, 6.11, 6.12
     display.fit, 22.8.13clip, 6.3.10, 6.13.1, 22.2.11
     draw, 10.4.1clipboard, 6.15.3, 17.7.3
     duplicates, 10.3.21clipping, 22.2.19
     editor, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6     planes, 6
     load, 10.1     tool, 6.13
     merge, 10.30     tools, 6.13
     new, 10.4.1clone, 3.6.1.2
     properties, 10.3.19close, 6.3.3, 6.3.4, 16.20
     query, 10.4.3, 10.5.1, 10.5.3     downstream cluster, 10.26.5
     read, 10.1     project, 16.20
     save, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6, 10.4.13     cavities, 5.6.6
     search, 10.4.3, 10.5, 10.5.1, 10.5.3cloud, 13.1.7, 13.1.7.2
     similarity, 10.4.3, 10.5, 10.5.1, 10.5.3cluster, 13.1.7, 13.1.9.7, 17.7.1
     spreadsheet, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6, 10.3     representative.center, 10.26.2
     structure, 10.4.13clustering, 17.7, 21.6.3
     superimpose, 10.35.1, 10.35.2, 10.35.3cns, 10.32
     superposition, 10.36, 10.36.3collada, 3.7.6, 6.3.7
     table, 10.3, 17.2color, 5.6.3, 6.3.2, 6.3.3, 6.3.4, 6.3.9.4, 6.4, 6.4.1, 6.8.2, 6.8.3, 8.8, 10.3.35, 10.14, 17.1.45, 17.7.4, 22.2.4, 22.2.5, 22.2.16, 22.2.20
cheminformatics, 10, 10.3, 22.8     alignment, 8.7.9

     by, 6.4connect, 6.3.9.1, 6.12, 6.12.7
          alignment, 8.8     object, 6.12.7
     chemical, 10.3.35connectivity, 10.4.3, 10.5.1
     faq, 22.2.20consensus, 10.37, 21.8.2
     key, 22.2.38     pharmacophore, 10.37.1
     scale, 22.2.38construct, 3.6.1.1, 6.10.7.1
     surface by proximity, 6.3.3     molecule, 3.6.1.1
               selection, 6.3.4     object, 3.6.1.1
     table, 10.3.27contact, 5.5, 5.5.3, 21.3.5
     2D sketch, 10.5.6.5     surface, 6.3.2
     background, 3.6.3.18, 6.4.2contacts, 6.3.3, 6.3.4, 10.6, 13.1.9.8, 16.3.12
     distance, 6.8.10contour, 5.3.6, 5.3.7
     mesh, 6.3.9.3convert, 5.1.2, 10.18.1, 10.18.5, 22.8.5
     table, 10.3.27     chemical, 10.3.24
coloring, 6.4.1          2D 3D, 10.7
column, 17, 17.1.6, 17.1.22, 17.1.25, 17.1.39, 17.1.40, 17.4, 17.4.1, 22.8.7          3D molecular editor, 10.4.16
     annotation, 17.1.41          from pdb, 5.1.3
     order, 17.1.29     local database, 3.6.1.6
     plot, 17.4.6     pdb, 21.3.2
     row width, 17.1.22          chem, 10.7.1
     statistics, 17.1.32     smiles to 2D, 22.8.11
     visibility order, 17.1.28     local.database, 3.6.1.6
     color, 17.1.10     smiles, 10.18, 10.18.3, 10.18.4
     hide, 10.3.8converting pdb, 5.1.2
     show, 10.3.8coordinates, 10.1.3
combinatorial chemistry, 10.33copy, 10.3.25, 10.4.11, 10.4.18, 10.5.6.2, 17.1.35
     library, 21.6.8     cell, 17.1.36
combine, 3.6.10.5     chemical, 10.3.25
     display style, 4.7.9     loop, 9.4
command, 22.5.16     paste row, 17.1.35
     line, 22.2.32     row, 17.1.36
commands, 22.10.1     rows, 17.1.44
compact tree, 10.26.5     selection to table, 17.1.37
compare, 10.3.29, 10.29, 10.30     chemical, 10.3.16
     table, 10.3.22covalent, 16.10.1
     tables, 10.29     bond, 5.6.2, 21.9.3
compatible, 3.6.1.10     docking, 12.4, 12.4.1, 16.16, 21.9.3
complex, 10.6, 13.1.9.5          tutorial, 21.9.3
compound, 4.2.1.3, 10.22, 17.2cpk, 6.1.5, 22.2.21
compounds, 22.9.3crash, 3.6.2.11
compress, 4.7.6creat, 7.6.1
compressed, 17.1.6create, 17.1.1
     table view, 17.1.6     markush, 10.33.3
conditions, 10.5.2     new objects, 4.3
     gen, 10.21cross, 22.2.10
configuration error, 22.1.19     section, 6.13
conformation, 10.21, 12.2.2cryptic, 5.6.6
conformational entropy, 10.25crystal, 5.3.2
conformations, 22.9.8crystallographic analysis, 5.3
conformers, 10.21          biomolecule, 5.3.3

          convert2grid, 5.3.7depth, 6.3.12, 6.10.5
          crystallographic cell, 5.3.2deselect, 22.2.7
          load eds, 5.3.4design loop, 9.3, 9.20.10
          maps cell, 5.3.5deviation, 22.4.7
          symmetry packing, 5.3.1dfa, 15.3.3
          tools, 21.3.8dfz, 15.3.2
     cell, 3.6.5dialog, 7.6.5
     neigbor, 5.3.1diffuse, 3.7.2
     neighbors, 3.6.5dihedral, 5.5.8, 6.8.5, 22.2.18
crystallography, 5.3.4, 5.3.6, 5.3.7, 22.2.27, 22.2.28     angle, 5.5
csv, 10.2.3, 17.1.2, 17.1.3, 17.1.21, 19.2dimensional, 22.8.6
current, 22.2.22directories preferences, 4.7.2
     slide, 7.13directory, 4.7
curves, 17.4.5disappearing labels, 22.1.12
custom, 6.12, 10.3.3, 10.35dislay ligand receptor interaction, 10.6
     actions, 17.1.40display, 4.1.4, 4.1.13.1, 4.7, 5.2.3, 5.2.3.1, 5.2.3.2, 6.8.14, 6.14, 10.23, 12.1.6.3, 22.2.4, 22.2.5, 22.2.8, 22.2.10, 22.2.11, 22.2.17, 22.2.21, 22.2.30, 22.2.32, 22.4.10, 22.4.11, 22.4.20, 22.8.4
     fragments, 10.13     delete distances, 6.9.4
     label, 6.8.8     dihedral, 6.9.3
     rotation, 6.12.2     distance restraints, 6.8.13
customized MPO score, 10.32.1     distance2, 6.9.1
cut, 17.1.35          angles, 6.9
     vertical alignment block, 8.3.11     formal charge, 6.1.9
cyclic peptide, 9.19     gradient, 6.8.16
cys, 5.6.2     hbond, 13.1.9.5
cysteine reactivity, 5.6.2     hbonds, 13.1.9.6, 16.3.4
damaged skin, 22.1.12     hydrogen, 6.1.7
dash, 22.2.12          atoms ligand editor, 16.3.3
database, 8.4, 10.10, 10.33.4, 13.1.3, 13.1.6, 18.1, 19     mesh, 6.3.5
     file format, 13.1.3     meshes, 6.3.8
     search and alignment, 8.4     options, 16.3
databases, 22.9.3     planar angle, 6.9.2
decompose.library, 21.6.9     tab, 3.7.1, 22.2.16
decomposition, 10.33.4, 10.34.1, 17.4.25     tether, 6.8.12
default, 4.1.13     toggle, 6.8.15
delete, 3.6.2.1, 4.6.6, 7.6.8, 22.4.9     CPK, 6.1.5
     alignment, 8.7.5     angle, 6.9.2
     all, 3.6.2.2     chemical, 10.3.3
     column row, 17.1.38     dihedral.angle, 6.9.3
     label, 6.8.9     distance, 6.8.10, 6.8.13, 6.9.1
     alignment, 8.7.5     electrostatic, 3.6.3.21
     all, 3.6.2.2     energy.gradient, 6.8.16
     angle.label, 6.9.4     hydrogen, 6.1.7
     column, 17.1.38          polar, 6.1.7
     distance.label, 6.9.4     macroshape, 6.3.6
     label, 6.8.9     meshes, 6.3.5
     row, 17.1.38          and display.macroshape, 3.7.6
     selection, 3.6.2.1     molecule, 10.3.24
     tether, 9.20.5     origin, 6.8.11
dendrogram, 10.28.1     potential, 3.6.3.21
density, 5.3.4, 5.3.6, 5.3.7, 22.2.27, 22.2.28     representations, 3.7.1

     ribbon, 6.1.3     flexible.rings, 22.5.20
     skin, 6.1.4     hitlist, 12.1.13
     status, 22.2.32     interactive, 12.1.9
     surface, 6.1.6, 6.3.1     preparation, 12.1.3
     surfaces, 3.7.6     procedure, 12.1.8
     table, 10.3.3     rank, 12.1.13
     tethers, 6.8.12     results, 12.1.12, 12.1.12.1, 12.1.12.2, 12.1.13
     wire, 6.1.1     sampling, 22.5.20
     xstick, 6.1.2     score, 12.1.13
distance, 5.5, 5.5.6, 6.8.10, 6.9, 10.29, 22.2.12, 22.4.8, 22.4.10     stack, 12.1.12.2
     faq, 22.4.10     template, 12.3
     restraint, 12.1.7document, 7.6.4, 7.6.5
     label, 4.7.7     navigation, 7.6.7
distances, 3.7.3documents, 6.15.3
disulfide, 9.9, 9.16dollar, 22.10.3
     bonds, 9.16donator, 10.4.9
diverse set, 17.7     envelope, 3.7.1
dock, 12, 12.1, 12.5, 16.10, 16.10.1, 21.9.3, 21.11.1, 21.11.2, 21.12.1, 22.5.3, 22.5.4, 22.5.5, 22.5.7, 22.5.8, 22.5.10, 22.5.11, 22.5.12, 22.5.13, 22.5.14, 22.5.15, 22.5.16, 22.5.21     surface, 4.7.5
     apf, 16.17dotted line, 6.1.3
     chemical table, 12.1.15     lines, 22.2.34
     command, 22.5.16double, 10.4.10
     macrocylce, 22.5.20doublet, 10.4.7
     table, 16.10download, 22.1.1, 22.9.3
          covalent, 16.10.1dpc, 15.3.4
docked ligand strain, 12.1.1.8drag, 4.1.11, 4.7.7, 6.8.3, 7.6.4, 8.6.6, 22.4.5
docking, 5.6.5, 12, 12.1.1, 12.1.2, 12.1.3, 12.1.16, 12.2, 12.2.1, 12.2.2, 12.2.3, 12.7, 12.7.1, 12.7.2, 12.7.3, 12.7.4, 12.7.5, 12.7.6, 12.7.8, 12.7.9, 12.7.10, 13.1, 13.1.1, 13.1.2, 13.1.6, 13.2, 16.10, 16.10.1, 16.11, 21.9, 21.9.1, 21.9.2, 21.11.3, 21.12, 21.12.2, 22.5, 22.5.1, 22.5.9, 22.5.17, 22.5.18     and drop sequences, 8.6.6
     batch index, 12.1.10.4     residue label, 3.6.3.16
     covalent, 12.4draganddrop, 4.1.11
     display, 12.1.17draw, 10.4.18, 10.33.5, 22.8.2
     explicit group, 21.12.2     chemical, 10.4.1
     from table, 12.1.9.1, 12.1.9.2drop, 4.1.11, 7.6.4, 8.6.6, 22.4.5
     introduction, 12.1.1drug, 10.11, 22.8.7, 22.8.9
     macrocycles, 12.1.6     bank, 4.2, 4.2.8, 10.1
     maps, 12.1.4, 12.1.5     like, 10.11.4
     preferences, 12.1.6drugbank, 10.1
          database scan, 12.1.6.2druglikeness, 10.4.9
          display, 12.1.6.3dsPocket, 4.1.8
          general, 12.1.6.1dual alanine scanning, 12.2.4
     project, 13.1.5easy rotate, 3.6.3.12
          table, 13.1.5ecfp, 11.3
     results display, 12.1.17edit, 5.2.3.1, 16.5.8, 22.8.3
     setup, 22.5.13     2D, 16.5.1
     start, 12.1.3     add sequence, 10.4.17
     steps, 12.1.2     alignment, 8.7.1
     template, 12.3     chemical moledit, 10.3.26
     templates, 16.12.3     ligand, 16.5, 16.5.1
     tutorials, 21.9          2D, 16.5.1
     background, 22.5.19          editor preferences, 16.2
     batch, 12.1.10          multiple substituents, 16.5.2
     conformations, 22.5.20          tools, 3.6.2.17

     molecular document, 7.6.1enumeration, 10.33.4
     molecule, 10.4eps, 10.2.6
     molt, 18.3epsilon, 22.4.15
     selection, 3.6.2.5eraser, 10.4.11
     slide, 7.4.1errno, 22.1.3
     table row, 17.1.24error, 22.1.3, 22.1.19, 22.2.35
     molecule, 10.3.26evaluate score strain, 16.4
     structure, 10.3.26exact, 10.29
editor, 22.4.12excel, 10.2.3
editpdbsearch, 3.6.2.12exclude fragment, 10.5.2
eds, 5.3.4, 5.3.6, 5.3.7     volume, 16.3.11
effect of mutation, 9.14, 9.15exit, 3.6.1.19
               on binding tutorial, 21.5.3explicit, 10.3.28, 12.2.1
                              example2, 21.5.3.1     flex, 12.2.1
                    stability tutorial, 21.5.4     group, 12.2.3
effort, 10.21, 10.35, 22.5.12          docking, 12.2.3
electron, 5.3.4, 5.3.6, 5.3.7, 22.2.27, 22.2.28     groups, 21.12.2
     denisty map, 5.3.5export, 5.5.10, 19.4
     density map, 3.6.1.7, 3.6.5, 5.3.4, 5.3.6, 12.5     dock project, 16.19
               contour, 3.6.5     pdb, 4.5
electrostatic coloring scale, 22.2.38extra windows, 6.2
     potential, 3.6.3.21extract, 4.4.2, 8.1, 10.1.3, 22.4.12, 22.8.8
     surface, 6.3     2D, 10.1.1
electrostatics, 6.3.1, 12.7.8     3d coordinates to spreadsheet, 10.1.3
elegant sketch, 6.10.4     icb, 3.6.1.5
element, 10.4.10     object icb, 4.4.2
eln, 19.7     sub alignment, 8.3.10
embed browser, 7.11     icb, 3.6.1.5
     powerpoint03, 7.8     pharmacophore, 10.5.6.4
     powerpoint07, 7.9faq, 22, 22.2, 22.2.13, 22.4, 22.5, 22.7, 22.10, 22.10.2
     powerpoint10, 7.10     ISISdraw, 22.8.3
     activeicm, 7.13     MolCart, 22.9
          script, 7.13     activeicm, 22.3
     browser, 7.7, 7.11          path, 22.3.3
     firefox, 7.7, 7.11     alignment secondary structure, 22.6.2
     internet.explorer, 7.7, 7.11     apf model, 22.8.12
     microsoft, 7.7     atom charge, 22.4.21
     powerpoint, 7.7, 7.8, 7.9, 7.10          display, 22.2.17
empty hostid, 22.1.18     autosave, 22.2.33
enamine, 10.5.5     backbone, 22.2.13
enantiomer, 22.5.21     background color, 22.2.2
enantiomers, 12.1.1.5          job, 22.5.19
energy, 5.6.3, 6.8.14, 10.25, 10.25.2, 12.1.12.2, 22.5.1, 22.5.2, 22.9.8     beep, 22.2.35
     circles, 13.1.10     binding energy, 22.5.2
     maps, 12.1.4, 12.1.5     blend transition, 22.2.31
     terms, 9.20.18     breaks, 22.2.34
ensemble, 12.2.2     change torsion, 22.4.16
entropy, 10.25.1     chem table display, 22.8.4
enumerate formal charge states, 10.16     chemical monitor, 22.8.10
     reaction, 21.6.10          query2, 22.8.1

     clipping plane, 22.2.11     nmr, 22.4.18
     closest, 22.4.22     nvidia error, 22.1.2
     color carbon, 22.2.4     origin, 22.2.10
          skin, 22.2.16     plist, 22.1.9
     command line display, 22.2.32     pmf score, 22.5.6
     convert chemical from pdb, 22.4.1     pockets, 22.2.14
     covalent bond, 22.4.2     preserve coordinates, 22.8.6
     delete, 22.4.9     quad buffer, 22.1.7
     descriptors, 22.8.15     receptor selection, 22.5.14
     deselect, 22.2.7     reload dock, 22.5.4
     dihedral, 22.2.18     remove salt, 22.8.14
     dock charge groups, 22.5.22          select, 22.2.6
          probe, 22.5.13     renumber, 22.4.4
          racemic, 22.5.21     residue number selection, 22.2.36
          repeat, 22.5.5     rmsd, 22.4.7
          working directory, 22.5.23     rmsdtips, 22.4.8
     docking, 22.5     rocking active ppt, 22.3.1
     docktime, 22.5.11          speed, 22.3.2
     dollar, 22.10.3     rotate chemical, 22.8.13
     download install, 22.1.1     scale display, 22.2.38
     druglikeness, 22.8.9     scanScoreExternal, 22.5.17
     energy, 22.5.1     scanScoreExternal2, 22.5.18
     error admin, 22.1.10     score, 22.5.8
     extract ligand, 22.8.8     script, 22.10
     flexible dock, 22.5.15     sequence secondary structure, 22.6.1
          ring docking, 22.5.20          alignments, 22.6
     font size, 22.2.1     smiles, 22.8.11
     foreground table, 22.10.4     solvent accessible surface table, 22.4.19
     gl failure, 22.1.11     ss, 22.4.17
     gui, 22.2     structure, 22.4
     guided dock, 22.5.3     superimpose, 22.4.6
     hitlist, 22.5.7     surface display, 22.2.37
     hydrogen bond acceptors, 22.8.17     thoroughness, 22.5.12
     iSee, 22.2.30     transparent ribbon, 22.2.3
     icmPocketFinder, 22.5.10     truncate mesh, 22.2.15
     insert column, 22.8.7     view stack, 22.9.8
     installation, 22.1     weak hydrogen bonds, 22.4.20
     interactions, 22.2.12     write pdb, 22.4.3
     ligandbox, 22.5.9faqcontour, 22.2.28
     measure distance ring, 22.8.16faqhbondstrength, 22.2.29
     merge, 22.4.5faqmaps, 22.2.27
     modeling, 22.7faqoda, 22.2.26
     molcart 64bit, 22.1.3faqstereo, 22.1.14
          query, 22.9.5fasta, 8.1.5
          sdf, 22.9.4fbdd, 13.2
          text search, 22.9.6fft, 12.7.1
     molecule c, 22.2.5     protein protein docking, 12.7.1
     moledit, 22.8.2file, 3.6.1.3
     movie planes, 22.2.19     close, 3.6.1.13
     newscript, 22.10.1     compatible, 3.6.1.10

     high quality image, 6.15.1     refinement, 9.1.3
     load, 3.6.1.7     scene antialias, 3.6.3.10
     menu, 3.6.1     screen, 3.6.3.8
     password, 3.6.1.11function, 17.1.26, 17.1.32
     preferences, 3.6.1.16functional.groups, 10.13
     quick image, 3.6.1.14fuzzy, 12.3
     icb, 4.1.10gap, 9.3
     recent, 3.6.1.17general preferences, 4.7.5
     bak, 3.6.2.11generalselecttools, 4.6.1
filter, 18.2, 22.2.4generator, 5.3.3, 10.21
     selection, 4.6.8getting started, 4
filters, 13.1.5giga search, 10.5.5
find chemical, 10.3.32          enamine, 10.5.5
fingerprint, 11, 11.3, 21.13, 22.8.1, 22.9.5glasses, 6.6, 22.1.6, 22.1.14
     method, 11.3glutamine proline, 9.20.2
fingerprints, 22.8.15google, 3.6.1.7
firefox, 22.3     objects, 6.3.7
fit, 10.3.34, 12.5, 22.5.15     3D, 3.7.6, 6.3.7
fitting, 12.5, 17.4.16gpcr_model, 21.5.1
flex super, 10.35.3graft loop, 9.4
flexibility, 5.6.4, 12.2.3, 21.12graphical, 22.2.4
flexible, 10.35, 12.2, 12.2.1, 12.2.2, 21.12.1, 22.5.15     display, 5.1.3.1, 5.1.3.2, 10.7.2, 10.7.3
     docking, 16.13          tutorial, 21.1
     receptor groups, 16.13               2D3D labels, 21.1.4
     ring sampling level, 12.1.6               annotation, 21.1.2
flood, 9.20.17               color representation, 21.1.1
fog, 3.6.3.5, 6, 6.10.1               labels, 21.1.3
font, 4.7, 4.7.7, 5.2.3.1, 6.8.2, 6.8.3, 8.7.7, 8.7.7.1, 10.3.28, 17.1.40, 17.7.4     user interface, 22.2
     preferences, 4.7.7graphics, 4.1
     size, 8.7, 22.1.16, 22.2.1     card, 22.1.2
form view, 17.1.5     controls, 6
formal, 5.1.3, 22.4.21     defects, 22.1.12
     charge, 6.1.9, 10.15, 10.16     effects, 6.10
format, 17.1.2, 17.1.40     panel, 6.2
formula, 10.4.9, 10.11     preferences, 4.7.3
fragment, 10.3.35, 10.34.1, 13, 13.2, 16.11     shadow, 3.6.3.13, 6.10.2
     linking, 16.11green arrows, 8.7.16, 22.6.2
     screening, 13.2     lines, 8.2, 22.6.1
fragments, 10.8grid, 10.3.3, 10.35, 21.12.1, 22.8.4
frame, 8.3.3grob, 4.7.5, 5.3.4, 5.3.6, 5.3.7, 6.3
free energy, 9.12, 9.13group, 10.34.1, 16.6
     radical, 10.4.7     column, 17.1.46
     wilson regression analysis, 10.34.2groups, 10.8, 10.11, 10.12
freeze column, 17.1.30guanidinium, 10.15
     row, 17.1.31gui, 4.1.1, 4.7.4
frequency, 10.3.35     menus, 3.6
front, 6.3.10, 6.13.1     preferences, 4.7.4
full model, 9.1.3     tabs, 3.7
          builder, 9.1.3guided docking, 12.1.7, 22.5.3
          multiple chain, 9.1.3.1h-bond, 5.2.3, 5.2.3.1, 5.2.3.2, 22.2.12

hardware stereo, 3.6.3.7, 22.1          tree, 10.26.4
hbond, 5.2, 21.3.6, 22.2.29     excel, 10.3.10
     strength, 22.2.29     extract 3D ph4, 10.5.6.4
header, 4.2.1.6, 17.4.9     filter, 10.3.12
health, 5.6.3     find replace, 10.3.13
heatmap, 17.4.7     mark row, 10.3.14
     example, 17.4.7.1     markush, 21.6.8
helix, 22.2.20          structure, 21.6.7
help, 2     merge tables, 10.3.23
     videos, 2     properties, 10.3.19
hetero, 10.3.28     reactions, 21.6.10
     scan, 16.7     reorder, 10.26.3
hidden block format, 8.7.11     sdf, 10.3.9
          width, 8.7.11     show hide, 10.3.8
hide, 17.1.39     sort column, 10.3.5
     column, 17.1.28     standardize, 10.3.18
high, 3.6.1.15     table hyperlinks, 10.3.15
     quality, 3.6.3.11          print, 10.3.11
highlight new data, 10.3.7.1          activeicm, 3.3
his, 22.4.15               create molecular documents, 3.3.3
histidine, 9.20.2, 22.4.15                    slides, 3.3.2
     tautomer, 22.4.15               getting started, 3.3.1
histogram, 13.1.9.2, 13.1.9.3, 17.4, 17.4.1, 17.4.9, 17.4.11, 17.4.13, 17.4.14, 17.4.15, 17.4.16, 17.4.17, 17.4.18, 17.4.20, 17.4.22               ppt, 3.3.4
     bins, 17.4.3               web, 3.3.5
     options, 17.4.2          chemical clusering, 10.26.1
     bin.size, 17.4.2          icm browser convert display pocket, 3.1.4
     bins, 17.4.3                    distances angles, 3.1.9
     color, 17.4.2                    get started, 3.1.1
     source, 17.4.2                    graphical display, 3.1.2
     style, 17.4.2                         effects, 3.1.5
     title, 17.4.2                    images, 3.1.7
historeceptomics, 4.2.10                    labels annotation, 3.1.6
hitlist, 12.1.12, 12.1.13, 13.1.8, 13.1.9.1, 13.1.9.3, 13.1.9.7, 22.5.7                    pro crystallographic tools, 3.2.6
     cluster apf, 13.1.9.7                         get started, 3.2.1
     columns, 12.1.13.1                         graphics, 3.2.2
     export, 12.1.14                         plots, 3.2.8
homology, 4.2.1.2, 4.2.5, 9, 9.1, 9.1.1, 9.1.1.1, 9.1.2.1, 9.1.2.2, 9.1.3.1, 9.2, 9.7, 21.5                         sequence analysis, 3.2.7
     model, 9.1, 9.1.1.2                         structure analysis, 3.2.3
          introduction, 9.1.1                         superimpose, 3.2.5
     older versions, 9.1.1.3                         surfaces, 3.2.4
hover, 17.4.26                    selections, 3.1.3
     3D editor, 21.7                    superimpose, 3.1.8
     add columns, 10.3.4          search, 4.2
     cluster center, 10.26.2          use gui, 4.1
     color 2D by ph4, 10.5.6.5hrydrogen.bond, 22.2.29
     copy 2D, 10.3.16html, 3.6.1.12, 4.3, 7.6.1, 7.6.7, 22.3
          paste, 10.3.6html-doc font size, 22.2.1
     decompose, 21.6.9hybridization, 10.4.3, 10.5.1
     duplicate chemicals, 10.3.21hydrogen, 5.2.3, 5.2.3.1, 5.2.3.2, 6.1.8, 10.4.3, 10.5.1, 21.3.6, 22.2.12, 22.8.7, 22.8.10
     edit table, 10.3.17     atom display, 16.3.3

          acceptors, 22.8.17in-a-window, 22.1.7
          donor, 10.37.1inchi, 10.18.3
          label edit, 5.2.3.1increment, 17.1.27
               move, 5.2.3.2     id, 17.1.27
     bonds, 5.2.4, 12.1.1.7index, 22.9.6
     bond, 10.4.9, 22.4.20     models, 15.1.2
hydrogens, 10.3.28induced, 22.5.15
     remove, 10.3.18     fit, 12.2, 12.2.1, 12.2.3, 16.13, 21.12, 21.12.1
hyperlink, 7.6.1, 7.6.2, 17.1.40insert, 7.6.4
hyrophobic, 10.37.1     column, 17.1.26
iSee, 3.6.1.5, 3.6.1.12, 4.1.10, 6.15.3, 21.2, 22.2.30, 22.2.31, 22.3.3     image, 7.6.3, 17.1.34
icb, 4.4.2, 4.5, 22.2.30, 22.3.3          table, 17.1.34
icm, 22.3.3     row, 17.1.33
     chemist howto chemical search, 3.4.3     script, 7.6.4
               cluster, 3.4.5install, 1, 10.10.1, 19.1, 22.1.3, 22.1.4
               combi library, 3.4.7installation, 22.1
               ph4, 3.4.4interaction, 5.5.3, 10.6, 22.2.12
               plots, 3.4.8     fingerprint, 13.1.9.8
               sketch, 3.4.1     fingerprints, 13.1.9.8
               spreadsheets, 3.4.2     restraint, 12.1.7
               stereoisomers tautomers, 3.4.6     restraints, 12.1.7
          pro 3D ligand editor, 3.5.1interactions, 16.3.12, 22.5.2
               chem3D, 3.5.2interactive, 12.1.9, 21.2
               chemsuper, 3.5.4     loaded ligand, 12.1.9.2
               energy, 3.5.3     loop, 9.1.4.2
               qsar, 3.5.5     modeling, 9.1.4
               tutorials, 3.5          table ligand, 12.1.9.1
          tutorials, 3.4     modeling, 9.1.4
     hanging, 22.1.13interface prediction, 21.10
     object, 5.1, 21.3.2internal hydrogen bonds, 12.1.1.7
     script, 17.1.40internet explorer, 22.3
icm-crash, 22.1.13interrupt, 6.10.7.3
icmFastAlignment, 8.4     animation, 6.10.7.3
icmPocketFinder, 5.6.6, 22.2.14, 22.5.10introduction, 1
icmdb, 19invert selection, 17.1.23
icmjs, 7.16invisible residue label, 22.1.12
icmpocketfinder, 21.3.7iqr, 17.4.23
id, 17.1.27isee, 7.6.5
identity, 4.2.1.2isis, 10.4.18
image, 4.1.14, 4.7, 4.7.5, 6.15.3, 7.6.3, 10.2, 10.2.6, 17.4.21, 22.1.20isostere, 13.4
     advanced, 6.15.3isotope, 10.4.3, 10.5.1
     distortion, 22.1.20iupac, 10.2.7, 10.3.20
     preferences, 4.7.6javascript, 7.16
     problem, 22.1.20job, 22.5.19
     multiple, 3.6.1.7join, 10.30
     quality, 3.6.3.11jpg, 6.15
     quick, 3.6.1.14, 6.15.2     means, 17.7.1
images, 6.15kcc, 15.3.1, 15.5
impose, 12.2.2keep carboxyls neutral, 12.1.6
improve model, 11.1.3kernel regression, 15.3.1

keyboard mouse, 6.11     considerations, 12.1.1.2
keystokes in chem-edit, 10.4.10     editor, 16, 16.10, 16.10.1, 16.16, 16.17
kmz, 3.7.6, 6.3.7          bioisostere, 16.8
knime, 20          covalent docking, 16.16
label, 4.7.7, 17.7.4, 22.2.17          mrc, 16.15
     atoms, 6.8.2          preferences, 3.6.2.18
     color, 6.8.7     energetics, 10.25
     move, 6.8.4          conformational entropy, 10.25.1
     residues, 6.8.3          strain, 10.25.2
     sites, 6.8.6     pocket, 5.2.4, 22.4.11
     variables, 6.8.5          surface, 16.3.2
     2D, 3.7.3     receptor contacts, 16.3.12
     3D, 3.7.3, 6.8.1          display, 5.2
     atom, 6.8.1          interaction, 10.6
     atoms, 6.8.2     strain, 16.3.10
     color, 6.8.7     surface, 5.2.2
     custom, 6.8.8     tether, 16.12
     delete, 6.8.1, 6.8.9ligand-based, 13, 13.3
     distance, 6.8.10     convert, 9.20.1
     drag, 3.6.3.16     editor, 16, 16.1
     move, 3.6.3.16, 6.8.4          binding.re-dock ligand, 16.9
     residue, 6.8.1          display, 16.3
     residues, 6.8.3          edit, 16.5
     site, 6.8.1          energy, 16.3
     sites, 6.8.6          hydrogen.bond, 16.3
     variable, 6.8.1          pocket, 16.3
     variables, 6.8.5, 22.2.18          preferences, 16.2
labeling, 6.8.1          restraint, 16.12
labels, 6.8, 10.3.28          surface, 16.3
     distances, 6.8.10          tether, 16.12
     tab, 3.7.3     optimization, 21.11.3
landscape, 4.7.6     pocket, 4.1.8
large chemical space, 21.6.4     receptor.contact, 5.5.3
     font, 22.1.16ligand_pocket_interactions, 5.2.4
          size, 22.1.9ligedit distance restraint, 16.12.2
     sdf, 10.1.2     tab, 3.7.5
layer, 6.14     tether, 16.12.1
layers, 6.14light, 3.7.2
learn, 10.19, 10.20, 11, 11.1, 17.6, 22.8.12     tab, 3.7.2
learning, 11lighting, 6.3.9.4, 6.5
     theory, 11.5likeness, 10.11, 22.8.9
least.squares, 17.4.16line, 4.7.5, 17.7.4, 22.2.12
library, 10.33.4lineWidth, 4.7.3
     reaction, 21.6.10link, 8.3.9
license, 22.1.4     structure to alignment, 21.4
ligand, 5.2.2, 10.6, 10.25, 10.25.1, 10.25.2, 12.1.1, 12.2, 12.7.6, 12.7.7, 16.3.12, 16.3.13, 16.5.8, 16.10, 16.11, 22.4.5, 22.4.11, 22.5.2, 22.5.9, 22.8.8linker, 12.8
     based screen, 10.37.3, 13.3links, 4.6.20
     best replace, 16.6linux, 10.10.1
     binding, 9.15lipinski rule, 10.32
     code, 4.2.1.3, 4.2.7list, 4.6.18

load, 3.6.1.3, 3.6.1.17, 5.3.4, 5.3.6, 5.3.7, 8.1     molt, 18.1
     example alignment, 8.3.14     receptor maps, 12.1.5
     nmr model, 4.2.1.4     selection, 4.6
     protein structure, 5.1.1     bond, 22.4.2
     sequence, 8.1     disulfide, 9.9, 22.4.17
          extract pdb, 8.1.3     molecule, 3.6.1.1
          from file, 8.1.4     object, 3.6.1.1
          paste, 8.1.2making molecular slides, 7.1
          swissprot, 8.1.1     html, 7.6
     libraries, 9.20.6manual change torsion, 16.5.4
local, 22.2.24, 22.2.25map, 4.7.7, 5.3.4, 5.3.6, 5.3.7
     databases, 18     cel, 5.3.5
     database.browse, 18.2maps, 12.1.4, 12.1.5, 12.7.8, 21.12.1, 22.2.27, 22.2.28, 22.5.9
          edit, 18.3mark, 17.1.45
          query, 18.4     row, 17.1.45
          row, 18.3     color, 17.4.14
localpdb, 22.2.24     shape, 17.4.13
localseq, 22.2.25     size, 17.4.13
lock, 6.3.10, 6.13.1, 10.3.31markush, 10.26.7, 10.33.1, 10.33.3, 10.34.1, 21.11.3
log, 17.4.6, 17.4.11     docking, 21.11.3
logD, 10.11.6     library, 21.6.8
logP, 10.4.9, 10.11mass, 22.4.22
logS, 10.4.9, 10.11matched pair, 10.34.6, 21.6.11
logarithmic, 17.4.11          analysis, 10.34.6
logout, 3.6.1.19materials, 3.7.6
loop, 9.2, 9.4, 22.2.20max, 17.7.1
     analysis, 9.6maxColorPotential, 4.7.10
     design, 9.3maximum common substructure, 10.26.6, 10.28, 10.28.1
     find pdb segments, 9.6               dendrogram, 10.28.1
     model, 9.2, 9.3, 21.5.2mcs, 10.26.6, 10.28.1
          tutorial, 21.5.2     rgroup decomposition, 10.26.7
     modeling, 9.1.4.2, 9.5, 9.6, 9.20.10mean, 17.4.6, 17.4.23, 22.4.7
     preferred residues, 9.5measure distance, 22.8.16
     model, 9.20.9          to ring, 22.8.16
     sample, 9.20.9median, 17.4.6, 17.4.23
     energy water, 9.20.17memory, 10.1.2
mac, 10.10.1, 22.1.9, 22.1.16menu, 7.6.5
     font, 22.1.16     chemistry, 3.6.14
          size, 22.1.16     docking, 3.6.15
machine learning, 21.13     homology, 3.6.13
macrocycles, 9.19     molmechanics, 3.6.16
macros, 7.14     tools chemical search, 3.6.11
macroshape, 3.6.3.22, 6.3, 6.3.6          molecular editor, 3.6.12
make, 6.10.7.1, 17.1.1     windows, 3.6.17
     alignment, 8.6.1merge, 10.30, 22.4.5
     animation, 6.10.7.1     two sets, 10.30
     apf docking sar model, 15.6mesh, 5.2.1, 5.2.2, 5.3.4, 5.3.6, 5.3.7, 6.3, 6.3.9.1, 6.3.9.2, 6.3.9.4, 6.3.10, 6.3.11, 6.3.12, 6.13.1
     complex, 13.1.9.6, 16.20     clip, 6.3.10
     flat, 22.8.13     color lighting, 6.3.9.4
     molecular document, 7.6     options, 6.3.9

     save, 6.3.11     graphics, 6
     options, 6.3.9     matched pairs, 21.6.11
meshes, 6.3.2, 6.10.5     mechanics, 9.20
     surfaces grobs, 6.3          convert, 9.20.1
     tab, 3.7.6          design loop, 9.20.10
metabolic oxidation, 15.7          edit structure, 9.20.5
min, 17.7.1          gamess, 9.20.16
minimization, 9.17          generate normal mode stack, 9.20.14
     cartesian, 9.20.8          his asn, 9.20.2
     global, 9.20.8          ic table, 9.20.13
     local, 9.20.8          impose conformation, 9.20.4
minimum specifications, 1          minimize, 9.20.8
mmff, 9.20.6, 10.4.16, 22.2.17, 22.8.5          mmff, 9.20.6
     type, 6.8.2          regularization, 9.20.3
mmp, 21.6.11          sample loop, 9.20.9
mnSolutions, 4.7.10               peptide, 9.20.12
model, 9, 9.1, 9.1.1, 9.1.1.1, 9.1.2, 9.1.2.1, 9.1.2.2, 9.1.3.1, 9.2, 9.7, 9.17, 21.5               protein, 9.20.11
     domain interaction, 9.17          terms, 9.20.18
     start, 9.1.1.2          view stack, 9.20.15
     weight, 11.1.2     modeling, 9
modelers view, 9.1.4.1     table, 10.18.2
     view, 9.1.4.1     weight, 10.4.9
modeling, 9.20.3molecule, 22.2.8, 22.8.3
     options, 9.1.1.1     editor, 10.4
modeller view, 9.1.4moledit, 10.4.8
modification history, 16.5.6molmechanics, 22.9.8
modify, 9.11     minimize, 9.20.8
     amino acid, 9.11     mmff, 9.20.6
     group, 9.10molscreen, 13, 15
mol, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6, 10.4.13, 21.11.2     custom model panel, 15.4
mol2, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6     load models, 15.1.1
molcart, 10.10, 10.10.1, 10.10.2, 10.10.3, 10.10.4, 10.10.5, 18, 19, 22.1.3, 22.8, 22.8.1, 22.9.3, 22.9.4, 22.9.5, 22.9.6               run, 15.1
     add database, 10.10.3     model type, 15.3
     administration, 10.10.5     results, 15.2
     connect, 22.9.2molskin, 6.3.2
     download dbs, 22.9.3molsynth, 10.11.5
     hostid, 22.9.1molt, 18, 18.4
     installation, 10.10.1monitor, 22.8.10
     license, 22.1.4monochrome, 10.3.28
     search, 10.10.4montecarlo, 22.9.7
     start, 10.10.2mouse, 4.1.3, 6.11, 6.12
     connect, 22.9.2mov, 6.16, 6.16.2
     hostid, 22.9.1move, 3.6.3.19, 4.1.11, 4.1.13, 5.2.3.2, 6.3.9.1, 6.3.9.2, 6.12, 6.12.7, 9.17, 22.4.5
     license, 22.9.1     column, 17.1.28
molclart, 22.1.4     mesh, 6.3.9.2
molecular, 10.3.30, 10.3.31, 10.3.34, 10.3.35, 10.21, 22.8.7, 22.8.10     slide, 7.4.2
     animations slides, 7     structure, 6.12
     documents, 21.2     tools, 6
     dynamics, 14     rotate, 6.11
     editor, 22.8.2     slab, 6.11

     z-rotation, 6.11numbers, 10.3.28
     zoom, 6.11nvidia, 22.1.2
movie, 6.16.1, 22.2.19, 22.9.7obj, 6.7
     montecarlo, 22.9.7object, 4.1.11, 4.5, 21.3, 22.2.8
     making, 6.16, 6.16.2objects, 5.1.2
     open, 6.16, 6.16.2     in table, 17.3
mpa, 21.6.11     in.table, 17.3
mpeg, 6.16, 6.16.1, 6.16.2occlusion, 6.3.12, 6.10.5
mpg, 6.16, 6.16.2     shading, 6.3.12
mpo, 10.32          effect, 6.10.5
     customized, 10.32.1occupancy, 6.1.3, 21.3.10
mtl, 6.7     display, 4.2.1.5
multi apf super, 10.36.3oda, 5.6.5, 12.7, 12.7.2, 12.7.3
     panel, 6.2older version, 3.6.1.10
     parameter optimization, 10.32omega, 6.8.5, 22.2.18
     template, 9.1.4.3online databases, 10.5.5
     windows, 6.2open, 3.6.1.3, 4.4, 17.1.2
multiple, 12.2.2, 21.12.1     file, 4.4
     chain, 9.1.2.2, 9.1.3.1     password, 4.4.1
     position group scan, 16.7     with password, 3.6.1.4
     rec, 12.2.2     movie, 6.16, 6.16.2
     receptor, 4.2.2, 21.12     password, 3.6.1.4, 4.4.1
          docking, 16.15optimal, 5.6.5, 12.7, 12.7.2, 12.7.3
     protein, 22.2.5optimize, 9.20.2
mutant, 9.10, 22.4.13, 22.4.14oracle, 19
mutate, 9.12, 9.13, 22.4.15orange, 4.6.5
     residue, 22.4.13     selection, 4.6.5
          N C, 22.4.14origin, 6.8.11, 22.2.10
mutation, 9.10, 9.12, 9.13, 9.15, 21.5.3, 21.5.4, 22.4.13, 22.4.14orthosteric, 5.6.6
     protein binding, 9.12other selection, 4.6.19
          ligand, 9.15outside, 22.5.9
          peptide, 9.14overlay, 21.3.3, 22.2.5, 22.4.6
          stability, 9.13pH, 10.17, 12.1.1.3
mysql, 19package.activeicm, 7.13
navigate workspace, 4.6.10packing, 5.3.1
nearest, 22.4.22pages, 19.7
neural network, 12.1.13.1pairwise, 10.36.1, 10.36.2
          Torsion Profile Neural Network Prediction Engine, 6.12.6.1     apf score, 10.37
new, 8.1parallelization, 13.1.7
     icm session, 3.6.1.2password, 10.10.5
     table, 17.1.1paste, 10.4.11, 10.4.18, 17.1.35
     table, 17.1.1pca, 17.5
nmr, 22.4.18pdb, 3.6.1.7, 4.2, 4.2.1.1, 4.2.7, 4.5, 5.1.3, 10.7.1, 21.3, 22.2.24, 22.2.25, 22.4.4
     model, 4.2.1.4     chem gl, 10.7.3
nntorsion, 6.12.6.1          iw, 10.7.2
nof, 10.11.2     dormat, 4.5
     chemical, 10.11.2     file, 22.4.3
non-contiguous selection, 4.6.18     html, 4.2.1.6
normal modes, 9.20.14     preparation, 21.3.11
number of sp3, 10.11.2     search, 4.2.1, 4.2.1.2, 4.2.1.3, 21.3.1

     recent, 3.6.1.18     logarithmic, 17.4.12
     search, 3.7.4, 4.1.2     mark, 17.4.13
pdbsearchfield, 3.6.2.13     mean median iqr, 17.4.23
pdbsearchhomology, 3.6.2.15     point label, 17.4.19
pdbsearchidentity, 3.6.2.14     preferences, 4.7.8
pdbsearcsequence, 3.6.2.16          groups, 17.4.25
peptide, 4.3, 9.14, 9.19, 12.6     regression, 17.4.16
     docking, 12.6     selection, 17.4.18
     modeling, 9.19     zoom translate, 17.4.17
percentage similarity, 8.7.15, 21.4.4     axis, 17.4.15
perspective, 3.6.3.9, 6.10.6     display, 17.4.15
ph4, 10.5.6     grid, 17.4.15
     draw 2d, 10.5.6.1     inline, 17.4.22
          3d, 10.5.6.2     logarithmic, 17.4.12
     search, 10.5.6.3pls, 10.19, 10.20, 11, 17.6, 21.13
pharmacophore, 10.3.35, 10.5.6.5, 21.8.2pmf, 22.5.6
     2D, 21.6.6png, 3.6.1.14, 6.15, 6.15.2, 7.6.3, 10.2, 10.2.6
     3D, 21.6.5pocket, 4.1.8, 5.2, 5.2.1, 5.2.2, 5.6.6, 12.1, 21.3.7, 22.2.14, 22.4.11, 22.5.10
     clone, 10.5.6.2     conservation, 22.4.12
     draw2D, 10.5.6.1     surface, 5.2.1, 13.1.10
     draw3D, 10.5.6.2     peptide, 4.1.8
     edit, 10.5.6.1, 10.5.6.2     properties, 4.1.8
     move, 10.5.6.2pocketome, 4.2, 4.2.2
     new, 10.5.6.2pockets, 5.6.6
     search, 10.5.6, 10.5.6.3, 21.6.5, 21.6.6point label, 17.4.19
phi, 6.8.5, 22.2.18portait, 4.7.6
phylogenetic, 8.7.8post edit ligand, 16.5.8
phylogeny, 8.7.8     screen, 13.1.9
pi, 5.2.5postscript, 4.7.6
     pi, 5.2.5potential mean force, 13.1.4
picking, 6ppbatch, 12.7.9
picture, 3.6.1.14, 4.1.14, 6.15.2, 7.6.3ppepitope, 12.7.7
     tips, 4.1.14ppmaps, 12.7.8
     chart, 17.4.8pprefine, 12.7.11
pipi, 5.2.5ppresults, 12.7.10
pka, 10.15pproc, 12.7.3
planar, 5.5.7, 6.8.5, 22.2.18ppsetligand, 12.7.6
     angle, 5.5ppsetproject, 12.7.4
     angle, 6.9.2ppsetreceptor, 12.7.5
plane, 6.3.10, 6.13, 6.13.1, 6.14, 22.2.11, 22.2.19, 22.2.21ppt, 7.12, 7.14, 22.3.3
     faq, 22.2.21predict, 8.3.2, 10.19, 10.20, 11, 11.2, 17.6, 22.8.9, 22.8.12
plot, 4.7, 4.7.8, 13.1.9.2, 17.4, 17.4.1, 17.4.4, 17.4.9, 17.4.11, 17.4.13, 17.4.14, 17.4.15, 17.4.16, 17.4.17, 17.4.18, 17.4.20, 17.4.21, 17.4.22, 17.4.23     disulfide, 9.16
     R group sar, 10.34.4     metabolic oxidation, 15.7
     axis, 17.4.11predicting bioassays, 11.2
     color, 17.4.14     compound properties, 11.2
     columns, 17.4.6prediction binding, 9.12
     function, 3.6.9, 3.6.9.1preferences, 4.7, 13.1.5, 22.2.24, 22.2.25
     grid, 17.4.15preferred residues, 9.5
     header, 17.4.9presentation, 7.6.5, 7.7, 7.12
     inline, 17.4.22presentations, 7

press-and-hold to rotate, 10.4.8               convert, 21.3.2
pretty view, 16.3.6               hydrogen bond, 21.3.6
primary aliphatic amines, 10.15               icmpocketfinder, 21.3.7
principal component analysis, 17.5               search, 21.3.1
          regression, 11               superimpose, 21.3.3
     components, 11.5     superposition, 5.4
print, 6.7, 17.4.20, 17.7.3          select, 5.4.1
     alignment, 8.7.4          sites by apf, 5.4.6
     plot, 17.4.20          superimpose 3D, 5.4.3
     alignment, 8.7.4               grid, 5.4.5
printer.resolution, 4.7.6               multiple proteins, 5.4.4
pro-drug, 10.24protein-protein, 5.6.5, 12.7, 12.7.1, 12.7.2, 12.7.3, 12.7.4, 12.7.5, 12.7.6, 12.7.8, 12.7.9, 12.7.10, 21.10
probe, 12.1.4, 22.5.13     docking refinement, 12.7.11
problem, 22.1.14protein-proteindocking, 12.7.7
     with selection, 22.1.12     convert, 9.20.1
prodrug, 10.24protonated, 22.4.15
profile, 4.2.10, 8.3.8protonation, 10.17, 12.1.1.6
project, 3.6.1.5, 12.7.4, 19.6, 21.6.4.6     state, 12.1.1.6
     close, 3.6.1.13protonation_ph, 10.17
     rename, 3.6.1.9protonation_ph_charge, 10.17.2
properties, 6.8.2, 10.11, 10.11.1, 22.8.7protonation_ph_concentration, 10.17.1
property, 10.4.9, 22.8.7, 22.8.8, 22.8.9, 22.8.10protprot, 12.7
     expression, 13.1.9.6proximity, 6.3.3, 6.3.4
     monitor, 10.4.9psa, 10.4.9
protac, 12.8psi, 6.8.5, 22.2.18
protect, 7.6.8pubchem, 10.1
protein, 5.4.6, 8, 9.14, 22.4.5publication quality images, 6.3.2
     chain, 9.3pubmed, 4.2.1.7
     health, 5.6.3purple box, 3.6.3.23, 12.1.4, 16.9.1
     model, 9.18qs hydrogen bond, 5.2.3
     protein docking, 21.10     pdb chem gl, 5.1.3.2
               tutorial, 21.10               iw, 5.1.3.1
     sculpting, 9.17qsar, 10.19, 10.20, 11.1, 21.13
     sequence, 10.4.17     learn predict, 10.19
     structure, 5     predict, 10.20
          analysis, 5.5quad buffer stereo, 22.1
               closed cavities, 5.5.4     buffer, 22.1.7
               contact areas, 5.5.3quality, 3.6.1.15, 4.7.5
               distance, 5.5.6query, 9.1.2, 19, 19.3, 22.8.1, 22.9.5, 22.9.6
               find related chains, 5.5.1     molt, 18.4
               finding dihedral angle, 5.5.8     processing, 10.5.3
                    planar angle, 5.5.7     setup, 10.5.1
               rama export, 5.5.10quick, 4.1.14
               ramachandran plot, 5.5.9     image, 6.15.2
               rmsd, 5.5.2     model multiple chain, 9.1.2.2
               surface area, 5.5.5          single chain, 9.1.2.1
          similarity, 5.7     start move structure, 4.1.3
          tutorials, 21.3          read pdb, 4.1.2
               analysis, 21.3.4          representation, 4.1.6
               contact area, 21.3.5          selection, 4.1.5

          what is selected, 4.6.4regul, 9.7
     display.distance, 6.9.1regularization, 9.7, 9.20.3
     start color, 4.1.7relationship, 11, 17.6
quit, 3.6.1.19     covalent geometry, 12.1.6
     group, 10.26.7, 10.33.4relaxed ligand, 16.3.9
          table, 10.33.2reload, 12.1.16, 22.5.4
     groups, 10.33.2     dock results, 12.1.16
r-group, 10.26.7, 10.33.2remove, 22.2.6, 22.2.7, 22.2.10
     decomposition, 10.26.7     salt, 22.8.14
     enumeration, 10.26.7     explixit.hydrogens, 10.12
r-groups, 17.4.25     salt, 10.12
racemic, 10.3.28, 10.18.5, 22.5.21rename, 17.1.25
radar, 17.4.6     column, 17.1.25
rainbow, 4.7.5, 6.8.15, 10.3.35, 22.2.38     project, 3.6.1.9
ramachandran plot, 5.5, 5.5.10renumber, 22.4.4
random forest, 11, 21.13reorder column, 17.1.29
range, 6.10.7.2replace chemical, 10.3.32
rapid isostere replacement, 13.4replacement, 16.6
ratio.selection, 4.7.5     group, 16.8
     dock ligand, 16.9report, 19.3
reactions, 10.8, 10.33.5representation, 3.6.3.19
reactive cysteine, 5.6.2residue, 4.7.7, 22.2.8, 22.4.15, 22.4.22
reactivity, 10.11.3     alternative orientation, 21.3.11
read, 3.6.1.3, 3.6.1.17, 4.4, 8.1, 10.3.1     content, 8.3.1
     chemical, 10.1     number selection, 22.2.36
          spreadsheet, 10.3.1     range, 4.6.18
     table, 17.1.2     content, 3.6.4, 8.3, 8.3.1
     pdb, 4.1.2     mutate, 22.4.13, 22.4.14
     table, 17residues, 5.2.1, 5.2.2, 22.2.14
reagent, 10.33.5resize, 6.3.9.1, 6.15.3
rear, 6.3.10, 6.13.1     mesh, 6.3.9.1
recent files, 3.6.1.17resolution, 4.2.1.3
     pdb codes, 3.6.1.18restore, 3.6.2.11, 6.3.10, 6.13.1
receptor, 5.2.1, 5.2.2, 10.6, 12.1.1, 12.2.2, 12.7.5, 12.7.7, 16.3.12, 21.12.1, 22.5.2, 22.5.14, 22.5.15     default, 22.1.9
     considerations, 12.1.1.1     recent backup, 3.6.2.11
     flexibility, 16.15restrained docking, 12.1.7
     pocket, 16.3.1restraint, 16.12.1, 16.12.2
          surface, 16.3.1, 16.3.2results, 12.7.10
     flexibility, 21.12.2     stack, 12.1.12.2
recover, 3.6.2.11retrieve columns, 22.5.24
     cylinders, 8.7.16, 22.6.2          from original database, 22.5.24
     lines, 8.2, 22.6.1review and adjust binding site, 12.1.4
redo, 3.6.2.10, 10.4.11, 16.5.5rgroup, 10.33.4
refine, 9.7, 9.8ribbon, 3.7.1, 4.7.9, 6.1.3, 22.2.23, 22.2.34
     loops, 9.1.3     as a mesh object, 22.2.3
     side chain, 9.8     faq, 22.2.23
     sidechains, 9.1.3     preferences, 4.7.9
refinement, 12.2.4     style, 4.7.9
region, 12.7.7     breaks, 6.1.3
regression, 10.34.2, 11.1, 11.5, 17.4.16, 21.13     cylinders, 6.1.3

     worm, 6.1.3     SMILES, 10.4.15
ribbonColorStyle, 4.7.9     alignment, 8.7.3
ride, 13.4          PDB, 4.5
     gpu benchmark, 13.4.1.2          pdb, 4.5
     server setup, 13.4.1.1     chemical mol, 10.4.13
     setup, 13.4.1          spreadsheet workspace, 10.2.1
right, 4.1.12          to chemical spreadsheet, 10.4.14
     click, 4.1.12     docked ligand, 16.18
rigid, 10.35     file, 4.5
     super, 10.35.2     hits, 16.5.7
          table, 10.35.1     image plot, 17.4.21
ring, 5.2.5, 10.4.3, 10.4.6, 10.5.1     ligand receptor complex, 16.18
     stacking, 5.2.5     object, 4.1.9
rings, 10.3.28, 10.21, 10.35     pdb, 4.5
rmsd, 5.5, 5.5.2, 22.4.7, 22.4.8     project icb, 4.1.10
rock, 3.6.3.15, 6.10.7, 6.10.7.1, 7     sequence, 8.1.5
     speed, 6.10.7.2     slide, 7.4
root, 22.4.7     smiles string, 10.4.15
     mean square deviation, 5.5.2     table, 17.1.21
rotate, 3.6.3.15, 4.1.3, 6, 6.10.7, 6.10.7.1, 6.12, 6.12.1, 6.12.2, 7, 10.3.34, 22.8.13          spreadsheet, 16.5.7
     chemical, 10.3.34     tree, 17.7.3
     when pasting, 10.4.8          sdf, 10.4.14
     easy, 3.6.3.12     image, 3.6.1.15, 4.1.14
     speed, 6.10.7.2     object, 4.1.9
rotating fragment in editor, 10.4.8     password, 3.6.1.11
rotation, 6.12.1     picture, 3.6.1.15
rough surface, 22.2.37     project, 3.6.1.8, 3.6.1.9, 3.6.1.10, 4.1.10
row, 17, 17.1.22, 17.1.35, 17.1.45     table.view, 17.1.8
     flag, 17.1.13saving, 3.6.1.8
     height, 17.1.7, 22.2.39     project, 3.6.1.8
     mark, 17.1.13scaffold, 10.14
     hide, 10.3.8     hopping, 16.8
     show, 10.3.8scale, 4.7.5, 22.2.38
ruler, 6.8.15scan, 9.20.7, 12.1.12.1
     molscreen, 15.1.3     hits, 12.1.12.1
rundock, 22.5.16          group, 16.7
rxn, 10.4.13scarab, 19
safari, 22.3     add user, 19.5
sali, 10.34.5     browse export data, 19.4
     bridge, 21.3.6     installation, 19.1
salts, 10.3.18     new project, 19.6
sample, 9.18, 10.35     pages, 19.7
     double bond cis trans, 12.1.6     query, 19.3
     peptide, 9.19, 9.20.12     upload data, 19.2
     protein, 9.18, 9.20.11scare, 12.2.4
     racemic centers, 12.1.6scatter, 13.1.9.2
sar, 10.26.7, 10.34, 17.4.25scatterplot, 13.1.9.4
     analysis, 10.34score, 12.1.13.1, 13.1.8, 16.4, 21.8.3, 21.8.5, 22.5.7, 22.5.8, 22.5.18
     table, 10.34.3     threshold, 13.1.4
save, 4.5, 6.3.11, 6.10.7.4, 8.1.5, 10.2.3, 17.4.21, 17.7.3, 22.2.33screen, 10.37, 21.8.4, 21.9, 21.11.1

screenshot, 6.16, 6.16.2     all, 3.6.2.3
     movie, 6.16.2     alter, 4.6.7
script, 4.3, 7.6.4, 7.6.5, 22.4.19, 22.10, 22.10.1, 22.10.2, 22.10.3     atom, 3.6.2.5
sculpting, 9.17     basic, 4.6.2
sdf, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6, 10.3.35, 10.10, 10.10.3, 10.18.1, 16.10, 18.1, 19.2, 21.11.2, 22.9.3, 22.9.4     change, 4.6.7
search, 5.7, 10.10, 10.10.4, 18.2, 19.3, 22.9.6     clear, 3.6.2.7
     chembl, 4.2.3     column, 17.1.23
     drugbank, 4.2.8     filter, 3.6.2.5, 4.6.8
     filter, 10.5.2     graphical, 4.6.16
     in workspace, 3.6.2.4     invert, 3.6.2.6, 17.1.23
     pdb, 4.2.1     level, 3.6.3.3
          chemical, 4.2.1     mode, 3.6.3.4
          ligand code, 4.2.7     near atoms, 3.6.2.8
     pocketome, 4.2.2     neighbors, 3.6.2.5, 3.6.2.8, 4.6.15, 4.6.17
     pubchem, 4.2.9     object, 4.6.11
     surechembl, 4.2.4     other, 4.6.19
     tab field, 4.2.1.3     properties, 3.6.2.5
          pdb chemical, 4.2.1.1     range, 17.1.23
               sequence, 4.2.1.2     residue, 3.6.2.5
     tautomer, 10.5.3     row, 17.1.23
     uniprot, 4.2.6     sphere, 4.6.15
     in.workspace, 3.6.2.4     spherical, 3.6.2.8
secondary aliphatic amines, 10.15     superposition, 5.4.1
     structure, 5.6.1, 22.2.20     table, 4.6.19, 17.1.23
     structure, 3.6.4, 6.1.3, 8.3, 8.3.2          elements, 17.1.23
select, 4.6.12, 4.6.13, 17, 17.1.45, 22.4.22     tools, 4.6.1, 4.6.2, 4.6.7, 4.6.8
     a tree branch, 17.7.2     whole, 4.6.11
     all, 4.6.14     workspace, 4.6.9, 4.6.17
     amino acid, 4.6.13selectioninvert, 3.6.2.6
     duplicates, 10.31selections, 4.6
     molecule, 4.6.12     links, 8.3.9
     neighbors, 4.6.15selectneighbors workspace, 4.6.17
          graphic, 4.6.16     organized network, 10.28
     object, 4.6.11sequence, 3.6.4, 4.2, 4.2.1.2, 4.2.5, 4.2.6, 4.3, 8, 8.1, 8.1.5, 8.2, 8.3, 8.3.7, 8.6.1, 8.6.5, 9.1.2, 10.4.17, 21.3, 21.4, 21.4.4, 22.4.12, 22.6, 22.6.1
     residue, 4.6.13, 4.6.18     analysis, 8.3
          by number, 4.6.18     editor, 8.5
          number, 4.6.18     identity, 8.7.15
     tree, 17.7.2     pattern, 4.2.1.2
     atom, 4.1.5, 4.6.3     reordering, 8.7.8
     graphical, 4.1.5, 4.6.3     secondary structure, 8.2, 22.6.1
     object, 4.1.5, 4.6.3     similarity, 8.7.15
     purple.box, 3.6.3.23     sites, 8.5
     residue, 4.1.5, 4.6.3     structure, 8.3.6
     workspace, 4.1.5, 4.6.3     type, 8.3.4
selectall, 3.6.2.3     DNA, 8.3.4
selecting.neighbors, 4.6.16     alignment, 8.3.5, 8.6.2, 8.6.6
selection, 4.6.4, 4.6.5, 4.6.21, 6.3.4, 10.4.11, 17.4.18, 17.7.2, 17.7.4, 22.2.4, 22.2.6, 22.2.7, 22.2.8, 22.2.13, 22.2.32, 22.4.9, 22.4.10, 22.4.22, 22.5.14     amino acid, 8.3.4
     clear, 3.6.2.7     nucleotide, 8.3.4
     neighbors, 3.6.2.8     protein, 8.3.4
     alignment, 4.6.19     search, 8.4

sequences, 8, 22.2.25size, 5.2.3.1
     unique, 8.3.13sketch accents, 6.10.3
     extract, 8.3.13     markush, 10.33.1
     unique, 8.3.13     reaction, 12.4.1
server, 13.1.7.2     smiles, 10.4.12
     error, 22.1.17     accents, 3.6.3.14, 6.10.3
set, 10.3.31, 22.4.21skin, 3.7.1, 6.1.4, 22.2.16
     formal charges, 10.15slab, 6.3.10, 6.13.1
     server, 22.1.17slice, 6.13
     bond type, 9.20.5slide, 6.10.7.4, 7.2, 7.3.1, 7.6.1, 22.2.31
     charges, 9.20.6     effects, 7.5
     chirality, 9.20.5     movie, 6.16.1
     disulfide, 9.9, 22.4.17          file, 7.2
          bond, 9.20.5     navigation, 7.3.2
     formal charge, 9.20.5     show, 7.3
     tether, 9.20.5     blend, 7.5
     types, 9.20.6     edit, 7.4.1
setAPFparams, 22.8.12     effect, 7.5
setup, 12.7.6     smooth, 7.5
     ligand receptor, 16.1     transition, 7.5
shade, 8.7.7, 8.7.7.1slides, 6.16.1, 7, 7.1, 7.3, 22.2.30
     alignment, 21.4.4smiles, 10.4.9, 10.11, 10.18, 10.18.3, 10.18.4
shading, 6.3.12smooth, 6.3.9.3
shadow, 6.10.2     surface, 22.2.37
share model, 11.1.4solid, 6.3.9.3
sheet, 22.2.20solvent.accessible.area, 22.4.19
shell preferences, 4.7.10sort hitlist, 13.1.9.1
shift, 6.8.3     table, 3.6.10.4
shine, 3.7.2, 4.7.5sorting, 13.1.9.1
shineStyle, 4.7.3     compounds, 17.7
show, 7.3.1, 17.1.39sp3, 10.11.2
     hide column, 17.1.39spec, 3.7.2
side, 10.3.29specifications, 22.1.5
     by side, 10.3.29specs, 1
               error, 22.1.19     faq, 22.1.5
               stereo, 3.6.3.6speed, 6.10.7.2
     chain refinement, 16.14sphere, 22.4.11
     chains, 9.8spherical, 22.4.9, 22.4.12
side-by-side, 22.1.19split, 10.34.1
side-chain sampling, 12.7.11spreadsheet, 10.18.2
side-chains, 12.2.1square, 22.4.7
sigmaLevel, 5.3.6, 5.3.7stability, 9.13, 21.5.3, 21.5.4
similarity, 10.29stack, 9.18, 12.1.12, 12.7.10, 22.9.8
simulation, 14, 22.9.8stacking, 5.2.5
     length, 22.5.12standalone hitlist, 12.1.14
simulations, 22.7standard table, 17.1
single, 10.4.10standardize, 10.12
     chain, 9.1.2.1     table, 10.12
singlet, 10.4.7start, 10.10.2
sites, 5.4.6     dock, 12.1

static, 22.4.8synthetic feasibility, 10.11.5
stereo, 4.7.6, 6.6, 10.3.28, 10.4.2, 22.1, 22.1.6, 22.1.7, 22.1.14system preferences, 4.7.11
     bond, 10.4.2tab, 17.1.2, 17.1.21
     hardware, 3.6.3.7     pdb, 3.7.4
     side-by-side, 3.6.3.6table, 4.3, 10.1.3, 10.3.24, 10.3.25, 10.3.28, 10.3.30, 10.3.31, 10.3.34, 10.3.35, 10.18.2, 10.21, 10.35.1, 16.10, 17, 17.1.6, 17.1.35, 17.1.40, 17.1.45, 17.4, 17.4.1, 17.4.4, 17.4.9, 17.4.11, 17.4.13, 17.4.14, 17.4.15, 17.4.16, 17.4.17, 17.4.18, 17.4.20, 17.7.1, 22.4.19, 22.8.4, 22.8.5, 22.8.7, 22.8.8
stereohard faq, 22.1.6     alignment, 17.1.12
stereoisomer, 10.18.5     clone, 17.1.16
stereoisomers, 10.23     color, 17.1.10
stick, 4.7.5     column format, 17.1.40
stl, 6.7     copy, 17.1.36, 17.1.37
stop, 6.10.7.3     delete, 17.1.17
store, 3.6.3.19, 6.10.7.4, 22.2.22     edit, 17.1.24
     current view, 3.6.3.19     filter, 17.1.43
               faq, 22.2.22     find, 17.1.9
strain, 5.6.3, 10.25, 10.25.2, 12.1.1.8, 16.4          replace, 10.3.32
strip, 22.4.9     font, 17.1.11
structure, 5.3.3, 11, 17.6, 21.3, 22.4          size, 22.2.1
     analysis, 21.3.4     grid, 17.1.5
     ensemble, 9.20.14     histogram, 17.4.1
     representation, 6.1     insert, 17.1.26
     smiles, 10.18.4     layout, 17.1.5
structure-based, 13     learning, 17.6
structures, 10, 10.1     mark, 17.1.13
style, 4.7.5          row, 17.1.13
substituent, 10.9.1, 10.9.2, 10.33.2, 16.5.2     mouse, 17.1.47
substructure, 10.10.4, 10.13, 12.3, 22.8.1, 22.9.5     navigation, 17.1.4
     template, 16.12.3     new column, 17.1.26
     alerts, 10.13     plot, 17.4
sulfur, 9.9     print, 17.1.19
superimpose, 3.6.8, 5.4.2, 5.4.6, 21.3.3, 22.2.5, 22.4.6, 22.4.7, 22.4.8     rename, 17.1.15
     3D, 5.4.3     rightclick, 17.1.14
     Calpha, 5.4.3     row height, 22.2.39
     arrange.grid, 5.4.5     save, 17.1.3
     backbone, 5.4.3          selection, 17.1.3
     flexible, 10.35.3     search, 17.1.9
     heavy atoms, 5.4.3     select, 17.1.23
     multiple, 5.4.4     setup, 17.1.18
     rigid, 10.35.1, 10.35.2     sort, 17.1.42
     substructure, 10.35.1, 10.35.2, 10.35.3     split fragments, 10.3.33
superposition, 10.35, 10.36.1, 10.36.2, 21.3.3, 21.8.1     view, 17.1.5
surface, 3.7.1, 4.7.5, 5.2.1, 5.2.2, 6.1.6, 6.3, 6.3.3, 6.3.4, 22.2.16, 22.2.37, 22.4.19          save, 17.1.8
     area, 5.5     zoom translate, 10.3.30
     area, 5.5.5     action, 17.1.47
surfaces, 5.2, 6.3.1, 6.3.2, 6.10.5     alignment, 17.1.12
surrounding, 22.4.11     append, 17.1.43
swissprot, 8.1, 8.5     clone, 17.1.16
sxstrace, 22.1.19     color, 17.1.10
symmetric oligomer, 9.1.3     column, 10.3.4, 17.1.26, 17.1.32, 17.1.39
symmetry, 5.3.1, 5.3.3, 21.3.8, 21.3.9     columns, 10.3.8
synthesize, 10.11.5     compare, 10.3.22

     cursor, 17.1.47templates, 10.4.6
     delete, 17.1.14, 17.1.17terminal, 10.3.28
     display, 22.10.4     font size, 22.2.1
     double.click, 17.1.47tether, 12.1.7, 16.12.1, 16.12.2
     edit, 10.3.17text, 4.7.7, 7.6, 7.6.1, 7.6.7, 10.3.28, 10.10.4, 17.4.24, 22.9.6
     excel, 10.3.10, 17.1.20     search, 10.5.4
     filter, 10.3.12, 17.1.43texture, 3.7.6
     find-replace, 10.3.13thoroughness, 10.21, 10.35, 22.5.12
          to screen, 17.1.4three, 10.3.24, 22.8.6
     font, 17.1.11threshold, 4.7.5
     foreground, 22.10.4tier, 4.1.13
     grid lines, 17.1.4time, 22.5.11
     hide, 17.1.39     machine, 22.1.15
     hyperlink, 10.3.15tissue, 4.2.10
     insert, 17.1.33     racemic, 10.18
     join, 3.6.10.5tools 3D, 3.6.6
     label, 10.3.14     analysis, 3.6.7
     landscape, 17.1.18     append rows, 3.6.10.7
     mark, 10.3.14     extras, 3.6.9
     merge, 3.6.10.5, 10.3.23, 10.30          plot function, 3.6.9.1
     mouse, 17.1.47     superimpose, 3.6.8
     name, 17.1.15     table, 3.6.10
     new, 17.1.1          Learn, 3.6.10.1
     options, 17.1.14          clustering, 3.6.10.3
     orientation, 17.1.18          merge, 3.6.10.5
     portrait, 17.1.18          predict, 3.6.10.2
     print, 10.3.11, 17.1.4, 17.1.19tooltip, 17.4.26
     read, 17.1.2     balloons, 17.4.26
     rename, 17.1.15torsion, 6.12.6, 9.20.7, 16.5.4, 22.4.16
     right click, 17.1.14     angles, 6.12, 6.12.6
     row, 17.1.33     scan, 9.20.7
     rows, 3.6.10.7toxscore, 10.11.3
     save, 10.3.9, 17.1.3, 17.1.4, 17.1.21trace, 6.1.10
     scale, 17.1.18transition.blend, 22.2.31
     scroll, 17.1.4transitions, 7, 22.2.30
     sdf, 10.3.9translate, 4.1.3, 6, 6.12, 10.3.30
     select, 17.1.23translation, 6.12.3, 8.3.3, 17.4.17
     setup, 17.1.18transparent, 6.3.9.3
     sort, 3.6.10.4, 10.3.5, 17.1.42     background, 6.15.3
     standard, 17.1     ribbon, 22.2.3
     view, 10.3.29     surface, 22.2.37
     width, 17.1.4tree, 8.7.8, 10.26.7, 17.7.2, 17.7.3, 17.7.4
tables, 10.29, 17     branch swapping, 8.7.8
tag, 4.6.21, 16.5.7, 17.1.46     distance, 10.26.3
tags, 4.6.21     edit, 10.26.4
tautomer, 10.22, 22.4.15     reorder, 10.26.3
tautomers, 10.22triplet, 10.4.7
temperature, 5.6.4trouble shooting, 22.1.11
template, 9.1.2, 10.4.6, 10.35trouble-shooting, 22.1.12
     docking, 22.5.3truncating a mesh object, 22.2.15

tsv, 17.1.21     animate view, 3.6.3.15
tut analyze alternative orientations, 21.3.11     center, 3.6.3.20
          occupancy, 21.3.10     color background, 3.6.3.18
          symmetry, 21.3.9     dock results, 12.1.12
     multiple receptor, 21.12.1     fog, 3.6.3.5
tut3, 21.5     macroshape, 3.6.3.22
tut3e, 21.3.12     menu, 3.6.3
tut5a, 21.9.1     mesh clip, 6.13.1
tut5b, 21.9.2     perspective, 3.6.3.9
tut5c, 21.11.1     selection level, 3.6.3.3
tut5e, 21.11.2          mode, 3.6.3.4
tutorial 2D pharmacophore, 21.6.6     shadow, 3.6.3.13
     3D pharmacophore, 21.6.5     sketch accents, 3.6.3.14
     chemical clustering, 21.6.3     slide show, 7.3.1
          search, 21.6.2     tools, 3.6.3
     molecular documents, 21.2     tree, 17.7.4
     sequence alignment, 21.4     undisplay all, 3.6.3.1
               link, 21.4.2     stach, 9.20.15
               load sequence, 21.4.1virtual, 13.1, 13.1.1, 13.1.2, 21.9, 21.11.1
               sequence conservation, 21.4.3     ligand screening, 15
tutorials, 21     screen, 13.3, 13.4
two, 10.3.24, 22.8.6     screening, 13, 13.2
ubuntu, 22.1.18          examples, 21.11
unclip, 6.3.10, 6.13.1virus, 5.3.3
undisplay, 4.1.4, 6.1.7, 22.2.10, 22.2.32visualize, 10.28
     box shade font, 8.7.7.1     apf fields, 16.3.11
undisplay-all, 3.6.3.1     chemical space, 10.28
     origin, 6.8.11     ligand strain, 16.3.10
undo, 3.6.2.9, 4.7, 10.4.11, 16.5.5vls, 12.2, 12.2.3, 13, 13.1, 13.1.6, 13.1.7.2, 13.1.9.6, 13.3, 21.11.2, 22.5.7, 22.5.8, 22.5.24
     redo, 16.5.5     analysis, 13.1.9.6
uniprot, 4.2.6, 8.5          display, 13.1.9.5
unique, 10.3.28, 10.31     command line, 13.1.7.2
unit, 5.3.3     getting started, 13.1.2
units, 22.5.1     histogram, 13.1.9.3
unix, 22.10.2          scatter plot, 13.1.9.2
unsatisfied hydrogen bonds, 16.3.8     introduction, 13.1.1
unusual peptide, 4.3     preferences, 13.1.4
upload, 19.2     results, 13.1.8
use activeicm, 7.12     run, 13.1.6
user, 10.10.5, 19.5     scatterplot, 13.1.9.4
     defined groups, 16.5.3     score, 12.1.1.4
     modifiers, 16.5.3     visualization, 13.1.10
user-defined groups, 10.4.5     results, 13.1.8
van der waal, 6.8.14volume, 10.4.9
variable, 4.7.7, 22.2.8water, 9.20.17
verbose, 10.21waters, 9.20.17
     large sdf files, 10.1.2wavefront, 3.7.6, 6.3.11, 6.7
vicinity, 10.21weak, 22.4.20
video, 2, 6.16, 6.16.1, 6.16.2web, 21.2
view, 3.6.3.19, 7.3.1, 10.3.28, 22.2.22, 22.9.8     browser, 3.6.1.12

weighted, 17.7.1 
width, 17.1.22 
window, 4.1.13 
windows, 4.1.13.1, 10.10.1 
wire, 3.7.1, 4.7.5, 6.1.1, 22.2.4, 22.2.21 
wireBondSeparation, 4.7.1 
working directory, 22.5.23 
workspace, 4.1.4, 5.1.3.1, 10.7.2 
     panel, 4.1.4 
     selection, 4.6.9 
     navigation, 4.6.10 
write, 4.1.14, 4.5, 17.4.21, 22.9.4, 22.9.7 
     alignment, 8.7.3 
     excel, 10.2.3 
     image, 3.6.1.15, 22.1.20 
     images, 6.15 
     pdb, 4.5 
     image, 3.6.1.15 
     object, 4.1.9 
     picture, 3.6.1.15 
     project, 3.6.1.8, 4.1.10 
     table, 17.1.3 
writing a pdb file, 22.4.3 
     ray, 3.6.5 
xi, 6.8.5, 22.2.18 
xls, 10.2.3 
xlsx, 10.2.3 
xml, 19.2 
xstick, 6.1.2, 22.2.21 
xyz, 22.2.10 
youtube, 2 
zoom, 4.1.3, 6, 6.12, 6.12.4, 10.3.30, 17.4.17 

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