Feb 16 2024 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, 10.19.2, 10.19.4     Search, 21.6.2
     Chemical Label, 6.8.11CisTransAmide Angle, 13.1.9.6
     Interaction Diagram, 16.3.7Clash Threshold, 4.7.10
     bioisostere, 10.9.1DNA, 4.3, 8, 8.3.3
     chemical label, 6.8.11Decomposition, 10.35.3
     from PDB, 10.1.1Display, 22.2.26
     screening, 15Distance, 13.1.9.6
     to 3D, 10.19, 10.19.3Dock Directory, 4.7.2
     depiction, 10.19.2Docking, 22.2.26
3D, 6.6, 6.8.8, 10.1.3, 10.3.24, 10.3.28, 10.3.31, 10.19.2, 21.2Drug Bank, 4.2.8
     QSAR, 10.37.4, 11.4, 21.14Editor, 4.7.2
     chemical, 10.4.16, 10.19.1Eintl, 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, 10.35.2
     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, 10.36.4, 10.36.7, 10.37.4, 11.4, 15, 15.6, 21.14     clashWidth, 4.7.3
     template, 10.36.3     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

     grobLineWidth, 4.7.3     max Nof Recent Files, 4.7.11
     hbond Ball Period, 4.7.1          Sequence Length, 4.7.4
               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, 10.19.3
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, 10.19.3
     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

LogP, 11, 17.6     Search, 3.6.2.12, 3.6.2.13, 3.6.2.14, 3.6.2.15, 3.6.2.16
LogS, 11, 17.6          Field, 3.6.2.13
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, 10.33PLOT.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, 22.8.10PSA, 10.11.7
Movie.fade Nof Frames, 4.7.4Pharmacophore RMSD, 13.1.9.6
     quality, 4.7.4PowerPoint, 21.2, 22.3
          Auto, 4.7.4Projects Directory, 4.7.2
NCBI, 22.2.25Prosite Dat, 4.7.2
NVIDIA, 22.1Protein, 22.2.26
Nof_Atoms, 10.11     Viewer, 4.7.2
Nof_Chirals, 10.11Pub Chem, 4.2.9
Nof_HBA, 10.11PubMed, 4.2.1.7
Nof_HBD, 10.11     Reference, 17.1.40
Nof_Rings, 10.11Pubchem, 4.2.9
Nof_RotBonds, 10.11QSAR, 11, 11.1, 17.6, 21.14
Non-overlap, 13.1.9.6R, 10.8, 10.35.1
Nvidia GL failutre, 22.1.11     and S, 22.5.21
ODA, 22.2.26R-Group, 10.35.3
Optimal, 22.2.26R-groups, 16.5.3
Output Directory, 4.7.2REAL, 10.5.5
PAINS, 10.4.9, 10.11.3RMSD, 5.4.2
     chemicals, 10.4.9RNA, 4.3
PCA, 11.1, 11.5, 21.6.4RTCNN, 12.1.1.4, 12.1.13.1
     analysis, 10.28Ramachandran Plot, 5.5.9
PDB, 4.2.1.6, 5.1.2, 5.3.3, 5.7, 8.1, 10.1.1, 16.18Real Format, 4.7.10
     Directory, 4.7.2     Label Shift, 4.7.7
          Style, 4.7.2          Style, 4.7.7
     link, 17.1.40RotB, 22.8.7, 22.8.10

SAR, 11, 15.6, 17.4.25, 17.6     cliff, 10.35.5, 10.35.6, 21.6.11
     table, 10.35.3, 21.6.9          tutorial, 21.6.11
SCARE, 12.2.4add database, 10.10.3
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, 10.36.5, 10.36.6, 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, 10.35.5     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, 10.35.2     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

     multiple, 8.3.7, 8.6.5          score, 21.8.3
     options, 8.7.10          screen, 21.8.4
     rename, 8.7.10          superposition, 21.8.1
     reorder, 8.3.12     alignment, 10.36.7
     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, 10.19.2
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, 10.16, 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, 10.36.5, 10.36.6, 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, 10.34.4
     alignment, 8.7.6author, 4.2.1.3
     by substructure, 10.13     close tree, 10.27.5
     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, 10.36.5, 10.36.6, 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, 10.36.6axes, 17.4.15
     pairwise, 10.36.5axis, 17.4.11
     super, 10.36.3     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

backup, 3.6.2.11     stack, 9.20.15
bad, 10.11build, 6.10.7.1
     groups, 10.4.9     homology model, 9.1.2
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, 10.22
begin docking simulation, 12.1.8cation, 5.2.5
best, 10.3.34cavities, 5.5
bicyclics, 10.4.6     closed, 5.5.4
binding, 21.5.3, 22.2.14, 22.5.2, 22.5.10ccp4, 22.2.27, 22.2.28
     properties, 6.3.1cell, 5.3.2
bioinfo align multiple, 8.3.7center, 3.6.3.20, 4.1.3, 6.12, 6.12.5, 16.3.13, 17.1.40, 22.4.22
          two sequences, 8.3.5     on ligand, 16.3.13
     links, 8.3.9     and representative members, 17.7.2
     menu, 3.6.4cereblon, 12.8
     secondary structure, 8.3.2chain.breaks, 22.2.34
     translation, 8.3.3chair, 22.5.20
bioisoester, 10.9change box size, 16.9.1
bioisostere, 10.9, 10.9.1, 10.9.2, 16.8     height of all rows, 17.1.7
biological, 5.3.3     ligand, 16.5.1
biomolecule, 3.6.5, 5.3.3, 21.3.8, 21.3.12     row height, 17.1.7
bit, 22.1.3     selection, 4.6.7
blast, 4.2.5, 8.4     speed range, 6.10.7.2
     search, 4.2.5changing font in alignment editor, 8.7
blood brain barrier, 10.11.4charge, 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
blue lines, 8.2     groups, 12.1.6, 22.5.22
boat, 22.5.20check box, 7.6.6
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     convert, 22.8.5
     covalent, 22.4.2     export excel, 10.2.3
     type, 5.1.3.1, 5.1.3.2, 10.7.1, 10.7.2, 10.7.3     save, 10.2
bonding, 6.1.8          3D, 10.2.5
     preferences, 4.7.1          editor, 10.2.4
box, 4.7.7, 6.8.16, 8.7.7, 8.7.7.1, 22.5.9          image, 10.2.6
     alignment, 21.4.4          table, 10.2.2
     size, 16.9.1     super, 10.36
browse, 10.3.31, 12.1.12.1, 19.4     view, 10.3.28
     mode, 10.3.31chembl, 4.2.3, 4.2.4
     molt, 18.2chemical, 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, 10.19.2, 10.23, 10.34.4, 10.34.5, 10.36, 10.36.5, 10.36.6, 17.7.1, 21.6.4, 22.8.4, 22.8.5, 22.8.7, 22.8.8, 22.8.9, 22.8.10

     descriptors, 22.8.15     superposition, 10.36.3, 10.36.7
     dictionary, 10.4.4, 10.4.5, 10.4.6     table, 10.3, 17.2
     draw, 21.6.1cheminformatics, 10, 10.3, 22.8
          spreadsheet tutorial, 21.6.1     tutorials, 21.6
     edit buttons, 10.4.11chemistry, 10.23, 22.8
     editor, 10.4, 10.4.8     convert, 10.19
          not starting, 22.1.13          2dto3d, 10.19.1
     fingerprint, 15     pca, 10.28
     fingerprints, 22.8.15     smiles, 10.19.3
     fragments, 10.3.33     duplicates, 10.32
     group, 10.4.5     remove.redundant, 10.32
     groups, 10.4.5, 10.4.8chemlib.so, 22.1.3
     modifiers, 10.34.2chemspace append, 21.6.4.4
     properties, 21.6.4     build visualize, 21.6.4.1
     right click, 10.4.3     compare, 21.6.4.8
     search, 10.5, 13.4     delete row, 21.6.4.3
          filter, 10.5.2     distinguish, 21.6.4.7
          text, 10.5.4     export, 21.6.4.5
     sketch, 21.6.1     project, 21.6.4.6
     space, 10.29     select, 21.6.4.2
     spreadsheet, 4.2.3, 10.1.3, 10.3.1, 10.4.14, 21.6.1, 22.8.13chi, 6.8.5, 22.2.18
          compare, 10.3.22chiral, 10.24, 12.1.1.5
          template, 10.3.2chirality, 10.24, 12.1.1.5
     spreadsheets, 10.3     considerations, 12.1.1.5
     substituent, 10.9chrome, 22.3
     substructure, 4.2.1.1cis trans proline, 21.5.2
     table, 16.10, 22.8.11clash, 4.7.5, 6.8.15
          display, 10.3.3     volumes, 13.1.10
     tables, 17.2classes, 10.3.28
     toxicity, 10.11.3classification model, 15.5
     2D, 10.7clear display and planes, 3.6.3.2
     3D, 10.7     selection, 4.6.6
     append, 10.4.13     planes, 3.6.3.2
     clustering, 10.27, 10.27.1click, 4.1.12, 6.11, 6.12
     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, 22.4.1clip, 6.3.10, 6.13.1, 22.2.11
     display.fit, 22.8.13clipboard, 6.15.3, 17.7.3
     draw, 10.4.1clipping, 22.2.19
     duplicates, 10.3.21     planes, 6
     editor, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6     tool, 6.13
     load, 10.1     tools, 6.13
     merge, 10.31clone, 3.6.1.2
     new, 10.4.1close, 6.3.3, 6.3.4, 16.20
     properties, 10.3.19     downstream cluster, 10.27.5
     query, 10.4.3, 10.5.1, 10.5.3     project, 16.20
     read, 10.1     cavities, 5.6.6
     save, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6, 10.4.13cloud, 13.1.7, 13.1.7.2
     search, 10.4.3, 10.5, 10.5.1, 10.5.3cluster, 13.1.7, 13.1.9.7, 17.7.1
     similarity, 10.4.3, 10.5, 10.5.1, 10.5.3     representative.center, 10.27.2
     spreadsheet, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6, 10.3clustering, 17.7, 21.6.3
     structure, 10.4.13cns, 10.33

color, 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, 22.2.20conformation, 9.20.18, 10.22, 12.2.2
     alignment, 8.7.9conformational entropy, 10.26
     background, 6.4.2conformations, 22.9.8
     by, 6.4conformers, 10.22
          alignment, 8.8connect, 6.3.9.1, 6.12, 6.12.7
     chemical, 10.3.35     object, 6.12.7
     faq, 22.2.20connectivity, 10.4.3, 10.5.1
     key, 22.2.38consensus, 10.37, 21.8.2
     scale, 22.2.38     pharmacophore, 10.37.1
     surface by proximity, 6.3.3construct, 3.6.1.1, 6.10.7.1
               selection, 6.3.4     molecule, 3.6.1.1
     table, 10.3.27     object, 3.6.1.1
     2D sketch, 10.5.6.5contact, 5.5, 5.5.3, 21.3.5
     background, 3.6.3.18, 6.4.2     surface, 6.3.2
     distance, 6.8.10contacts, 6.3.3, 6.3.4, 10.6, 13.1.9.8, 16.3.12
     mesh, 6.3.9.3contour, 5.3.6, 5.3.7
     table, 10.3.27convert, 5.1.2, 10.19.1, 10.19.5, 22.8.5
coloring, 6.4.1     chemical, 10.3.24
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          2D 3D, 10.7
     annotation, 17.1.41          3D molecular editor, 10.4.16
     order, 17.1.29          from pdb, 5.1.3
     plot, 17.4.6     local database, 3.6.1.6
     row width, 17.1.22     pdb, 21.3.2
     statistics, 17.1.32          chem, 10.7.1
     visibility order, 17.1.28     smiles to 2D, 22.8.11
     color, 17.1.10     local.database, 3.6.1.6
     hide, 10.3.8     smiles, 10.19, 10.19.3, 10.19.4
     show, 10.3.8converting pdb, 5.1.2
combinatorial chemistry, 10.34coordinates, 10.1.3
     library, 21.6.8copy, 10.3.25, 10.4.11, 10.4.18, 10.5.6.2, 17.1.35
combine, 3.6.10.5     cell, 17.1.36
     display style, 4.7.9     chemical, 10.3.25
command, 22.5.16     loop, 9.4
     line, 22.2.32     paste row, 17.1.35
commands, 22.10.1     row, 17.1.36
common substructure, 10.36.1     rows, 17.1.44
compact tree, 10.27.5     selection to table, 17.1.37
compare, 10.3.29, 10.30, 10.31     chemical, 10.3.16
     table, 10.3.22covalent, 16.10.1
     tables, 10.30     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, 10.23, 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, 10.34.3
conditions, 10.5.2     new objects, 4.3
     gen, 10.22cross, 22.2.10
configuration error, 22.1.19     section, 6.13

crystal, 5.3.2     selection, 3.6.2.1
crystallographic analysis, 5.3     tether, 9.20.5
          biomolecule, 5.3.3dendrogram, 10.29.1
          contour map, 5.3.6density, 5.3.4, 5.3.6, 5.3.7, 22.2.27, 22.2.28
          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, 10.36dislay 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, 6.8.15, 6.14, 10.24, 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     chemical, 6.8.11
     label, 6.8.8     delete distances, 6.9.4
     rotation, 6.12.2     dihedral, 6.9.3
customized MPO score, 10.33.1     distance restraints, 6.8.14
cut, 17.1.35     distance2, 6.9.1
     vertical alignment block, 8.3.11          angles, 6.9
cyclic peptide, 9.19     formal charge, 6.1.9
cys, 5.6.2     gradient, 6.8.17
cysteine reactivity, 5.6.2     hbond, 13.1.9.5
damaged skin, 22.1.12     hbonds, 13.1.9.6, 16.3.4
dash, 22.2.12     hydrogen, 6.1.7
database, 8.4, 10.10, 10.34.4, 13.1.3, 13.1.6, 18.1, 19          atoms ligand editor, 16.3.3
     file format, 13.1.3     mesh, 6.3.5
     search and alignment, 8.4     meshes, 6.3.8
databases, 22.9.3     options, 16.3
decompose.library, 21.6.9     planar angle, 6.9.2
decomposition, 10.34.4, 10.35.1, 17.4.25     tab, 3.7.1, 22.2.16
default, 4.1.13     tether, 6.8.13
delete, 3.6.2.1, 4.6.6, 7.6.8, 22.4.9     toggle, 6.8.16
     alignment, 8.7.5     CPK, 6.1.5
     all, 3.6.2.2     angle, 6.9.2
     column row, 17.1.38     chemical, 10.3.3
     label, 6.8.9     dihedral.angle, 6.9.3
     alignment, 8.7.5     distance, 6.8.10, 6.8.14, 6.9.1
     all, 3.6.2.2     electrostatic, 3.6.3.21
     angle.label, 6.9.4     energy.gradient, 6.8.17
     column, 17.1.38     hydrogen, 6.1.7
     distance.label, 6.9.4          polar, 6.1.7
     label, 6.8.9     macroshape, 6.3.6
     row, 17.1.38     meshes, 6.3.5

     molecule, 10.3.24     templates, 16.12.3
     origin, 6.8.12     tutorials, 21.9
     potential, 3.6.3.21     background, 22.5.19
     representations, 3.7.1     batch, 12.1.10
     restraints, 6.8.14     conformations, 22.5.20
     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, 6.8.13     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, 10.30, 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, 10.34.5, 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

          2D, 16.5.1     terms, 9.20.19
          editor preferences, 16.2ensemble, 9.20.18, 12.2.2
          multiple substituents, 16.5.2entropy, 10.26.1
          tools, 3.6.2.17enumerate formal charge states, 10.17
     menu, 3.6.2     reaction, 21.6.10
     molecular document, 7.6.1enumeration, 10.34.4
     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, 10.30
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, 10.22, 10.36, 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, 6.8.15, 10.26, 10.26.2, 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

     change torsion, 22.4.16          text search, 22.9.6
     chem table display, 22.8.4     molecule c, 22.2.5
     chemical monitor, 22.8.10     moledit, 22.8.2
          query2, 22.8.1     movie planes, 22.2.19
     cheminformatics, 22.8     newscript, 22.10.1
     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

     protein protein docking, 12.7.1frequency, 10.3.35
file, 3.6.1.3front, 6.3.10, 6.13.1
     close, 3.6.1.13full model, 9.1.3
     compatible, 3.6.1.10          builder, 9.1.3
     export, 3.6.1.12          multiple chain, 9.1.3.1
     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, 10.22
     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
flexibility, 5.6.4, 12.2.3, 21.12graft loop, 9.4
flexible, 10.36, 12.2, 12.2.1, 12.2.2, 21.12.1, 22.5.15graphical, 22.2.4
     APF superposition to template, 10.36.4     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, 10.17     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, 10.35.1, 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, 10.36, 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, 10.35.1, 16.6
     radical, 10.4.7     column, 17.1.46
     wilson regression analysis, 10.35.2groups, 10.8, 10.11, 10.12
freeze column, 17.1.30guanidinium, 10.15
     row, 17.1.31gui, 4.1.1, 4.7.4

     preferences, 4.7.4     copy 2D, 10.3.16
     tabs, 3.7          paste, 10.3.6
guided docking, 12.1.7, 22.5.3     decompose, 21.6.9
h-bond, 5.2.3, 5.2.3.1, 5.2.3.2, 22.2.12     duplicate chemicals, 10.3.21
halogen, 10.11.2     edit table, 10.3.17
hardware stereo, 3.6.3.7, 22.1          tree, 10.27.4
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, 10.27.3
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, 10.27.1
     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, 10.27.2          use gui, 4.1
     color 2D by ph4, 10.5.6.5hrydrogen.bond, 22.2.29

html-doc font size, 22.2.1     quality, 3.6.3.11
hybridization, 10.4.3, 10.5.1     quick, 3.6.1.14, 6.15.2
hydrogen, 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, 22.8.10images, 6.15
     atom display, 16.3.3impose, 12.2.2
     bond, 5.2, 6.1.8, 10.6, 13.1.9.5, 21.3.6improve model, 11.1.3
          acceptors, 22.8.17in-a-window, 22.1.7
          donor, 10.37.1inchi, 10.19.3
          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, 10.31

     means, 17.7.1ligand, 5.2.2, 10.6, 10.26, 10.26.1, 10.26.2, 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, 22.8.8
kcc, 15.3.1, 15.5     based screen, 10.37.3, 13.3
keep carboxyls neutral, 12.1.6     best replace, 16.6
kernel regression, 15.3.1     binding, 9.15
     chemical, 10.4.10     code, 4.2.1.3, 4.2.7
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, 10.26
     move, 6.8.4          conformational entropy, 10.26.1
     residues, 6.8.3          strain, 10.26.2
     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, 10.20, 10.21, 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, 10.34.4lineWidth, 4.7.3
     reaction, 21.6.10link, 8.3.9
license, 22.1.4     structure to alignment, 21.4

links, 4.6.20     animation, 6.10.7.1
linux, 10.10.1     apf docking sar model, 15.6
lipinski rule, 10.33     complex, 13.1.9.6, 16.20
list, 4.6.18     flat, 22.8.13
lmhostid, 22.1.18     molecular document, 7.6
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, 10.27.7, 10.34.1, 10.34.3, 10.35.1, 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, 10.35.6, 21.6.11
logarithmic, 17.4.11          analysis, 10.35.6
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, 10.27.6, 10.29, 10.29.1
     find pdb segments, 9.6               dendrogram, 10.29.1
     model, 9.2, 9.3, 21.5.2mcs, 10.27.6, 10.29.1
          tutorial, 21.5.2     rgroup decomposition, 10.27.7
     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, 10.31, 22.4.5

mesh, 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, 6.13.1molecular, 10.3.30, 10.3.31, 10.3.34, 10.3.35, 10.22, 22.8.7, 22.8.10
     clip, 6.3.10     animations slides, 7
     color lighting, 6.3.9.4     documents, 21.2
     options, 6.3.9     dynamics, 14
     representation, 6.3.9.3     editor, 22.8.2
     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, 9.20.19
     start, 9.1.1.2          view stack, 9.20.15
     weight, 11.1.2     modeling, 9
modelers view, 9.1.4.1     table, 10.19.2
     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

     structure, 6.12nof, 10.11.2
     tools, 6     chemical, 10.11.2
     rotate, 6.11non-contiguous selection, 4.6.18
     slab, 6.11normal modes, 9.20.14
     translate, 6.11number of sp3, 10.11.2
     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, 10.33          effect, 6.10.5
     customized, 10.33.1occupancy, 6.1.3, 21.3.10
mtl, 6.7     display, 4.2.1.5
multi apf super, 10.36.7oda, 5.6.5, 12.7, 12.7.2, 12.7.3
     panel, 6.2older version, 3.6.1.10
     parameter optimization, 10.33omega, 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, 6.8.12, 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, 10.18, 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, 10.36.5, 10.36.6
          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

     file, 22.4.3     color, 17.4.14
     html, 4.2.1.6     columns, 17.4.6
     preparation, 21.3.11     function, 3.6.9, 3.6.9.1
     search, 4.2.1, 4.2.1.2, 4.2.1.3, 21.3.1     grid, 17.4.15
     convert, 9.20.1     header, 17.4.9
     recent, 3.6.1.18     inline, 17.4.22
     search, 3.7.4, 4.1.2     logarithmic, 17.4.12
pdbsearchfield, 3.6.2.13     mark, 17.4.13
pdbsearchhomology, 3.6.2.15     mean median iqr, 17.4.23
pdbsearchidentity, 3.6.2.14     point label, 17.4.19
pdbsearcsequence, 3.6.2.16     preferences, 4.7.8
peptide, 4.3, 9.14, 9.19, 12.6          groups, 17.4.25
     docking, 12.6     regression, 17.4.16
     modeling, 9.19     selection, 17.4.18
percentage similarity, 8.7.15, 21.4.4     zoom translate, 17.4.17
perspective, 3.6.3.9, 6.10.6     axis, 17.4.15
ph4, 10.5.6     display, 17.4.15
     draw 2d, 10.5.6.1     grid, 17.4.15
          3d, 10.5.6.2     inline, 17.4.22
     search, 10.5.6.3     logarithmic, 17.4.12
pharmacophore, 10.3.35, 10.5.6.5, 21.8.2pls, 10.20, 10.21, 11, 17.6, 21.13
     2D, 21.6.6pmf, 22.5.6
     3D, 21.6.5png, 3.6.1.14, 6.15, 6.15.2, 7.6.3, 10.2, 10.2.6
     clone, 10.5.6.2pocket, 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
     draw2D, 10.5.6.1     conservation, 22.4.12
     draw3D, 10.5.6.2     surface, 5.2.1, 13.1.10
     edit, 10.5.6.1, 10.5.6.2     peptide, 4.1.8
     move, 10.5.6.2     properties, 4.1.8
     new, 10.5.6.2pocketome, 4.2, 4.2.2
     search, 10.5.6, 10.5.6.3, 21.6.5, 21.6.6pockets, 5.6.6
phi, 6.8.5, 22.2.18point label, 17.4.19
phylogenetic, 8.7.8portait, 4.7.6
phylogeny, 8.7.8post edit ligand, 16.5.8
pi, 5.2.5     screen, 13.1.9
     cation, 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, 10.20, 10.21, 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, 10.35.4     metabolic oxidation, 15.7
     axis, 17.4.11predicting bioassays, 11.2

prediction binding, 9.12               rmsd, 5.5.2
preferences, 4.7, 13.1.5, 22.2.24, 22.2.25               surface area, 5.5.5
preferred residues, 9.5          similarity, 5.7
presentation, 7.6.5, 7.7, 7.12          tutorials, 21.3
presentations, 7               analysis, 21.3.4
preserve, 22.8.6               contact area, 21.3.5
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, 10.25protein-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, 10.25protonated, 22.4.15
profile, 4.2.10, 8.3.8protonation, 10.18, 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, 10.18
     rename, 3.6.1.9protonation_ph_charge, 10.18.2
properties, 6.8.2, 10.11, 10.11.1, 22.8.7protonation_ph_concentration, 10.18.1
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, 10.11.7
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, 10.20, 10.21, 11.1, 21.13
     sequence, 10.4.17     learn predict, 10.20
     structure, 5     predict, 10.21
          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

          single chain, 9.1.2.1     loops, 9.1.3
     start move structure, 4.1.3     side chain, 9.8
          read pdb, 4.1.2     sidechains, 9.1.3
          representation, 4.1.6refinement, 12.2.4
          selection, 4.1.5region, 12.7.7
               level, 4.6.3regression, 10.35.2, 11.1, 11.5, 17.4.16, 21.13
          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, 10.27.7, 10.34.4relaxed ligand, 16.3.9
          table, 10.34.2reload, 12.1.16, 22.5.4
     groups, 10.34.2     dock results, 12.1.16
r-group, 10.27.7, 10.34.2remove, 22.2.6, 22.2.7, 22.2.10
     decomposition, 10.27.7     salt, 22.8.14
     enumeration, 10.27.7     explixit.hydrogens, 10.12
r-groups, 17.4.25     salt, 10.12
racemic, 10.3.28, 10.19.5, 22.5.21rename, 17.1.25
radar, 17.4.6     column, 17.1.25
rainbow, 4.7.5, 6.8.16, 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, 10.34.5representation, 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, 10.34.5resize, 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, 10.34.4
refine, 9.7, 9.8ribbon, 3.7.1, 4.7.9, 6.1.3, 22.2.23, 22.2.34

     faq, 22.2.23     racemic centers, 12.1.6
     preferences, 4.7.9sar, 10.27.7, 10.35, 17.4.25
     style, 4.7.9     analysis, 10.35
     breaks, 6.1.3     table, 10.35.3
     cylinders, 6.1.3save, 4.5, 6.3.11, 6.10.7.4, 8.1.5, 10.2.3, 17.4.21, 17.7.3, 22.2.33
     smooth, 6.1.3     SMILES, 10.4.15
     worm, 6.1.3     alignment, 8.7.3
ribbonColorStyle, 4.7.9          PDB, 4.5
ride, 13.4          pdb, 4.5
     gpu benchmark, 13.4.1.2     chemical mol, 10.4.13
     server setup, 13.4.1.1          spreadsheet workspace, 10.2.1
     setup, 13.4.1          to chemical spreadsheet, 10.4.14
right, 4.1.12     docked ligand, 16.18
     click, 4.1.12     file, 4.5
rigid, 10.36     hits, 16.5.7
     substructure superposition to template, 10.36.2     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, 10.22, 10.36     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, 6.8.16scan, 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, 10.35.5     browse export data, 19.4
     bridge, 21.3.6     installation, 19.1
salts, 10.3.18     new project, 19.6
sample, 9.18, 10.36     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

scatterplot, 13.1.9.4selecting.neighbors, 4.6.16
score, 12.1.13.1, 13.1.8, 16.4, 21.8.3, 21.8.5, 22.5.7, 22.5.8, 22.5.18selection, 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
     threshold, 13.1.4     clear, 3.6.2.7
screen, 10.37, 21.8.4, 21.9, 21.11.1     neighbors, 3.6.2.8
screening, 13.1, 13.1.1, 13.1.2, 21.12     alignment, 4.6.19
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, 10.19.1, 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, 10.32selections, 4.6
     molecule, 4.6.12     links, 8.3.9
     neighbors, 4.6.15selectneighbors workspace, 4.6.17
          graphic, 4.6.16     organized network, 10.29
     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

     amino acid, 8.3.4simulations, 22.7
     nucleotide, 8.3.4single, 10.4.10
     protein, 8.3.4     chain, 9.1.2.1
     search, 8.4singlet, 10.4.7
     structure.alignment, 8.3.6, 8.6.3sites, 5.4.6
sequences, 8, 22.2.25size, 5.2.3.1
     unique, 8.3.13sketch accents, 6.10.3
     extract, 8.3.13     markush, 10.34.1
     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, 10.19, 10.19.3, 10.19.4
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, 10.35.1
side-chain sampling, 12.7.11spreadsheet, 10.19.2
side-chains, 12.2.1square, 22.4.7
sigmaLevel, 5.3.6, 5.3.7stability, 9.13, 21.5.3, 21.5.4
similarity, 10.30stack, 9.18, 9.20.18, 12.1.12, 12.7.10, 22.9.8
simulation, 14, 22.9.8stacking, 5.2.5
     length, 22.5.12stacks, 9.20.18

standard table, 17.1symmetric oligomer, 9.1.3
standardize, 10.12symmetry, 5.3.1, 5.3.3, 21.3.8, 21.3.9
     table, 10.12synthesize, 10.11.5
start, 10.10.2synthetic feasibility, 10.11.5
     dock, 12.1system preferences, 4.7.11
startup, 22.10.2tab, 17.1.2, 17.1.21
static, 22.4.8     pdb, 3.7.4
stereo, 4.7.6, 6.6, 10.3.28, 10.4.2, 22.1, 22.1.6, 22.1.7, 22.1.14table, 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, 10.19.2, 10.22, 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
     bond, 10.4.2     alignment, 17.1.12
     hardware, 3.6.3.7     clone, 17.1.16
     side-by-side, 3.6.3.6     color, 17.1.10
stereohard faq, 22.1.6     column format, 17.1.40
stereoisomer, 10.19.5     copy, 17.1.36, 17.1.37
stereoisomers, 10.24     delete, 17.1.17
stick, 4.7.5     edit, 17.1.24
stl, 6.7     filter, 17.1.43
stop, 6.10.7.3     find, 17.1.9
store, 3.6.3.19, 6.10.7.4, 22.2.22          replace, 10.3.32
     current view, 3.6.3.19     font, 17.1.11
               faq, 22.2.22          size, 22.2.1
strain, 5.6.3, 10.26, 10.26.2, 12.1.1.8, 16.4     grid, 17.1.5
strip, 22.4.9     histogram, 17.4.1
structure, 5.3.3, 11, 17.6, 21.3, 22.4     insert, 17.1.26
     analysis, 21.3.4     layout, 17.1.5
     ensemble, 9.20.14     learning, 17.6
     representation, 6.1     mark, 17.1.13
     smiles, 10.19.4          row, 17.1.13
structure-based, 13     mouse, 17.1.47
structures, 10, 10.1     navigation, 17.1.4
style, 4.7.5     new column, 17.1.26
substituent, 10.9.1, 10.9.2, 10.34.2, 16.5.2     plot, 17.4
substructure, 10.10.4, 10.13, 10.36.1, 10.36.2, 12.3, 22.8.1, 22.9.5     print, 17.1.19
     template, 16.12.3     rename, 17.1.15
     alerts, 10.13     rightclick, 17.1.14
sulfur, 9.9     row height, 22.2.39
superimpose, 3.6.8, 5.4.2, 5.4.6, 10.36.4, 21.3.3, 22.2.5, 22.4.6, 22.4.7, 22.4.8     save, 17.1.3
     3D, 5.4.3          selection, 17.1.3
     Calpha, 5.4.3     search, 17.1.9
     arrange.grid, 5.4.5     select, 17.1.23
     backbone, 5.4.3     setup, 17.1.18
     heavy atoms, 5.4.3     sort, 17.1.42
     multiple, 5.4.4     split fragments, 10.3.33
superposition, 10.36, 10.36.1, 10.36.2, 10.36.5, 10.36.6, 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

     columns, 10.3.8temperature, 5.6.4
     compare, 10.3.22template, 9.1.2, 10.4.6, 10.36
     copy, 10.3.6     docking, 22.5.3
     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, 10.22, 10.36, 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, 10.19
     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, 10.31          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     analysis, 10.16
     row, 17.1.33     angles, 6.12, 6.12.6
     rows, 3.6.10.7     scan, 9.20.7
     save, 10.3.9, 17.1.3, 17.1.4, 17.1.21toxscore, 10.11.3
     scale, 17.1.18trace, 6.1.10
     scroll, 17.1.4transition.blend, 22.2.31
     sdf, 10.3.9transitions, 7, 22.2.30
     select, 17.1.23translate, 4.1.3, 6, 6.12, 10.3.30
     setup, 17.1.18translation, 6.12.3, 8.3.3, 17.4.17
     sort, 3.6.10.4, 10.3.5, 17.1.42transparent, 6.3.9.3
     standard, 17.1     background, 6.15.3
     view, 10.3.29     ribbon, 22.2.3
     width, 17.1.4     surface, 22.2.37
tables, 10.30, 17tree, 8.7.8, 10.27.7, 17.7.2, 17.7.3, 17.7.4
tag, 4.6.21, 16.5.7, 17.1.46     branch swapping, 8.7.8
tags, 4.6.21     distance, 10.27.3
tautomer, 10.23, 22.4.15     edit, 10.27.4
tautomers, 10.23     reorder, 10.27.3

trouble shooting, 22.1.11     large sdf files, 10.1.2
trouble-shooting, 22.1.12vicinity, 10.22
truncating a mesh object, 22.2.15video, 2, 6.16, 6.16.1, 6.16.2
     crash qlock, 22.1.13view, 3.6.3.19, 7.3.1, 10.3.28, 22.2.22, 22.9.8
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, 10.29
     box shade font, 8.7.7.1     apf fields, 16.3.11
undisplay-all, 3.6.3.1     chemical space, 10.29
     origin, 6.8.12     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, 10.32     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, 6.8.15volume, 10.4.9
variable, 4.7.7, 22.2.8water, 9.20.17
verbose, 10.22waters, 9.20.17

weak, 22.4.20 
web, 21.2 
     browser, 3.6.1.12 
weight, 10.11, 22.8.7, 22.8.10 
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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