May 8 2008
Contents
 
Introduction
Overview - RECOMMENDED READING FOR NEW ICM USERS
File Menu
Graphics Move Tools
Display Tab
Light Tab
Labels Tab
PDB Search Tab
Meshes Tab
View Menu
Selections
Tables
Sequences
Bioinfo Menu
Tools Menu - Xray
Tools Menu - 3D Predict
Tools Menu - Analysis
Tools Menu - Superimpose
Homology and Modelling
Working with Chemistry Tools
Chemsitry Menu
Docking
Animations, Slides, & Documents
Movie Making
Frequently Asked Questions
Tutorial - Graphical Display
Molecular Document
Tutorial - Working with PDB Protein Structures
Tutorial - Working with Sequence Alignments
Tutorial - Ligand Binding Pocket Analysis
Tutorial - Homology and Modeling Tools
Tutorial - Crystallographic Analysis Tools
Tutorial - Working with Chemical Tables
Tutorial - Working with the Molecular Editor
Tutorial - Chemical Searching
Tutorial - Docking and Virtual Ligand Screening
 
Index

Index

2D, 2.16.5, 2.16.6, 7.1, 20.2.2, 20.2.7, 21.5, 21.6, 21.7, 21.13, 26.8.4     displayLineLabels, 3.9.7
     3d labels, 26.8.4     displayMapBox, 3.9.3
     depiction, 21.7     distance Label Drag, 3.9.1
3D, 2.16.5, 2.16.6, 7.1, 20.2.2, 20.2.7, 20.2.10, 21.7, 26.8.4     dnaBallRadius, 3.9.9
     browse, 2.16.13     dnaRibbonRatio, 3.9.9
     graphics.main, 2.12     dnaRibbonWidth, 3.9.9
3Dlabel, 3.1.12     dnaRibbonWorm, 3.9.9
3d, 3.1.12     dnaStickRadius, 3.9.9
4D, 36.6     dnaWormRadius, 3.9.9
64, 25.1.2     font Scale, 3.9.7
APF, 21.22.5     fontColor, 3.9.7
     template, 21.22.4     fontLineSpacing, 3.9.7
Area, 25.3.27     grobLineWidth, 3.9.3
Atom Single Style, 3.9.3     hbond Ball Period, 3.9.1
Bad Groups, 25.6.12, 25.6.15               Style, 3.9.1
Beep, 3.9.11     hbondAngleSharpness, 3.9.1
Binding pocket, 2.13.8     hbondMinStrength, 3.9.1
Blast, 25.3.26     hbondStyle, 3.9.1
BlastDB Directory, 3.9.2     hbondWidth, 3.9.1
     alphas, 5.5.2     hetatmZoom, 3.9.1
CPK, 5, 5.2     hydrogenDisplay, 3.9.1
Clash Threshold, 3.9.10     light, 3.9.3
DNA, 3.1.4, 13, 14.3     lightPosition, 3.9.3
Display, 25.3.27     mapLineWidth, 3.9.3
Dock Directory, 3.9.2     occupancy Radius Ratio, 3.9.3
Docking, 25.3.27     occupancyDisplay, 3.9.3
Editor, 3.9.2     quality, 3.9.3
FILTER.Z, 3.9.2     rainbow Bar Style, 3.9.4
     gz, 3.9.2     resLabelDrag, 3.9.7
     uue, 3.9.2     resize Keep Scale, 3.9.3
FTP.createFile, 3.9.11     ribbonRatio, 3.9.9
     keep File, 3.9.11     ribbonWidth, 3.9.9
     proxy, 3.9.11     ribbonWorm, 3.9.9
Filter.zip, 3.9.2     rocking, 3.9.4
Force Auto Bond Typing, 3.9.11          Range, 3.9.4
Formula, 25.6.12, 25.6.15          Speed, 3.9.4
Frequently Asked Questions, 25     selectionStyle, 3.9.3
GIF, 3.8, 24, 24.1     site Label Drag, 3.9.7
GRAPHIC.store Display, 3.9.3               Shift, 3.9.7
     NtoC Rainbow, 3.9.4     siteArrow, 3.9.7
     alignment Rainbow, 3.9.4     stereoMode, 3.9.3
     atomLabelShift, 3.9.7     stickRadius, 3.9.1
     ballStickRatio, 3.9.1     surfaceDotDensity, 3.9.3
     center Follows Clipping, 3.9.3     surfaceDotSize, 3.9.3
     clash Style, 3.9.3     surfaceProbeRadius, 3.9.3
     clashWidth, 3.9.3     transparency, 3.9.3
     clip Grobs, 3.9.3     wire Width, 3.9.1
          Skin, 3.9.3     wormRadius, 3.9.9
          Static, 3.9.3     xstick Backbone Ratio, 3.9.1
     discrete Rainbow, 3.9.4          Hydrogen Ratio, 3.9.1
          Vw Ratio, 3.9.1LogP, 12.5
GROB.arrowRadius, 3.9.3LogS, 12.5
     atomSphereRadius, 3.9.3MOL, 12.2, 20, 20.1.1, 20.2.1, 20.2.2, 20.2.3, 20.2.4, 20.2.5, 22.4.3
     contourSigmaIncrement, 3.9.3MOL2, 20.1.1, 22.4.3
     relArrow Size, 3.9.3MOVIE.frame Grab Mode, 3.9.4
     relArrowHead, 3.9.3MW, 33.2, 33.4, 33.5, 33.6
GUI, 1Map Atom Margin, 3.9.10
     Overview, 2     Sigma Level, 3.9.10
     auto Save, 3.9.4     File Size Mb, 3.9.11
               Interval, 3.9.4Max_Fused_Rings, 21.1
     enumberation Memory Limit, 3.9.11Mnconf, 3.9.10
     max Nof Recent Files, 3.9.11MolIPSA, 2.16.6, 25.6.12, 25.6.15
          Sequence Length, 3.9.4MolLogP, 2.16.6, 25.6.12, 25.6.15
     splash Screen Delay, 3.9.11MolLogS, 2.16.6, 25.6.12, 25.6.15
               Image, 3.9.11MolPSA, 21.1, 33.2, 33.4, 33.5, 33.6
     table Row Mark Colors, 3.9.4MolVol, 21.1
     workspace Folder Style, 3.9.4Molcart, 21.23.2
     workspaceTabStyle, 3.9.4MoldHf, 2.16.6, 21.1, 25.6.12, 25.6.15
HBA, 2.16.6, 25.6.12, 25.6.15Molecular Document, 27
HBD, 2.16.6, 25.6.12, 25.6.15Movie.fade Nof Frames, 3.9.4
HTTP.proxy, 3.9.11     quality, 3.9.4
     support Cookies, 3.9.11          Auto, 3.9.4
     user Agent, 3.9.11NCBI, 25.3.26
Html, 8.6.2NMR, 8.1
Http Read Style, 3.9.11Nof_Atoms, 21.1
Hydrogen.bond, 3.9.5Nof_Chirals, 21.1
ICM, 1Nof_HBA, 21.1
     graphics crash, 25.9.1Nof_HBD, 21.1
IMAGE.bondLength2D, 3.9.6Nof_Rings, 21.1
     color, 3.9.6Nof_RotBonds, 21.1
     compress, 3.9.6Nvidia GL failutre, 25.9.1
     gammaCorrection, 3.9.6ODA, 25.3.27
     generateAlpha, 3.9.6Optimal, 25.3.27
     lineWidth, 3.9.6Output Directory, 3.9.2
     lineWidth2D, 3.9.6PBS, 22.4.6
     orientation, 3.9.6PCA, 12.5.3
     paper Size, 3.9.6PDB, 8.2, 8.6.1, 8.6.2, 8.7, 13.1, 15.3
     previewResolution, 3.9.6     Directory, 3.9.2
     previewer, 3.9.6          Style, 3.9.2
     print, 3.9.6     convert, 8.7, 28.2
     printerDPI, 3.9.6     pattern, 8.4
     scale, 3.9.6     query, 8.3, 8.4
     stereoAngle, 3.9.6     search, 8.1, 8.3, 8.4, 8.5, 8.6, 28.1
     stereoBase, 3.9.6     sensitive search, 8.5
     stereoText, 3.9.6     sequence, 8.4
ISIS, 25.6.8     similarity, 8.5
Icm Prompt, 3.9.10PFAM, 3.4
Inx Directory, 3.9.2PLOT.Yratio, 3.9.8
JPEG, 3.8     color, 3.9.8
Log Directory, 3.9.2     date, 3.9.8
     font, 3.9.8     phone, 3.9.11
     fontSize, 3.9.8VLS, 22.4, 22.4.1, 22.4.2, 22.4.6, 22.4.10
     labelFont, 3.9.8     preferences, 22.4.4
     lineWidth, 3.9.8Var Label Style, 3.9.7
     logo, 3.9.8Volume, 2.16.6, 25.6.12, 25.6.15
     markSize, 3.9.8Water Radius, 3.9.10
     orientation, 3.9.8Wire Style, 3.9.1
     paper Size, 3.9.8X-ray, 8.1, 22.1.1
     previewer, 3.9.8XPDB Directory, 3.9.2
     rainbowStyle, 3.9.8Xstick, 5, 5.2
     seriesLabels, 3.9.8a-bright, 6
PLS, 12.5.1acceptor, 20.3.5
PNG, 2.13.7, 3.8, 24, 24.1acid, 3.1.4
Projects Directory, 3.9.2activityy, 12.5
Prosite Dat, 3.9.2adding fragment, 20.3.4
Protein, 25.3.27          in editor, 20.3.4
     Viewer, 3.9.2administration, 21.27.4
QSAR, 12.5, 12.5.1advanced alignment selectioection, 13.2.18
R, 21.20, 21.26alias, 20.3.3
R-group, 21.25align, 2.13.2, 13.2.1, 21.13, 29.1
RMSD, 5.8     color 2D scaffold, 21.13
Ramachandran Plot, 17.8     dna protein, 13.2.3
Real Format, 3.9.10     multiple sequences, 13.2.4
Receptor Setup, 22.1.5     two sequences, 13.2.2
     Label Shift, 3.9.7     DNA to protein, 13.2.3, 14.7
          Style, 3.9.7     annotate, 29.4
RotB, 2.16.6, 25.6.12, 25.6.15     box, 29.4
SAR, 12.5     multiple, 13.2.4, 29.3
SCORE, 25.5.7, 25.5.18     sequence, 13.2, 13.2.5
SDF, 12.2, 20, 20.1.1, 20.2.2, 20.2.3, 20.2.4, 20.2.5, 22.4.3     shade, 29.4
SEQUENCE.site Colors, 3.9.4     two sequences, 13.2.2, 14.5
SITE.label Style, 3.9.7alignment, 2.14.5, 25.4.12, 30, 30.2
     labelOffset, 3.9.7     comment, 13.2.9
     wrap Comment, 3.9.7     editing, 13.2.7
SLIDE.ignore Background Color, 3.9.4     editor, 13.2.6
          Fog, 3.9.4     font size, 25.3.1
SMILES, 20.4.2     format, 13.2.14
SVM, 12.5.1     gaps, 13.2.14
     kernels, 12.5.3     introduction, 13.2.1
Select Min Grad, 3.9.10     reorder, 14.12
Show Res Code In Selection, 3.9.7     search, 13.2.15
Smiles, 2.16.6, 25.6.12, 25.6.15     selection, 13.2.16
Swissprot, 3.4     view options, 13.2.13
     Dat, 3.9.2     box, 13.2.12
Temp Directory, 3.9.2     color, 13.2.11, 13.2.12
UNIX, 22.4.6     comment, 13.2.9
USER.email, 3.9.11     consensus, 13.2.11, 13.2.18
     friends, 3.9.11     cut, 14.11
     full Name, 3.9.11     delete, 13.2.8
     organization, 3.9.11     display title, 13.2.13
     extract, 14.10atom, 3.9.5, 20.2.7, 25.3.4, 25.3.5, 25.3.8, 25.3.15, 25.3.16, 25.4.10, 26.2.1, 26.3, 26.8, 26.8.2
     gaps, 13.2.14     label, 26.8.2
     linked, 31.1.1     charge, 25.4.21
     multiple, 14.8atomLabelStyle, 3.9.7
     options, 13.2.13attachment, 20.3.2, 21.23.1
     print, 13.2.8     point, 21.19
     rename, 13.2.13autofit, 22.5
     reorder, 14.12ave, 12.6
     ruler, 13.2.13avi, 24, 24.1, 24.2
     save, 13.2.8axes, 12.3.7
     search, 13.2.15axis, 12.3.4
     selection, 13.2.16, 13.2.17, 13.2.18b-factor, 16.3, 22.1.1, 28.4
     sequence offset, 13.2.13backbone, 25.3.12
     shade, 13.2.12background, 5.4.1, 26.7.1
     table, 13.2.13     color shortcut, 25.3.2
     view, 13.2.13     jobs, 2.12
alignments, 2.14, 13.2, 29bad, 21.1
     main, 2.12     groups, 2.16.6
alpha, 6     groups, 20.3.5
     channel, 3.9.6ball, 3.9.5
ambient, 6     and stick, 5, 5.2
amino, 3.1.4bank, 8.1
analysis, 14basic alignment selection, 13.2.17
angle, 4.2.6, 5.5.4, 17.6, 17.7, 25.3.17, 25.4.16basicsel, 11.1.2
angstrom, 2.15.9, 25.4.7batch, 22.1.10, 22.4.6, 22.6.8
animate, 10.14begin docking simulation, 22.1.8
     view, 10.14best, 20.2.13
animation, 23.1, 23.1.1, 23.1.2, 23.1.3, 23.1.4binding, 2.15.7, 25.3.13, 25.5.2, 25.5.11
     store, 23.1.4     pocket, 30
animations, 23bioinfo align dna protein, 14.7
annotate, 26.8.3          multiple, 14.8
annotation, 26, 26.8, 26.8.3          two sequences, 14.5
antialias, 3.8, 10.10     links, 14.9
     lines, 10.16     secondary structure, 14.2
     lines, 10.16     translation, 14.3
apf super, 21.22.4biological, 15.3
     alignment, 21.22.5biomolecule, 15, 15.3, 32, 32.2
applying prediction models, 12.5.2bit, 25.1.2
area, 16.4, 17.2, 22.6, 22.6.1, 22.6.2blast, 14.14
aromatic, 20.2.7boat, 25.5.20
arrange, 2.13.5bond, 2.15.3, 2.15.8, 2.16.6, 19.7, 20.3.6, 25.4.1, 25.6.12, 25.6.15, 30.3
     window, 2.13.5     covalent, 25.4.2
arrow, 3.1.5, 3.1.9, 26.8.3     type, 2.15.4, 2.15.5, 21.8.1, 21.8.2, 21.8.3
     graph, 25.3.8bonding, 5.3
as_graph, 25.3.8     preferences, 3.9.1
asn, 8.7.1box, 3.1.5, 3.1.10, 3.9.7, 25.5.10
assign, 5.2.3bpmc, 31.2
     2D coordinates, 21.7branch, 2.16.12
     helices, 16.1browse, 20.2.10, 22.1.12
     strands, 16.1     mode, 20.2.10
build, 2.16.1, 23.1.1     clustering, 21.14
     homology model, 19.2     convert, 2.15.3, 2.15.4, 2.15.5, 21.8, 21.8.1, 21.8.2, 21.8.3, 25.4.1
bye, 3.12     display, 33.1, 33.2, 33.3, 33.4, 33.5, 33.6
calculate, 2.15.9, 25.5.2     draw, 20.3.1, 34.1
     properties, 21.1     edit, 20.3.8, 34.2
     startup, 25.8.2     editor, 20.4, 20.4.1, 20.4.2, 20.4.3, 20.4.4
carbon, 25.3.4, 25.3.5     load, 20.1, 20.1.1
cartesian, 21.9     merge, 21.16
cavities.closed, 17.3     new, 20.3.1
ccp4, 25.3.28, 25.3.29     query, 20.3.2, 21.23.1, 21.23.2
cell, 15.2          results, 21.23.3
center, 2.2, 4.2, 4.2.5, 10.19, 12.1.26     read, 20.1, 20.1.1, 33.1, 33.2, 33.3, 33.4, 33.5, 33.6
centers, 2.16.12     redo, 20.3.11
     and representative members, 12.6.1     save, 20.3.7, 20.4, 20.4.1, 20.4.2, 20.4.3, 20.4.4
chair, 25.5.20     search, 20.3.2, 21.23, 21.23.1, 21.23.2, 21.23.3, 35.1, 35.2
chair-boat, 25.5.3     similarity, 20.3.2, 21.23, 21.23.1, 21.23.2, 21.23.3, 35.1, 35.2
change, 2.16.7, 2.16.8, 2.16.11     smiles, 20.1.2
     selection, 11.1.3     spreadsheet, 20.2, 20.4, 20.4.1, 20.4.2, 20.4.3, 20.4.4, 33.2, 33.4, 33.5, 33.6
     speed range, 23.1.2     structure, 20.1.1, 20.3.7, 20.3.8
changing font in alignment editor, 13.2.6     substructure, 35.2
charge, 2.15.3, 2.15.4, 2.15.5, 5.5.1, 20.3.2, 21.8.1, 21.8.2, 21.8.3, 21.23.1, 25.4.1     superimpose, 21.22.1, 21.22.2, 21.22.3
chem convert, 25.6.10     superposition, 21.22.4, 21.22.5
     save, 20.4     table, 12.2, 20.2, 33.2, 33.4, 33.5, 33.6, 34.1, 34.2
          editor, 20.4.2     undo, 20.3.11
          image, 20.4.4chemicals, 2.16
          table, 20.4.1cheminformatics, 2.16, 20.2, 25.6
          workspace, 20.4.3chemistry, 21.10, 25.6
     super, 21.22     menu, 21
     view, 20.2.7     smiles, 21.5
chemical, 2.16.1, 2.16.2, 2.16.3, 2.16.4, 2.16.5, 2.16.6, 2.16.7, 2.16.8, 2.16.9, 2.16.10, 2.16.11, 2.16.12, 12.6, 20, 20.2.6, 20.2.7, 20.2.9, 20.2.10, 20.2.13, 20.2.14, 20.3.6, 21.7, 21.10, 21.19, 21.21, 21.22, 21.26, 21.27.3, 25.6.9, 25.6.10, 25.6.12, 25.6.13, 25.6.14, 25.6.15     duplicates, 21.18
     browse, 2.16.13     remove.redundant, 21.18
     clustering, 21.14chemlib.so, 25.1.2
     dictionary, 20.3.3chi, 5.5.4, 25.3.17
     draw load, 20.1chiral, 21.12
     editor, 20.3, 20.3.4chirality, 21.12
          not starting, 25.9.3clash, 3.9.5, 5.9
     find replace, 21.25classes, 20.2.7
     fragments, 20.2.12clear display and planes, 10.2
     group, 20.3.3     planes, 10.2
     groups, 20.3.3, 20.3.4click, 2.13.3, 4.1, 4.2, 12.1.9
     right click, 20.3.2clip, 9.2.4, 10.23, 25.3.10
     search, 21.23clipboard, 12.6.2
     smiles, 20.1.2clipping, 25.3.20
     spreadsheets, 20.2, 33     planes, 2.13.1, 4
     structure, 20     tool, 10.22
     table display, 20.2.1     tools, 10.22
     tables, 12.2, 33closed cavities, 16.5, 17.3
     2D, 21.8cluster, 2.16.12, 12.6, 22.4.6
     3D, 21.8clustering, 12.5.4
     append, 20.3.7color, 5.4, 5.5.1, 5.5.2, 12.1.29, 12.6.3, 16.2, 20.2.14, 21.13, 25.3.4, 25.3.5, 25.3.15, 25.3.21, 26, 26.7, 26.7.1, 30
     background, 5.4.1converting pdb, 8.7
     chemical, 20.2.14copy, 12.1.21, 20.2.3, 20.3.12, 21.24.2
     display mesh, 9.2.3     cell, 12.1.22
     faq, 25.3.21     chemical, 20.2.3
     table, 20.2.5     paste row, 12.1.21
     background, 5.4.1, 10.17          structure, 20.3.10
     mesh, 9.2.3     row, 12.1.22
     table, 20.2.5     selection to table, 12.1.23
coloring, 5.4cpk, 5.2.5, 25.3.22, 26.7.2
column, 12, 12.1.15, 12.1.25, 12.1.26, 12.3, 12.3.1, 25.6.12, 33.2, 33.4, 33.5, 33.6creat, 23.3.1, 23.3.2
     row width, 12.1.15     molecular document, 23.3.1
     statistics, 12.1.19cross, 25.3.9
     filter, 33.5, 33.6     section, 10.22
     rename, 33.6crystal, 15.2
combo display style, 3.9.9crystallographic, 32.1
command, 25.5.17     analysis tools, 32
commands, 3.1.6, 25.8.1     cell, 15.2
compare, 20.2.8, 21.15, 21.16     cell, 15
     tables, 21.15     neigbor, 15.1
compound, 2.16, 12.2, 21.10     neighbors, 15
compounds, 25.6.3crystallography, 15.4, 15.6, 15.7, 25.3.28, 25.3.29
compress, 3.9.6csv, 12.1.2, 12.1.3, 12.1.14
conf gen, 21.9current, 25.3.23
conformation, 21.9, 22.2.2custom, 4.2, 20.2.1, 21.22
conformations, 25.7.2     label, 7.1
conformers, 21.9     rotation, 4.2.2
connect, 4.2, 4.2.7, 9.2.2cut, 12.1.21
     object, 4.2.7     vertical alignment block, 14.11
connectivity, 20.3.2, 21.23.1damaged skin, 25.9.2
conservation, 30dash, 25.3.11
construct, 3.1, 3.1.1, 3.1.5, 23.1.1data, 8.1
     DNA, 3.1.3databank, 2.15.1
     RNA, 3.1.3database, 14.14, 21.19, 21.27, 22.1.2, 22.4.3, 22.4.5
     chemical, 3.1.2     file format, 22.4.3
     compound, 3.1.2     seach and alignment, 14.14
     molecule, 3.1databases, 25.6.3
     nucleic, 3.1.4decomposition, 21.19, 21.20
     object, 3.1default, 2.13.4
     protein, 3.1.4delete, 25.4.9
     sequence, 3.1.4     column row, 12.1.24
contact, 17.2     label, 7.1.1
     areads, 17.2     column, 12.1.24
contour, 15.6, 15.7     label, 7.1.1
     map, 15.6     row, 12.1.24
convert, 2.15.2, 2.16.5, 8.7, 21.11, 25.6.10density, 15.4, 15.6, 15.7, 25.3.28, 25.3.29
     chemical, 20.2.2deselect, 25.3.7
          2D 3D, 21.8deviation, 25.4.7
     pdb chem, 21.8.1dialog, 23.3.5
     smiles, 21.5, 21.6diffuse, 6
convert2grid, 15.7dihedral, 5.5.4, 17.7, 25.3.17
directories preferences, 3.9.2     interactive, 22.1.9
directory, 3.9     maps, 22.1.7
disappearing labels, 25.9.2     preparation, 22.1.3
display, 2.6, 2.13.5, 2.15.8, 3.9, 5.9, 20.2.6, 21.12, 25.3.4, 25.3.5, 25.3.8, 25.3.9, 25.3.10, 25.3.16, 25.3.22, 25.3.31, 25.4.10, 25.4.11, 25.4.20, 25.6.9, 26.2, 30.1, 30.3     procedure, 22.1.8
     chemical, 20.2.6     project name, 22.1.4
     distance restraints, 5.7     rank, 22.1.14
     hydrogen, 5.1     receptor setup, 22.1.5
     mesh, 9.2     results, 22.1.11, 22.1.12, 22.1.13, 22.1.14
     structure, 2.7     sampling, 25.5.20
     tab, 5, 25.3.15     score, 22.1.14
     tether, 5.6     stack, 22.1.13
     CPK, 5.2.5     template, 22.3
     alignment, 2.12document, 3.1.7, 23.3.4, 23.3.5, 26
     chemical, 20.2.1     navigation, 23.3.6
     distance, 5.7documents, 25.3.19
     html, 2.12dollar, 25.8.3
     hydrogen, 5.1donator, 20.3.5
          polar, 5.1     envelope, 5, 5.2
     macroshape, 9.2.1     surface, 3.9.5
     meshes, 9.2double, 20.3.6
          and display.macroshape, 9download, 1.3, 25.6.3
     molecule, 20.2.2drag, 2.13.2, 2.14.5, 3.9.7, 5.5.2, 13.2.5, 23.3.4, 25.4.5, 29.2
     origin, 7.3     and drop sequences, 13.2.5
     representations, 5, 5.2     residue label, 10.15
     restraints, 5.7draganddrop, 2.13.2
     ribbon, 5.2.3draw, 20.3.12, 21.21, 25.6.7
     skin, 5.2.4     chemical, 20.3.1
     surface, 5.2.6, 9.1drop, 2.13.2, 2.14.5, 13.2.5, 23.3.4, 25.4.5, 29.2
     surfaces, 9drug, 21.1, 25.6.12, 25.6.14
     table, 2.12, 20.2.1druglikeness, 20.3.5
     tethers, 5.6easy, 2.13.8
     wire, 5.2.1     rotate, 10.12
     xstick, 5.2.2edit, 2.16.7, 2.16.8, 2.16.11, 25.6.8
distance, 2.15.9, 7.2, 17.5, 21.15, 25.3.11, 25.4.8, 25.4.10     alignment, 13.2.7
     faq, 25.4.10     chemical, 20.3.8
     label, 3.9.7          moledit, 20.2.4
distances, 7     molecular document, 23.3.2
disulfide, 19.7     molecule, 20.3
diverse set, 12.5.4     movie, 24.3.7
dock, 22, 22.1, 22.1.2, 22.5, 25.5.3, 25.5.4, 25.5.5, 25.5.6, 25.5.8, 25.5.9, 25.5.11, 25.5.12, 25.5.13, 25.5.14, 25.5.15, 25.5.16, 25.5.17, 36.3, 36.4, 36.6     slide description, 23.2.3
     command, 25.5.17     table row, 12.1.17
docking, 2.15.2, 16.4, 22, 22.1.3, 22.1.15, 22.2, 22.2.1, 22.2.2, 22.4, 22.4.1, 22.4.2, 22.4.5, 22.6, 22.6.1, 22.6.2, 22.6.3, 22.6.4, 22.6.5, 22.6.7, 22.6.8, 22.6.9, 25.5, 25.5.1, 25.5.10, 25.5.18, 25.5.19, 36, 36.1, 36.2, 36.5     molecule, 20.2.4
     start, 22.1.3     movie, 24.3.7
     template, 22.3     structure, 20.2.4
     adjust, 22.1.6editor, 2.16.1, 2.16.2, 2.16.7, 2.16.8, 2.16.11, 25.4.12, 30.2
     batch, 22.1.10eds, 15.4, 15.6, 15.7
     binding, 22.1.6electron, 15.4, 15.6, 15.7, 25.3.28, 25.3.29
     conformations, 25.5.20     denisty map, 15.5
     flexible.rings, 25.5.20     densitry map.contour, 15
     hitlist, 22.1.14          map, 15, 22.5
electrostatics, 22.6.7     gui, 25.3
element, 20.3.6     guided dock, 25.5.4
energy, 2.15.2, 5.9, 16.2, 22.1.13, 25.3.19, 25.5.1, 25.5.2, 25.7.2     hardware, 25.2
     mesh, 25.3.19     hitlist, 25.5.8
enumeration, 21.19     iSee, 25.3.31
eps, 20.4.4     icmPocketFinder, 25.5.11
epsilon, 25.4.15     insert column, 25.6.12
errno, 25.1.2     installation, 25.1
error, 25.1.2     interactions, 25.3.11
escaping, 2.13.1     ligandbox, 25.5.10
exact, 21.15     merge, 25.4.5
exit, 3.12     molcart 64bit, 25.1.2
explicit, 20.2.7, 22.2.1          query, 25.6.6
     flex, 22.2.1          sdf, 25.6.4
extract, 2.14.4, 2.16.4, 13.1, 25.4.12, 25.6.13, 30.2          text search, 25.6.16
     icb, 3.3     molecule c, 25.3.5
     sub alignment, 14.10     moledit, 25.6.7
     icb, 3.3     movie planes, 25.3.20
faq, 25, 25.2, 25.3, 25.3.12, 25.4, 25.5, 25.7, 25.8, 25.8.2     newscript, 25.8.1
     ISISdraw, 25.6.8     nmr, 25.4.18
     atom charge, 25.4.21     nvidia error, 25.1.1
          display, 25.3.16     origin, 25.3.9
     backbone, 25.3.12     pmf score, 25.5.7
     background color, 25.3.2     pockets, 25.3.13
     binding energy, 25.5.2     preserve coordinates, 25.6.11
     change torsion, 25.4.16     receptor selection, 25.5.15
     chem table display, 25.6.9     reload dock, 25.5.5
     chemical monitor, 25.6.15     remove select, 25.3.6
          query2, 25.6.5     renumber, 25.4.4
     cheminformatics, 25.6     ringflex dock, 25.5.3
     clipping plane, 25.3.10     rmsd, 25.4.7
     color carbon, 25.3.4     rmsdtips, 25.4.8
          skin, 25.3.15     scanScoreExternal, 25.5.18
     convert chemical from pdb, 25.4.1     scanScoreExternal2, 25.5.19
     covalent bond, 25.4.2     score, 25.5.9
     delete, 25.4.9     script, 25.8
     deselect, 25.3.7     sgi, 25.1.3
     dihedral, 25.3.17     simulations, 25.7
     dock probe, 25.5.14     solvent accessible surface table, 25.4.19
          repeat, 25.5.6     ss, 25.4.17
     docking, 25.5     structure, 25.4
     docktime, 25.5.12     superimpose, 25.4.6
     dollar, 25.8.3     thoroughness, 25.5.13
     druglikeness, 25.6.14     transparent ribbon, 25.3.3
     energy, 25.5.1     truncate mesh, 25.3.14
     extract ligand, 25.6.13     view stack, 25.7.2
     flexible dock, 25.5.16     weak hydrogen bonds, 25.4.20
          ring docking, 25.5.20     write pdb, 25.4.3
     font size, 25.3.1faqcontour, 25.3.29
     gl failure, 25.9.1faqhbondstrength, 25.3.30
faqoda, 25.3.27graphics, 26.7
faqstereo, 25.9.4     card, 25.1.1
fasta, 2.14, 2.14.2     controls, 4
features, 1.2     defects, 25.9.2
file, 3.2, 8.6.1     preferences, 3.9.3
     load, 3.4     tips, 2.13.1
     menu, 3     shadow, 10.13
     quick image, 3.7grid, 20.2.1, 21.22, 25.6.9, 36.6
     icb, 2.11grob, 3.9.5, 15.4, 15.6, 15.7
     recent, 3.10group, 21.20
filter, 25.3.4groups, 21.1, 21.2, 21.26
     selection, 11.1.4gui, 3.9.4
          tut, 26.5     preferences, 3.9.4
find, 8.2     overview, 2
     chemical, 20.2.11guided docking, 25.5.4
     pdb, 8.2h, 25.3.19
finding dihedral angle, 17.7h-bond, 2.15.8, 25.3.11, 25.3.19, 30.3
     planar angle, 17.6hardware, 25.2
fingerprint, 25.6.5, 25.6.6     stereo, 10.7
fit, 20.2.13, 22.5, 25.5.16hbond, 25.3.30
fitting, 12.3.8, 22.5     strength, 25.3.30
flex super, 21.22.3header, 8.6.2, 12.3.3
flexibility, 16.3health, 16.2, 31.3
flexible, 21.22, 22.2, 22.2.1, 22.2.2, 25.5.16, 36.6helices strands, 16.1
     rings, 25.5.3helix, 25.3.21
fog, 4, 10.5hetero, 20.2.7
font, 3.9, 3.9.7, 5.5.1, 5.5.2, 12.1.26, 12.6.3, 20.2.7hidden block format, 13.2.14
     preferences, 3.9.7          width, 13.2.14
     size, 13.2.6, 25.3.1hide, 12.1.25
foreground, 26.7.1high, 3.8
formal, 2.15.3, 25.4.21     quality, 10.11
format, 12.1.26hints, 2.13
formula, 2.16.6, 20.3.5, 21.1his, 8.7.1, 25.4.15
fragment, 20.2.14, 21.20histidine, 25.4.15
fragments, 21.26     tautomer, 25.4.15
frame, 14.3histogram, 12.3, 12.3.1, 12.3.3, 12.3.4, 12.3.5, 12.3.6, 12.3.7, 12.3.8, 12.3.9, 12.3.10, 12.3.11, 12.3.13, 22.4.10, 22.4.11
frequency, 20.2.14hitlist, 22.1.11, 22.1.14, 22.4.8, 22.4.9, 22.4.11, 25.5.8
front, 9.2.4, 10.23homology, 19, 19.1, 19.1.1, 19.4, 19.5, 31, 31.1
full scene antialias, 10.10     loops, 19.3
     screen, 10.8     model introduction, 19.1
function, 12.1.18, 12.1.19</