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Contents
 
Introduction
Help Videos
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Molecular Dynamics
Tutorials
 
Index

Index

2D, 6.8.8     dnaRibbonWidth, 4.7.9
     Chemical Label, 6.8.11     dnaRibbonWorm, 4.7.9
     chemical label, 6.8.11     dnaStickRadius, 4.7.9
3D, 6.6, 6.8.8, 9.2     dnaWormRadius, 4.7.9
     interactive ligand editor, 3.5.5     font Scale, 4.7.7
     object, 6.3.9     fontColor, 4.7.7
     print, 6.7     fontLineSpacing, 4.7.7
     printing, 6.7     grobLineWidth, 4.7.3
     stereo, 6.6     hbond Ball Period, 4.7.1
3D_Similarity_PDB_Search, 5.6               Style, 4.7.1
4D docking, 4.2.2     hbondAngleSharpness, 4.7.1
ActiveICM, 3.4.1.12     hbondMinStrength, 4.7.1
Atom Single Style, 4.7.3     hbondStyle, 4.7.1
Beep, 4.7.11     hbondWidth, 4.7.1
BlastDB Directory, 4.7.2     hetatmZoom, 4.7.1
     alphas, 6.8.3     hydrogenDisplay, 4.7.1
COLLADA, 3.4.1.7     light, 4.7.3
CPK, 3.5.1     lightPosition, 4.7.3
ChEMBL, 4.2.3     mapLineWidth, 4.7.3
Clash Threshold, 4.7.10     occupancy Radius Ratio, 4.7.3
DNA, 4.3     occupancyDisplay, 4.7.3
Dock Directory, 4.7.2     quality, 4.7.3
Drug Bank, 4.2.8     rainbow Bar Style, 4.7.4
Editor, 4.7.2     resLabelDrag, 4.7.7
FILTER.Z, 4.7.2     resize Keep Scale, 4.7.3
     gz, 4.7.2     ribbonRatio, 4.7.9
     uue, 4.7.2     ribbonWidth, 4.7.9
FTP.createFile, 4.7.11     ribbonWorm, 4.7.9
     keep File, 4.7.11     rocking, 4.7.4
     proxy, 4.7.11          Range, 4.7.4
Filter.zip, 4.7.2          Speed, 4.7.4
Force Auto Bond Typing, 4.7.11     selectionStyle, 4.7.3
GIF, 3.4.1.15, 6.16, 6.16.2     site Label Drag, 4.7.7
GRAPHIC.store Display, 4.7.3               Shift, 4.7.7
     NtoC Rainbow, 4.7.4     siteArrow, 4.7.7
     alignment Rainbow, 4.7.4     stereoMode, 4.7.3
     atomLabelShift, 4.7.7     stickRadius, 4.7.1
     ballStickRatio, 4.7.1     surfaceDotDensity, 4.7.3
     center Follows Clipping, 4.7.3     surfaceDotSize, 4.7.3
     clash Style, 4.7.3     surfaceProbeRadius, 4.7.3
     clashWidth, 4.7.3     transparency, 4.7.3
     clip Grobs, 4.7.3     wire Width, 4.7.1
          Skin, 4.7.3     wormRadius, 4.7.9
          Static, 4.7.3     xstick Backbone Ratio, 4.7.1
     discrete Rainbow, 4.7.4          Hydrogen Ratio, 4.7.1
     displayLineLabels, 4.7.7          Style, 4.7.1
     displayMapBox, 4.7.3          Vw Ratio, 4.7.1
     distance Label Drag, 4.7.1GROB.arrowRadius, 4.7.3
     dnaBallRadius, 4.7.9     atomSphereRadius, 4.7.3
     dnaRibbonRatio, 4.7.9     contourSigmaIncrement, 4.7.3
     relArrowHead, 4.7.3          Auto, 4.7.4
GUI.auto Save, 4.7.4Output Directory, 4.7.2
               Interval, 4.7.4PDB, 4.2.1.6, 5.1.2, 5.3.3, 5.6
     enumeration Memory Limit, 4.7.11     Directory, 4.7.2
     max Nof Recent Files, 4.7.11          Style, 4.7.2
          Sequence Length, 4.7.4     Search, 3.4.2.12, 3.4.2.13, 3.4.2.14, 3.4.2.15, 3.4.2.16
     splash Screen Delay, 4.7.11          Field, 3.4.2.13
               Image, 4.7.11          Homology, 3.4.2.15
     table Row Mark Colors, 4.7.4          Identity, 3.4.2.14
     workspace Folder Style, 4.7.4          Sequence, 3.4.2.16
     workspaceTabStyle, 4.7.4     convert, 5.1.2
HTTP.proxy, 4.7.11PFAM, 3.4.1.7
     support Cookies, 4.7.11PLOT.Yratio, 4.7.8
     user Agent, 4.7.11     color, 4.7.8
How To Guide, 3     date, 4.7.8
Html, 4.2.1.6     draw Tics, 4.7.8
Http Read Style, 4.7.11     font, 4.7.8
Hydrogen.bond, 4.7.5     fontSize, 4.7.8
ICM Browser How To, 3.1     labelFont, 4.7.8
          Pro How To, 3.2     lineWidth, 4.7.8
IMAGE.bondLength2D, 4.7.6     logo, 4.7.8
     color, 4.7.6     markSize, 4.7.8
     compress, 4.7.6     orientation, 4.7.8
     gammaCorrection, 4.7.6     paper Size, 4.7.8
     generateAlpha, 4.7.6     previewer, 4.7.8
     lineWidth, 4.7.6     rainbowStyle, 4.7.8
     lineWidth2D, 4.7.6     seriesLabels, 4.7.8
     orientation, 4.7.6PNG, 3.4.1.15, 4.1.14, 6.16, 6.16.2
     paper Size, 4.7.6PowerPoint, 9.2
     previewResolution, 4.7.6Projects Directory, 4.7.2
     previewer, 4.7.6Prosite Dat, 4.7.2
     print, 4.7.6     Viewer, 4.7.2
     printerDPI, 4.7.6Pub Chem, 4.2.9
     scale, 4.7.6PubMed, 4.2.1.7
     stereoAngle, 4.7.6Pubchem, 4.2.9
     stereoBase, 4.7.6RMSD, 5.4.2
     stereoText, 4.7.6RNA, 4.3
Icm Prompt, 4.7.10Ramachandran Plot, 5.5.9
Inx Directory, 4.7.2Real Format, 4.7.10
JPEG, 3.4.1.15     Label Shift, 4.7.7
KMZ, 3.4.1.7          Style, 4.7.7
Log Directory, 4.7.2SEQUENCE.site Colors, 4.7.4
MD, 8, 8.1, 8.2, 8.3, 8.4SITE.label Style, 4.7.7
MOVIE.frame Grab Mode, 4.7.4     labelOffset, 4.7.7
Map Atom Margin, 4.7.10     wrap Comment, 4.7.7
     Sigma Level, 4.7.10SLIDE.ignore Background Color, 4.7.4
     File Size Mb, 4.7.11          Fog, 4.7.4
Mnconf, 4.7.10Select Min Grad, 4.7.10
Movie.fade Nof Frames, 4.7.4Show Res Code In Selection, 4.7.7
     quality, 4.7.4SureChEMBL, 4.2.4
     Dat, 4.7.2avi, 6.16, 6.16.2
Temp Directory, 4.7.2b-factor, 9.3.10
USER.email, 4.7.11backbone, 6.1.10
     friends, 4.7.11background, 6.4.2, 6.4.3
     full Name, 4.7.11     images activeicm, 7.15
     organization, 4.7.11     image, 6.4.3
     phone, 4.7.11backup, 3.4.2.11
Var Label Style, 4.7.7ball, 4.7.5
Water Radius, 4.7.10     and stick, 3.5.1
Wire Style, 4.7.1basicsel, 4.6.2
XPDB Directory, 4.7.2binding properties, 6.3.1
Xstick, 3.5.1bioinfo menu, 3.4.4
a-bright, 3.5.2biological, 5.3.3
active, 7.7biomolecule, 3.4.5, 5.3.3, 9.3.8, 9.3.12
activeICM, 7.8blast, 4.2.5
activeicm, 7.7, 7.12, 7.14, 7.14.1     search, 4.2.5
     advanced, 7.14bond, 5.2.3, 5.2.3.1, 5.2.3.2
     background images, 7.15bonding, 6.1.8
     control, 7.13     preferences, 4.7.1
activeicmjs, 7.16box, 4.7.7, 6.8.16
album, 6.15.3build, 6.10.7.1
align, 4.1.11buttons, 7.14
alpha, 3.5.2bye, 3.4.1.19
     channel, 4.7.6     alpha, 6.1.10
ambient, 3.5.2     trace, 6.1.10
amino acid, 4.3ca-trace, 6.1.10
anaglyph, 6.6cache, 7.14.1
analysis, 3.4.4cation, 5.2.5
angle, 5.5.7, 5.5.8, 6.8.5, 6.9, 6.12.6cavities, 5.5
animate, 3.4.3.15, 6.10.7     closed, 5.5.4
     view, 6.10.7cell, 5.3.2
animation, 6.10.7.1, 6.10.7.2, 6.10.7.3, 6.10.7.4center, 3.4.3.20, 4.1.3, 6.12, 6.12.5
     store, 6.10.7.4change selection, 4.6.7
animations, 7     speed range, 6.10.7.2
annotate, 4.6.21charge, 3.4.3.21, 6.8.2
antialias, 3.4.1.15, 3.4.3.10check box, 7.6.6
     lines, 3.4.3.17chembl, 4.2.3, 4.2.4
     lines, 3.4.3.17chemical spreadsheet, 4.2.3
apf, 5.4.6, 5.7     substructure, 4.2.1.1
append.rows, 3.4.10.7chi, 6.8.5
area, 5.5.3, 9.3.5clash, 4.7.5, 6.8.15
arrange, 4.1.13.1clear display and planes, 3.4.3.2
     window, 4.1.13.1     selection, 4.6.6
as2_graph, 4.6.5     planes, 3.4.3.2
assign, 6.1.3click, 4.1.12, 6.11, 6.12
atom, 4.7.5clip, 6.3.10, 6.13.1
atomLabelStyle, 4.7.7clipboard, 6.15.3
atomic property fields, 5.4.6, 5.7clipping planes, 6
author, 4.2.1.3     tool, 6.13
     play slide, 7.13     tools, 6.13
close, 6.3.3, 6.3.4custom, 6.12
collada, 3.5.6, 6.3.7     label, 6.8.8
color, 6.3.2, 6.3.3, 6.3.4, 6.3.9.4, 6.4, 6.4.1, 6.8.2, 6.8.3     rotation, 6.12.2
     background, 6.4.2default, 4.1.13
     by, 6.4delete, 3.4.2.1, 4.6.6, 7.6.8
     surface by proximity, 6.3.3     all, 3.4.2.2
               selection, 6.3.4     label, 6.8.9
     background, 3.4.3.18, 6.4.2     all, 3.4.2.2
     distance, 6.8.10     angle.label, 6.9.4
     mesh, 6.3.9.3     distance.label, 6.9.4
coloring, 6.4.1     label, 6.8.9
combine, 3.4.10.5     selection, 3.4.2.1
     display style, 4.7.9density, 5.3.4, 5.3.6, 5.3.7
compatible, 3.4.1.10depth, 6.3.12, 6.10.5
compound, 4.2.1.3dialog, 7.6.5
compress, 4.7.6diffuse, 3.5.2
connect, 6.3.9.1, 6.12, 6.12.7dihedral, 5.5.8, 6.8.5
     object, 6.12.7     angle, 5.5
construct, 3.4.1.1, 6.10.7.1directories preferences, 4.7.2
     molecule, 3.4.1.1directory, 4.7
     object, 3.4.1.1display, 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
contact, 5.5, 5.5.3, 9.3.5     chemical, 6.8.11
     surface, 6.3.2     delete distances, 6.9.4
contacts, 6.3.3, 6.3.4     dihedral, 6.9.3
contour, 5.3.6, 5.3.7     distance restraints, 6.8.14
convert, 5.1.2     distance2, 6.9.1
     local database, 3.4.1.6          angles, 6.9
     pdb, 9.3.2     formal charge, 6.1.9
     local.database, 3.4.1.6     gradient, 6.8.17
converting pdb, 5.1.2     hydrogen, 6.1.7
cpk, 6.1.5     mesh, 6.3.5
crash, 3.4.2.11     meshes, 6.3.8
creat, 7.6.1     planar angle, 6.9.2
     new objects, 4.3     tab, 3.5.1
cross section, 6.13     tether, 6.8.13
crystal, 5.3.2     toggle, 6.8.16
crystallographic analysis, 5.3     CPK, 6.1.5
          biomolecule, 5.3.3     angle, 6.9.2
          contour map, 5.3.6     dihedral.angle, 6.9.3
          convert2grid, 5.3.7     distance, 6.8.10, 6.8.14, 6.9.1
          crystallographic cell, 5.3.2     electrostatic, 3.4.3.21
          load eds, 5.3.4     energy.gradient, 6.8.17
          maps cell, 5.3.5     hydrogen, 6.1.7
          symmetry packing, 5.3.1          polar, 6.1.7
          tools, 9.3.8     macroshape, 6.3.6
     cell, 3.4.5     meshes, 6.3.5
     neigbor, 5.3.1          and display.macroshape, 3.5.6
     neighbors, 3.4.5     origin, 6.8.12
crystallography, 5.3.4, 5.3.6, 5.3.7     potential, 3.4.3.21
current.slide, 7.13     representations, 3.5.1
     ribbon, 6.1.3energy, 6.8.15
     skin, 6.1.4exit, 3.4.1.19
     surface, 6.1.6, 6.3.1export, 5.5.10
     surfaces, 3.5.6     pdb, 4.5
     tethers, 6.8.13extra windows, 6.2
     wire, 6.1.1extract, 4.4.2
     xstick, 6.1.2     icb, 3.4.1.5
distance, 5.5, 5.5.6, 6.8.10, 6.9     object icb, 4.4.2
     label, 4.7.7     icb, 3.4.1.5
distances, 3.5.3file, 3.4.1.3
document, 7.6.4, 7.6.5     close, 3.4.1.13
     navigation, 7.6.7     compatible, 3.4.1.10
documents, 6.15.3     export, 3.4.1.12
     envelope, 3.5.1     high quality image, 6.15.1
     surface, 4.7.5     load, 3.4.1.7
dotted line, 6.1.3     menu, 3.4.1
drag, 4.1.11, 4.7.7, 6.8.3, 7.6.4     password, 3.4.1.11
     residue label, 3.4.3.16     preferences, 3.4.1.16
draganddrop, 4.1.11     quick image, 3.4.1.14
drop, 4.1.11, 7.6.4     icb, 4.1.10
drug bank, 4.2, 4.2.8     recent, 3.4.1.17
dsPocket, 4.1.8     bak, 3.4.2.11
easy rotate, 3.4.3.12filter selection, 4.6.8
edit, 5.2.3.1fog, 3.4.3.5, 6, 6.10.1
     ligand tools, 3.4.2.17font, 4.7, 4.7.7, 5.2.3.1, 6.8.2, 6.8.3
     menu, 3.4.2     preferences, 4.7.7
     molecular document, 7.6.1formal charge, 6.1.9
     selection, 3.4.2.5front, 6.3.10, 6.13.1
     slide, 7.4.1full scene antialias, 3.4.3.10
editpdbsearch, 3.4.2.12     screen, 3.4.3.8
eds, 5.3.4, 5.3.6, 5.3.7general preferences, 4.7.5
electron, 5.3.4, 5.3.6, 5.3.7generalselecttools, 4.6.1
     denisty map, 5.3.5generator, 5.3.3
     density map, 3.4.1.7, 3.4.5, 5.3.4, 5.3.6getting started, 4
               contour, 3.4.5glasses, 6.6
electrostatic potential, 3.4.3.21google, 3.4.1.7
     surface, 6.3     objects, 6.3.7
electrostatics, 6.3.1     3D, 3.5.6, 6.3.7
elegant sketch, 6.10.4graphical display tutorial, 9.1
embed browser, 7.11               2D3D labels, 9.1.4
     powerpoint03, 7.8               annotation, 9.1.2
     powerpoint07, 7.9               color representation, 9.1.1
     powerpoint10, 7.10               labels, 9.1.3
     activeicm, 7.13graphics, 4.1
          script, 7.13     controls, 6
     browser, 7.7, 7.11     effects, 6.10
     firefox, 7.7, 7.11     panel, 6.2
     internet.explorer, 7.7, 7.11     preferences, 4.7.3
     microsoft, 7.7     shadow, 3.4.3.13, 6.10.2
     powerpoint, 7.7, 7.8, 7.9, 7.10grob, 4.7.5, 5.3.4, 5.3.6, 5.3.7, 6.3
     menus, 3.4icmpocketfinder, 9.3.7
     preferences, 4.7.4identity, 4.2.1.2
     tabs, 3.5image, 4.1.14, 4.7, 4.7.5, 6.15.3, 7.6.3
h-bond, 5.2.3, 5.2.3.1, 5.2.3.2     advanced, 6.15.3
hardware stereo, 3.4.3.7     preferences, 4.7.6
hbond, 5.2, 9.3.6     multiple, 3.4.1.7
header, 4.2.1.6     quality, 3.4.3.11
help, 2     quick, 3.4.1.14, 6.15.2
     videos, 2images, 6.15
high, 3.4.1.15insert, 7.6.4
     quality, 3.4.3.11     image, 7.6.3
historeceptomics, 4.2.10     script, 7.6.4
hitlist, 8.4interaction, 5.5.3
homology, 4.2.1.2, 4.2.5interactive, 9.2
     to activeicm, 3.3interrupt, 6.10.7.3
               create molecular documents, 3.3.3     animation, 6.10.7.3
                    slides, 3.3.2introduction icm browser, 1
               getting started, 3.3.1isee, 7.6.5
               ppt, 3.3.4javascript, 7.16
               web, 3.3.5jpg, 6.15
          icm browser convert display pocket, 3.1.4keyboard mouse, 6.11
                    distances angles, 3.1.9kmz, 3.5.6, 6.3.7
                    get started, 3.1.1label, 4.7.7
                    graphical display, 3.1.2     atoms, 6.8.2
                         effects, 3.1.5     color, 6.8.7
                    images, 3.1.7     move, 6.8.4
                    labels annotation, 3.1.6     residues, 6.8.3
                    pro crystallographic tools, 3.2.6     sites, 6.8.6
                         get started, 3.2.1     variables, 6.8.5
                         graphics, 3.2.2     2D, 3.5.3
                         plots, 3.2.8     3D, 3.5.3, 6.8.1
                         sequence analysis, 3.2.7     atom, 6.8.1
                         structure analysis, 3.2.3     atoms, 6.8.2
                         superimpose, 3.2.5     color, 6.8.7
                         surfaces, 3.2.4     custom, 6.8.8
                    selections, 3.1.3     delete, 6.8.1, 6.8.9
                    superimpose, 3.1.8     distance, 6.8.10
          search, 4.2     drag, 3.4.3.16
          use gui, 4.1     move, 3.4.3.16, 6.8.4
html, 3.4.1.12, 4.3, 7.6.1, 7.6.7     residue, 6.8.1
hydrogen, 5.2.3, 5.2.3.1, 5.2.3.2, 6.1.8, 9.3.6     residues, 6.8.3
     bond, 5.2, 6.1.8, 9.3.6     site, 6.8.1
          label edit, 5.2.3.1     sites, 6.8.6
               move, 5.2.3.2     variable, 6.8.1
     bonds, 5.2.4     variables, 6.8.5
hyperlink, 7.6.1, 7.6.2labeling, 6.8.1
iSee, 3.4.1.5, 3.4.1.12, 4.1.10, 6.15.3, 9.2labels, 6.8
icb, 4.4.2, 4.5     distances, 6.8.10
     object, 5.1, 9.3.2     tab, 3.5.3
icmjs, 7.16landscape, 4.7.6
layers, 6.14     representation, 6.3.9.3
ligand, 5.2.2     save, 6.3.11
     code, 4.2.1.3, 4.2.7     options, 6.3.9
     editor preferences, 3.4.2.18meshes, 6.3.2, 6.10.5
     pocket, 5.2.4     surfaces grobs, 6.3
     receptor display, 5.2     tab, 3.5.6
     surface, 5.2.2mmff type, 6.8.2
     pocket, 4.1.8mnSolutions, 4.7.10
     receptor.contact, 5.5.3molecular animations slides, 7
ligand_pocket_interactions, 5.2.4     documents, 9.2
ligedit tab, 3.5.5     dynamics, 8, 8.1, 8.2, 8.3, 8.4
light, 3.5.2          membrane, 8.3
     tab, 3.5.2          restraints, 8.2
lighting, 6.3.9.4, 6.5          run, 8.1
line, 4.7.5          vls, 8.4
lineWidth, 4.7.3     graphics, 6
links, 4.6.20molskin, 6.3.2
list, 4.6.18mouse, 4.1.3, 6.11, 6.12
load, 3.4.1.3, 3.4.1.17, 5.3.4, 5.3.6, 5.3.7mov, 6.16, 6.16.2
     nmr model, 4.2.1.4move, 3.4.3.19, 4.1.11, 4.1.13, 5.2.3.2, 6.3.9.1, 6.3.9.2, 6.12, 6.12.7
     protein structure, 5.1.1     mesh, 6.3.9.2
lock, 6.3.10, 6.13.1     slide, 7.4.2
logout, 3.4.1.19     structure, 6.12
macros, 7.14     tools, 6
macroshape, 3.4.3.22, 6.3, 6.3.6     rotate, 6.11
make, 6.10.7.1     slab, 6.11
     animation, 6.10.7.1     translate, 6.11
     molecular document, 7.6     z-rotation, 6.11
     selection, 4.6     zoom, 6.11
     molecule, 3.4.1.1movie, 6.16.1
     object, 3.4.1.1     making, 6.16, 6.16.2
making molecular slides, 7.1     open, 6.16, 6.16.2
     html, 7.6mpeg, 6.16, 6.16.1, 6.16.2
map, 4.7.7, 5.3.4, 5.3.6, 5.3.7mpg, 6.16, 6.16.2
     cel, 5.3.5mtl, 6.7
materials, 3.5.6multi panel, 6.2
maxColorPotential, 4.7.10     windows, 6.2
membrane, 8.3multiple receptor, 4.2.2
menu, 7.6.5navigate workspace, 4.6.10
     chemistry, 3.4.14neural network Torsion Profile Neural Network Prediction Engine, 6.12.6.1
     docking, 3.4.15     icm session, 3.4.1.2
     homology, 3.4.13nmr model, 4.2.1.4
     molmechanics, 3.4.16nntorsion, 6.12.6.1
     tools chemical search, 3.4.11non-contiguous selection, 4.6.18
          molecular editor, 3.4.12obj, 6.7
     windows, 3.4.17object, 4.1.11, 4.5, 9.3
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, 6.13.1objects, 5.1.2
     clip, 6.3.10occlusion, 6.3.12, 6.10.5
     color lighting, 6.3.9.4     shading, 6.3.12
     options, 6.3.9          effect, 6.10.5
     display, 4.2.1.5pocketome, 4.2, 4.2.2, 5.7
older version, 3.4.1.10portait, 4.7.6
omega, 6.8.5postscript, 4.7.6
open, 3.4.1.3, 4.4ppt, 7.12, 7.14
     file, 4.4preferences, 4.7
     password, 4.4.1presentation, 7.6.5, 7.7, 7.12
     with password, 3.4.1.4presentations, 7
     movie, 6.16, 6.16.2print, 6.7
     password, 3.4.1.4, 4.4.1printer.resolution, 4.7.6
orange, 4.6.5profile, 4.2.10
     selection, 4.6.5project, 3.4.1.5
origin, 6.8.12     close, 3.4.1.13
other selection, 4.6.19     rename, 3.4.1.9
overlay, 9.3.3properties, 6.8.2
package.activeicm, 7.13protect, 7.6.8
packing, 5.3.1protein, 5.4.6
pdb, 3.4.1.7, 4.2, 4.2.1.1, 4.2.7, 4.5, 9.3     structure, 5
     dormat, 4.5          analysis, 5.5
     html, 4.2.1.6               closed cavities, 5.5.4
     preparation, 9.3.11               contact areas, 5.5.3
     search, 4.2.1, 4.2.1.2, 4.2.1.3, 9.3.1               distance, 5.5.6
     recent, 3.4.1.18               find related chains, 5.5.1
     search, 3.5.4, 4.1.2               finding dihedral angle, 5.5.8
pdbsearchfield, 3.4.2.13                    planar angle, 5.5.7
pdbsearchhomology, 3.4.2.15               rama export, 5.5.10
pdbsearchidentity, 3.4.2.14               ramachandran plot, 5.5.9
pdbsearcsequence, 3.4.2.16               rmsd, 5.5.2
peptide, 4.3               surface area, 5.5.5
perspective, 3.4.3.9, 6.10.6          similarity, 5.6
phi, 6.8.5          tutorials, 9.3
pi, 5.2.5               analysis, 9.3.4
     cation, 5.2.5               contact area, 9.3.5
     pi, 5.2.5               convert, 9.3.2
picking, 6               hydrogen bond, 9.3.6
picture, 3.4.1.14, 4.1.14, 6.15.2, 7.6.3               icmpocketfinder, 9.3.7
     tips, 4.1.14               search, 9.3.1
pipi, 5.2.5               superimpose, 9.3.3
planar, 5.5.7, 6.8.5     superposition, 5.4
     angle, 5.5          select, 5.4.1
     angle, 6.9.2          sites by apf, 5.4.6
plane, 6.3.10, 6.13, 6.13.1, 6.14          superimpose 3D, 5.4.3
plot, 4.7, 4.7.8               grid, 5.4.5
     function, 3.4.9, 3.4.9.1               multiple proteins, 5.4.4
     preferences, 4.7.8proximity, 6.3.3, 6.3.4
png, 3.4.1.14, 6.15, 6.15.2, 7.6.3psi, 6.8.5
pocket, 4.1.8, 5.2, 5.2.1, 5.2.2, 9.3.7publication quality images, 6.3.2
     properties, 5.7pubmed, 4.2.1.7
     surface, 5.2.1purple box, 3.4.3.23
     peptide, 4.1.8qs hydrogen bond, 5.2.3
     properties, 4.1.8quality, 3.4.1.15, 4.7.5
     image, 6.15.2root mean square deviation, 5.5.2
     start move structure, 4.1.3rotate, 3.4.3.15, 4.1.3, 6, 6.10.7, 6.10.7.1, 6.12, 6.12.1, 6.12.2, 7
          read pdb, 4.1.2     torsion, 6.12.6.1
          representation, 4.1.6     easy, 3.4.3.12
          selection, 4.1.5     speed, 6.10.7.2
               level, 4.6.3rotation, 6.12.1
          what is selected, 4.6.4ruler, 6.8.16
     display.distance, 6.9.1salt bridge, 9.3.6
     start color, 4.1.7save, 4.5, 6.3.11, 6.10.7.4
quit, 3.4.1.19     as PDB, 4.5
rainbow, 4.7.5, 6.8.16          pdb, 4.5
ramachandran plot, 5.5, 5.5.10     file, 4.5
range, 6.10.7.2     object, 4.1.9
ratio.selection, 4.7.5     pdb, 4.5
read, 3.4.1.3, 3.4.1.17, 4.4     project icb, 4.1.10
     pdb, 4.1.2     slide, 7.4
rear, 6.3.10, 6.13.1     image, 3.4.1.15, 4.1.14
recent files, 3.4.1.17     object, 4.1.9
     pdb codes, 3.4.1.18     password, 3.4.1.11
receptor, 5.2.1, 5.2.2     picture, 3.4.1.15
recover, 3.4.2.11     project, 3.4.1.8, 3.4.1.9, 3.4.1.10, 4.1.10
redo, 3.4.2.10saving, 3.4.1.8
rename project, 3.4.1.9     project, 3.4.1.8
representation, 3.4.3.19scale, 4.7.5
residue, 4.7.7scan_pockets, 5.7
     alternative orientation, 9.3.11screening, 8.4
     range, 4.6.18screenshot, 6.16, 6.16.2
     content, 3.4.4     movie, 6.16.2
residues, 5.2.1, 5.2.2script, 4.3, 7.6.4, 7.6.5
resize, 6.3.9.1, 6.15.3search, 5.6
     mesh, 6.3.9.1     chembl, 4.2.3
resolution, 4.2.1.3     drugbank, 4.2.8
restore, 3.4.2.11, 6.3.10, 6.13.1     in workspace, 3.4.2.4
     recent backup, 3.4.2.11     pdb, 4.2.1
restraints, 8.2          chemical, 4.2.1
ribbon, 3.5.1, 4.7.9, 6.1.3          ligand code, 4.2.7
     preferences, 4.7.9     pocketome, 4.2.2
     style, 4.7.9     pubchem, 4.2.9
     breaks, 6.1.3     surechembl, 4.2.4
     cylinders, 6.1.3     tab field, 4.2.1.3
     smooth, 6.1.3          pdb chemical, 4.2.1.1
     worm, 6.1.3               sequence, 4.2.1.2
ribbonColorStyle, 4.7.9     uniprot, 4.2.6
right, 4.1.12     in.workspace, 3.4.2.4
     click, 4.1.12secondary.structure, 3.4.4, 6.1.3
ring, 5.2.5select, 4.6.12, 4.6.13
     stacking, 5.2.5     all, 4.6.14
rmsd, 5.5, 5.5.2     amino acid, 4.6.13
rock, 3.4.3.15, 6.10.7, 6.10.7.1, 7     molecule, 4.6.12
     speed, 6.10.7.2     neighbors, 4.6.15
     object, 4.6.11shineStyle, 4.7.3
     residue, 4.6.13, 4.6.18show, 7.3.1
          by number, 4.6.18side by side stereo, 3.4.3.6
          number, 4.6.18sigmaLevel, 5.3.6, 5.3.7
     atom, 4.1.5, 4.6.3simulation, 8, 8.1, 8.2, 8.3, 8.4
     graphical, 4.1.5, 4.6.3sites, 5.4.6
     object, 4.1.5, 4.6.3size, 5.2.3.1
     purple.box, 3.4.3.23sketch accents, 6.10.3
     residue, 4.1.5, 4.6.3     accents, 3.4.3.14, 6.10.3
     workspace, 4.1.5, 4.6.3skin, 3.5.1, 6.1.4
selectall, 3.4.2.3slab, 6.3.10, 6.13.1
selecting.neighbors, 4.6.16slice, 6.13
selection, 4.6.4, 4.6.5, 4.6.21, 6.3.4slide, 6.10.7.4, 7.2, 7.3.1, 7.6.1
     clear, 3.4.2.7     effects, 7.5
     neighbors, 3.4.2.8     movie, 6.16.1
     alignment, 4.6.19          file, 7.2
     all, 3.4.2.3     navigation, 7.3.2
     alter, 4.6.7     show, 7.3
     atom, 3.4.2.5     blend, 7.5
     basic, 4.6.2     edit, 7.4.1
     change, 4.6.7     effect, 7.5
     clear, 3.4.2.7     smooth, 7.5
     filter, 3.4.2.5, 4.6.8     transition, 7.5
     graphical, 4.6.16slides, 6.16.1, 7, 7.1, 7.3
     invert, 3.4.2.6smooth, 6.3.9.3
     level, 3.4.3.3solid, 6.3.9.3
     mode, 3.4.3.4sort table, 3.4.10.4
     near atoms, 3.4.2.8spec, 3.5.2
     neighbors, 3.4.2.5, 3.4.2.8, 4.6.15, 4.6.17speed, 6.10.7.2
     object, 4.6.11stacking, 5.2.5
     other, 4.6.19stereo, 4.7.6, 6.6
     properties, 3.4.2.5     hardware, 3.4.3.7
     residue, 3.4.2.5     side-by-side, 3.4.3.6
     sphere, 4.6.15stick, 4.7.5
     spherical, 3.4.2.8stl, 6.7
     superposition, 5.4.1stop, 6.10.7.3
     table, 4.6.19store, 3.4.3.19, 6.10.7.4
     tools, 4.6.1, 4.6.2, 4.6.7, 4.6.8     current view, 3.4.3.19
     whole, 4.6.11strain, 6.12.6.1
     workspace, 4.6.9, 4.6.17structure, 5.3.3, 9.3
selectioninvert, 3.4.2.6     analysis, 9.3.4
selections, 4.6     representation, 6.1
selectneighbors workspace, 4.6.17style, 4.7.5
sequence, 3.4.4, 4.2, 4.2.1.2, 4.2.5, 4.2.6, 4.3, 9.3superimpose, 3.4.8, 5.4.2, 5.4.6, 9.3.3
     pattern, 4.2.1.2     3D, 5.4.3
shading, 6.3.12     Calpha, 5.4.3
shadow, 6.10.2     arrange.grid, 5.4.5
shell preferences, 4.7.10     backbone, 5.4.3
shift, 6.8.3     heavy atoms, 5.4.3
shine, 3.5.2, 4.7.5     multiple, 5.4.4
surface, 3.5.1, 4.7.5, 5.2.1, 5.2.2, 6.1.6, 6.3, 6.3.3, 6.3.4unit, 5.3.3
     area, 5.5unusual peptide, 4.3
     area, 5.5.5     activeicm, 7.12
surfaces, 5.2, 6.3.1, 6.3.2, 6.10.5van der waal, 6.8.15
symmetry, 5.3.1, 5.3.3, 9.3.8, 9.3.9variable, 4.7.7
system preferences, 4.7.11video, 2, 6.16, 6.16.1, 6.16.2
tab pdb, 3.5.4view, 3.4.3.19, 7.3.1
table, 4.3     animate view, 3.4.3.15
     join, 3.4.10.5     center, 3.4.3.20
     merge, 3.4.10.5     color background, 3.4.3.18
     rows, 3.4.10.7     fog, 3.4.3.5
     sort, 3.4.10.4     macroshape, 3.4.3.22
tag, 4.6.21     menu, 3.4.3
tags, 4.6.21     mesh clip, 6.13.1
text, 4.7.7, 7.6, 7.6.1, 7.6.7     perspective, 3.4.3.9
texture, 3.5.6     selection level, 3.4.3.3
threshold, 4.7.5          mode, 3.4.3.4
tier, 4.1.13     shadow, 3.4.3.13
tissue, 4.2.10     sketch accents, 3.4.3.14
tools 3D, 3.4.6     slide show, 7.3.1
     analysis, 3.4.7     tools, 3.4.3
     append rows, 3.4.10.7     undisplay all, 3.4.3.1
     extras, 3.4.9virus, 5.3.3
          plot function, 3.4.9.1vls, 8.4
     superimpose, 3.4.8wavefront, 3.5.6, 6.3.11, 6.7
     table, 3.4.10web, 9.2
          Learn, 3.4.10.1     browser, 3.4.1.12
          clustering, 3.4.10.3window, 4.1.13
          merge, 3.4.10.5windows, 4.1.13.1
          predict, 3.4.10.2wire, 3.5.1, 4.7.5, 6.1.1
torsion, 6.12.6, 6.12.6.1wireBondSeparation, 4.7.1
     angles, 6.12, 6.12.6workspace, 4.1.4
trace, 6.1.10     panel, 4.1.4
transitions, 7     selection, 4.6.9
translate, 4.1.3, 6, 6.12     navigation, 4.6.10
translation, 6.12.3write, 4.1.14, 4.5
transparent, 6.3.9.3     image, 3.4.1.15
     background, 6.15.3     images, 6.15
tut analyze alternative orientations, 9.3.11     pdb, 4.5
          occupancy, 9.3.10     image, 3.4.1.15
          symmetry, 9.3.9     object, 4.1.9
tut3e, 9.3.12     picture, 3.4.1.15
tutorial molecular documents, 9.2     project, 3.4.1.8, 4.1.10
tutorials, 9     ray, 3.4.5
unclip, 6.3.10, 6.13.1xi, 6.8.5
undisplay, 4.1.4, 6.1.7xstick, 6.1.2
undisplay-all, 3.4.3.1youtube, 2
     origin, 6.8.12zoom, 4.1.3, 6, 6.12, 6.12.4
undo, 3.4.2.9, 4.7 
uniprot, 4.2.6 

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