Mar 8 2017 Feedback.
Contents
 
Introduction
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Tutorials
 
Index

Index

2D, 5.8.8     dnaRibbonRatio, 3.7.9
3D, 5.6, 5.8.8, 7.2     dnaRibbonWidth, 3.7.9
     QSAR, 7.5     dnaRibbonWorm, 3.7.9
     interactive ligand editor, 2.5.5     dnaStickRadius, 3.7.9
     object, 5.3.9     dnaWormRadius, 3.7.9
     print, 5.7     font Scale, 3.7.7
     printing, 5.7     fontColor, 3.7.7
     stereo, 5.6     fontLineSpacing, 3.7.7
3Dqsar tutorial, 7.5     grobLineWidth, 3.7.3
4D docking, 3.2.2     hbond Ball Period, 3.7.1
APF, 7.5               Style, 3.7.1
ActiveICM, 2.4.1.12     hbondAngleSharpness, 3.7.1
Atom Single Style, 3.7.3     hbondMinStrength, 3.7.1
Atomic Property Fields, 7.5     hbondStyle, 3.7.1
Beep, 3.7.11     hbondWidth, 3.7.1
BlastDB Directory, 3.7.2     hetatmZoom, 3.7.1
     alphas, 5.8.3     hydrogenDisplay, 3.7.1
COLLADA, 2.4.1.7     light, 3.7.3
CPK, 2.5.1     lightPosition, 3.7.3
ChEMBL, 3.2.3     mapLineWidth, 3.7.3
Clash Threshold, 3.7.10     occupancy Radius Ratio, 3.7.3
DNA, 3.3     occupancyDisplay, 3.7.3
Dock Directory, 3.7.2     quality, 3.7.3
Drug Bank, 3.2.8     rainbow Bar Style, 3.7.4
Editor, 3.7.2     resLabelDrag, 3.7.7
FILTER.Z, 3.7.2     resize Keep Scale, 3.7.3
     gz, 3.7.2     ribbonRatio, 3.7.9
     uue, 3.7.2     ribbonWidth, 3.7.9
FTP.createFile, 3.7.11     ribbonWorm, 3.7.9
     keep File, 3.7.11     rocking, 3.7.4
     proxy, 3.7.11          Range, 3.7.4
Filter.zip, 3.7.2          Speed, 3.7.4
Force Auto Bond Typing, 3.7.11     selectionStyle, 3.7.3
GIF, 2.4.1.15, 5.16, 5.16.2     site Label Drag, 3.7.7
GRAPHIC.store Display, 3.7.3               Shift, 3.7.7
     NtoC Rainbow, 3.7.4     siteArrow, 3.7.7
     alignment Rainbow, 3.7.4     stereoMode, 3.7.3
     atomLabelShift, 3.7.7     stickRadius, 3.7.1
     ballStickRatio, 3.7.1     surfaceDotDensity, 3.7.3
     center Follows Clipping, 3.7.3     surfaceDotSize, 3.7.3
     clash Style, 3.7.3     surfaceProbeRadius, 3.7.3
     clashWidth, 3.7.3     transparency, 3.7.3
     clip Grobs, 3.7.3     wire Width, 3.7.1
          Skin, 3.7.3     wormRadius, 3.7.9
          Static, 3.7.3     xstick Backbone Ratio, 3.7.1
     discrete Rainbow, 3.7.4          Hydrogen Ratio, 3.7.1
     displayLineLabels, 3.7.7          Style, 3.7.1
     displayMapBox, 3.7.3          Vw Ratio, 3.7.1
     distance Label Drag, 3.7.1GROB.arrowRadius, 3.7.3
     dnaBallRadius, 3.7.9     atomSphereRadius, 3.7.3
     relArrow Size, 3.7.3          Auto, 3.7.4
     relArrowHead, 3.7.3Output Directory, 3.7.2
GUI.auto Save, 3.7.4PDB, 3.2.1.6, 4.1.2, 4.3.3
               Interval, 3.7.4     Directory, 3.7.2
     enumberation Memory Limit, 3.7.11          Style, 3.7.2
     max Nof Recent Files, 3.7.11     Search, 2.4.2.12, 2.4.2.13, 2.4.2.14, 2.4.2.15, 2.4.2.16
          Sequence Length, 3.7.4          Field, 2.4.2.13
     splash Screen Delay, 3.7.11          Homology, 2.4.2.15
               Image, 3.7.11          Identity, 2.4.2.14
     table Row Mark Colors, 3.7.4          Sequence, 2.4.2.16
     workspace Folder Style, 3.7.4     convert, 4.1.2
     workspaceTabStyle, 3.7.4PFAM, 2.4.1.7
HTTP.proxy, 3.7.11PLOT.Yratio, 3.7.8
     support Cookies, 3.7.11     color, 3.7.8
     user Agent, 3.7.11     date, 3.7.8
How To Guide, 2     draw Tics, 3.7.8
Html, 3.2.1.6     font, 3.7.8
Http Read Style, 3.7.11     fontSize, 3.7.8
Hydrogen.bond, 3.7.5     labelFont, 3.7.8
ICM Browser How To, 2.1     lineWidth, 3.7.8
          Pro How To, 2.2     logo, 3.7.8
IMAGE.bondLength2D, 3.7.6     markSize, 3.7.8
     color, 3.7.6     orientation, 3.7.8
     compress, 3.7.6     paper Size, 3.7.8
     gammaCorrection, 3.7.6     previewer, 3.7.8
     generateAlpha, 3.7.6     rainbowStyle, 3.7.8
     lineWidth, 3.7.6     seriesLabels, 3.7.8
     lineWidth2D, 3.7.6PNG, 2.4.1.15, 3.1.14, 5.16, 5.16.2
     orientation, 3.7.6Projects Directory, 3.7.2
     paper Size, 3.7.6Prosite Dat, 3.7.2
     previewResolution, 3.7.6     Viewer, 3.7.2
     previewer, 3.7.6Pub Chem, 3.2.9
     print, 3.7.6PubMed, 3.2.1.7
     printerDPI, 3.7.6Pubchem, 3.2.9
     scale, 3.7.6QSAR, 7.5
     stereoAngle, 3.7.6RMSD, 4.4.2
     stereoBase, 3.7.6RNA, 3.3
     stereoText, 3.7.6Ramachandran Plot, 4.5.9
Icm Prompt, 3.7.10Real Format, 3.7.10
Inx Directory, 3.7.2     Label Shift, 3.7.7
JPEG, 2.4.1.15          Style, 3.7.7
KMZ, 2.4.1.7SEQUENCE.site Colors, 3.7.4
Log Directory, 3.7.2SITE.label Style, 3.7.7
MOVIE.frame Grab Mode, 3.7.4     labelOffset, 3.7.7
Map Atom Margin, 3.7.10     wrap Comment, 3.7.7
     Sigma Level, 3.7.10SLIDE.ignore Background Color, 3.7.4
     File Size Mb, 3.7.11          Fog, 3.7.4
Mnconf, 3.7.10Select Min Grad, 3.7.10
Movie.fade Nof Frames, 3.7.4Show Res Code In Selection, 3.7.7
     quality, 3.7.4SureChEMBL, 3.2.4
     Dat, 3.7.2avi, 5.16, 5.16.2
Temp Directory, 3.7.2b-factor, 7.3.10
USER.email, 3.7.11backbone, 5.1.10
     friends, 3.7.11background, 5.4.2, 5.4.3
     full Name, 3.7.11     images activeicm, 6.15
     organization, 3.7.11     image, 5.4.3
     phone, 3.7.11backup, 2.4.2.11
Var Label Style, 3.7.7ball, 3.7.5
Water Radius, 3.7.10     and stick, 2.5.1
Wire Style, 3.7.1basicsel, 3.6.2
XPDB Directory, 3.7.2binding properties, 5.3.1
Xstick, 2.5.1bioinfo menu, 2.4.4
a-bright, 2.5.2biological, 4.3.3
active, 6.7biomolecule, 2.4.5, 4.3.3, 7.3.8, 7.3.12
activeICM, 6.8blast, 3.2.5
activeicm, 6.7, 6.12, 6.14, 6.14.1     search, 3.2.5
     advanced, 6.14bond, 4.2.3, 4.2.3.1, 4.2.3.2
     background images, 6.15bonding, 5.1.8
     control, 6.13     preferences, 3.7.1
activeicmjs, 6.16box, 3.7.7, 5.8.15
album, 5.15.3build, 5.10.7.1
align, 3.1.11buttons, 6.14
alpha, 2.5.2bye, 2.4.1.19
     channel, 3.7.6     alpha, 5.1.10
ambient, 2.5.2     trace, 5.1.10
amino acid, 3.3ca-trace, 5.1.10
anaglyph, 5.6cache, 6.14.1
analysis, 2.4.4cavities, 4.5
angle, 4.5.7, 4.5.8, 5.8.5, 5.9, 5.12.6     closed, 4.5.4
animate, 2.4.3.15, 5.10.7cell, 4.3.2
     view, 5.10.7center, 2.4.3.20, 3.1.3, 5.12, 5.12.5
animation, 5.10.7.1, 5.10.7.2, 5.10.7.3, 5.10.7.4change selection, 3.6.7
     store, 5.10.7.4     speed range, 5.10.7.2
animations, 6charge, 2.4.3.21, 5.8.2
annotate, 3.6.21chembl, 3.2.3, 3.2.4
antialias, 2.4.1.15, 2.4.3.10chemical spreadsheet, 3.2.3
     lines, 2.4.3.17     substructure, 3.2.1.1
     lines, 2.4.3.17chi, 5.8.5
apf, 4.4.6clash, 3.7.5, 5.8.14
append.rows, 2.4.10.7clear display and planes, 2.4.3.2
area, 4.5.3, 7.3.5     selection, 3.6.6
arrange, 3.1.13.1     planes, 2.4.3.2
     window, 3.1.13.1click, 3.1.12, 5.11, 5.12
as2_graph, 3.6.5clip, 5.3.10, 5.13.1
assign, 5.1.3clipboard, 5.15.3
atom, 3.7.5clipping planes, 5
atomLabelStyle, 3.7.7     tool, 5.13
atomic property fields, 4.4.6     tools, 5.13
author, 3.2.1.3clone, 2.4.1.2
     play slide, 6.13close, 5.3.3, 5.3.4
color, 5.3.2, 5.3.3, 5.3.4, 5.3.9.4, 5.4, 5.4.1, 5.8.2, 5.8.3     rotation, 5.12.2
     background, 5.4.2default, 3.1.13
     by, 5.4delete, 2.4.2.1, 3.6.6, 6.6.7
     surface by proximity, 5.3.3     all, 2.4.2.2
               selection, 5.3.4     label, 5.8.9
     background, 2.4.3.18, 5.4.2     all, 2.4.2.2
     distance, 5.8.10     angle.label, 5.9.4
     mesh, 5.3.9.3     distance.label, 5.9.4
coloring, 5.4.1     label, 5.8.9
combine, 2.4.10.5     selection, 2.4.2.1
     display style, 3.7.9density, 4.3.4, 4.3.6, 4.3.7
compatible, 2.4.1.10depth, 5.3.12, 5.10.5
compound, 3.2.1.3dialog, 6.6.5
compress, 3.7.6diffuse, 2.5.2
connect, 5.3.9.1, 5.12, 5.12.7dihedral, 4.5.8, 5.8.5
     object, 5.12.7     angle, 4.5
construct, 2.4.1.1, 5.10.7.1directories preferences, 3.7.2
     molecule, 2.4.1.1directory, 3.7
     object, 2.4.1.1display, 3.1.4, 3.1.13.1, 3.7, 4.2.3, 4.2.3.1, 4.2.3.2, 5.8.14, 5.14
contact, 4.5, 4.5.3, 7.3.5     delete distances, 5.9.4
     surface, 5.3.2     dihedral, 5.9.3
contacts, 5.3.3, 5.3.4     distance restraints, 5.8.13
contour, 4.3.6, 4.3.7     distance2, 5.9.1
convert, 4.1.2          angles, 5.9
     local database, 2.4.1.6     formal charge, 5.1.9
     pdb, 7.3.2     gradient, 5.8.16
     local.database, 2.4.1.6     hydrogen, 5.1.7
converting pdb, 4.1.2     mesh, 5.3.5
cpk, 5.1.5     meshes, 5.3.8
crash, 2.4.2.11     planar angle, 5.9.2
creat, 6.6.1     tab, 2.5.1
     new objects, 3.3     tether, 5.8.12
cross section, 5.13     toggle, 5.8.15
crystal, 4.3.2     CPK, 5.1.5
crystallographic analysis, 4.3     angle, 5.9.2
          biomolecule, 4.3.3     dihedral.angle, 5.9.3
          contour map, 4.3.6     distace, 5.8.10
          convert2grid, 4.3.7     distance, 5.8.13, 5.9.1
          crystallographic cell, 4.3.2     electrostatic, 2.4.3.21
          load eds, 4.3.4     energy.gradient, 5.8.16
          maps cell, 4.3.5     hydrogen, 5.1.7
          symmetry packing, 4.3.1          polar, 5.1.7
          tools, 7.3.8     macroshape, 5.3.6
     cell, 2.4.5     meshes, 5.3.5
     neigbor, 4.3.1          and display.macroshape, 2.5.6
     neighbors, 2.4.5     origin, 5.8.11
crystallography, 4.3.4, 4.3.6, 4.3.7     potential, 2.4.3.21
current.slide, 6.13     representations, 2.5.1
custom, 5.12     restraints, 5.8.13
     label, 5.8.8     ribbon, 5.1.3
     surface, 5.1.6, 5.3.1export, 4.5.10
     surfaces, 2.5.6extra windows, 5.2
     tethers, 5.8.12extract, 3.4.2
     wire, 5.1.1     icb, 2.4.1.5
     xstick, 5.1.2     object icb, 3.4.2
distance, 4.5, 4.5.6, 5.8.10, 5.9     icb, 2.4.1.5
     label, 3.7.7file, 2.4.1.3
distances, 2.5.3     close, 2.4.1.13
document, 6.6.4, 6.6.5     compatible, 2.4.1.10
     navigation, 6.6.6     export, 2.4.1.12
documents, 5.15.3     high quality image, 5.15.1
     envelope, 2.5.1     load, 2.4.1.7
     surface, 3.7.5     menu, 2.4.1
dotted line, 5.1.3     password, 2.4.1.11
drag, 3.1.11, 3.7.7, 5.8.3, 6.6.4     preferences, 2.4.1.16
     residue label, 2.4.3.16     quick image, 2.4.1.14
draganddrop, 3.1.11     icb, 3.1.10
drop, 3.1.11, 6.6.4     recent, 2.4.1.17
drug bank, 3.2, 3.2.8     bak, 2.4.2.11
dsPocket, 3.1.8filter selection, 3.6.8
easy rotate, 2.4.3.12fingerprint, 7.4
edit, 4.2.3.1fog, 2.4.3.5, 5, 5.10.1
     ligand tools, 2.4.2.17font, 3.7, 3.7.7, 4.2.3.1, 5.8.2, 5.8.3
     menu, 2.4.2     preferences, 3.7.7
     molecular document, 6.6.1formal charge, 5.1.9
     selection, 2.4.2.5front, 5.3.10, 5.13.1
     slide, 6.4.1full scene antialias, 2.4.3.10
editpdbsearch, 2.4.2.12     screen, 2.4.3.8
eds, 4.3.4, 4.3.6, 4.3.7general preferences, 3.7.5
electron, 4.3.4, 4.3.6, 4.3.7generalselecttools, 3.6.1
     denisty map, 4.3.5generator, 4.3.3
     densitry map.contour, 2.4.5getting started, 3
          map, 2.4.1.7, 2.4.5, 4.3.4, 4.3.6glasses, 5.6
electrostatic potential, 2.4.3.21google, 2.4.1.7
     surface, 5.3     objects, 5.3.7
electrostatics, 5.3.1     3D, 2.5.6, 5.3.7
elegant sketch, 5.10.4graphical display tutorial, 7.1
embed browser, 6.11               2D3D labels, 7.1.4
     powerpoint03, 6.8               annotation, 7.1.2
     powerpoint07, 6.9               color representation, 7.1.1
     powerpoint10, 6.10               labels, 7.1.3
     activeicm, 6.13graphics, 3.1
          script, 6.13     controls, 5
     browser, 6.7, 6.11     effects, 5.10
     firefox, 6.7, 6.11     panel, 5.2
     internet.explorer, 6.7, 6.11     preferences, 3.7.3
     microsoft, 6.7     shadow, 2.4.3.13, 5.10.2
     powerpoint, 6.7, 6.8, 6.9, 6.10grob, 3.7.5, 4.3.4, 4.3.6, 4.3.7, 5.3
energy, 5.8.14gui, 3.1.1, 3.7.4
exit, 2.4.1.19     menus, 2.4
     tabs, 2.5     quality, 2.4.3.11
h-bond, 4.2.3, 4.2.3.1, 4.2.3.2     quick, 2.4.1.14, 5.15.2
hardware stereo, 2.4.3.7images, 5.15
hbond, 4.2, 7.3.6insert, 6.6.4
header, 3.2.1.6     image, 6.6.3
high, 2.4.1.15     script, 6.6.4
     quality, 2.4.3.11interaction, 4.5.3
homology, 3.2.1.2, 3.2.5interactive, 7.2
     to activeicm, 2.3interrupt, 5.10.7.3
               create molecular documents, 2.3.3     animation, 5.10.7.3
                    slides, 2.3.2introduction icm browser, 1
               getting started, 2.3.1isee, 6.6.5
               ppt, 2.3.4javascript, 6.16
               web, 2.3.5jpg, 5.15
          icm browser convert display pocket, 2.1.4keyboard mouse, 5.11
                    distances angles, 2.1.9kmz, 2.5.6, 5.3.7
                    get started, 2.1.1label, 3.7.7
                    graphical display, 2.1.2     atoms, 5.8.2
                         effects, 2.1.5     color, 5.8.7
                    images, 2.1.7     move, 5.8.4
                    labels annotation, 2.1.6     residues, 5.8.3
                    pro crystallographic tools, 2.2.6     sites, 5.8.6
                         get started, 2.2.1     variables, 5.8.5
                         graphics, 2.2.2     2D, 2.5.3
                         plots, 2.2.8     3D, 2.5.3, 5.8.1
                         sequence analysis, 2.2.7     atom, 5.8.1
                         structure analysis, 2.2.3     atoms, 5.8.2
                         superimpose, 2.2.5     color, 5.8.7
                         surfaces, 2.2.4     custom, 5.8.8
                    selections, 2.1.3     delete, 5.8.1, 5.8.9
                    superimpose, 2.1.8     distance, 5.8.10
          search, 3.2     drag, 2.4.3.16
          use gui, 3.1     move, 2.4.3.16, 5.8.4
html, 2.4.1.12, 3.3, 6.6.1, 6.6.6     residue, 5.8.1
hydrogen, 4.2.3, 4.2.3.1, 4.2.3.2, 5.1.8, 7.3.6     residues, 5.8.3
     bond, 4.2, 5.1.8, 7.3.6     site, 5.8.1
          label edit, 4.2.3.1     sites, 5.8.6
               move, 4.2.3.2     variable, 5.8.1
     bonds, 4.2.4     variables, 5.8.5
hyperlink, 6.6.1, 6.6.2labeling, 5.8.1
iSee, 2.4.1.5, 2.4.1.12, 3.1.10, 5.15.3, 7.2labels, 5.8
icb, 3.4.2, 3.5     distances, 5.8.10
     object, 4.1, 7.3.2     tab, 2.5.3
icmjs, 6.16landscape, 3.7.6
icmpocketfinder, 7.3.7layer, 5.14
identity, 3.2.1.2layers, 5.14
image, 3.1.14, 3.7, 3.7.5, 5.15.3, 6.6.3ligand, 4.2.2
     advanced, 5.15.3     code, 3.2.1.3, 3.2.7
     preferences, 3.7.6     editor preferences, 2.4.2.18
     multiple, 2.4.1.7     pocket, 4.2.4
     surface, 4.2.2mmff type, 5.8.2
     pocket, 3.1.8mnSolutions, 3.7.10
     receptor.contact, 4.5.3molecular animations slides, 6
ligand_pocket_interactions, 4.2.4     documents, 7.2
ligedit tab, 2.5.5     graphics, 5
light, 2.5.2molskin, 5.3.2
     tab, 2.5.2mouse, 3.1.3, 5.11, 5.12
lighting, 5.3.9.4, 5.5mov, 5.16, 5.16.2
line, 3.7.5move, 2.4.3.19, 3.1.11, 3.1.13, 4.2.3.2, 5.3.9.1, 5.3.9.2, 5.12, 5.12.7
lineWidth, 3.7.3     mesh, 5.3.9.2
links, 3.6.20     slide, 6.4.2
list, 3.6.18     structure, 5.12
load, 2.4.1.3, 2.4.1.17, 4.3.4, 4.3.6, 4.3.7     tools, 5
     nmr model, 3.2.1.4     rotate, 5.11
     protein structure, 4.1.1     slab, 5.11
lock, 5.3.10, 5.13.1     translate, 5.11
logout, 2.4.1.19     z-rotation, 5.11
machine learning, 7.4     zoom, 5.11
macros, 6.14movie, 5.16.1
macroshape, 2.4.3.22, 5.3, 5.3.6     making, 5.16, 5.16.2
make, 5.10.7.1     open, 5.16, 5.16.2
     animation, 5.10.7.1mpeg, 5.16, 5.16.1, 5.16.2
     molecular document, 6.6mpg, 5.16, 5.16.2
     selection, 3.6multi panel, 5.2
     molecule, 2.4.1.1     windows, 5.2
     object, 2.4.1.1multiple receptor, 3.2.2
making molecular slides, 6.1navigate workspace, 3.6.10
     html, 6.6new icm session, 2.4.1.2
map, 3.7.7, 4.3.4, 4.3.6, 4.3.7nmr model, 3.2.1.4
     cel, 4.3.5non-contiguous selection, 3.6.18
materials, 2.5.6object, 3.1.11, 3.5, 7.3
maxColorPotential, 3.7.10objects, 4.1.2
menu, 6.6.5occlusion, 5.3.12, 5.10.5
     chemistry, 2.4.14     shading, 5.3.12
     docking, 2.4.15          effect, 5.10.5
     homology, 2.4.13occupancy, 5.1.3, 7.3.10
     molmechanics, 2.4.16     display, 3.2.1.5
     tools chemical search, 2.4.11older version, 2.4.1.10
          molecular editor, 2.4.12omega, 5.8.5
     windows, 2.4.17open, 2.4.1.3, 3.4
mesh, 4.2.1, 4.2.2, 4.3.4, 4.3.6, 4.3.7, 5.3, 5.3.9.1, 5.3.9.2, 5.3.9.4, 5.3.10, 5.3.11, 5.3.12, 5.13.1     file, 3.4
     clip, 5.3.10     password, 3.4.1
     color lighting, 5.3.9.4     with password, 2.4.1.4
     options, 5.3.9     movie, 5.16, 5.16.2
     representation, 5.3.9.3     password, 2.4.1.4, 3.4.1
     save, 5.3.11orange, 3.6.5
     options, 5.3.9     selection, 3.6.5
meshes, 5.3.2, 5.10.5origin, 5.8.11
     surfaces grobs, 5.3other selection, 3.6.19
     tab, 2.5.6overlay, 7.3.3
packing, 4.3.1               contact areas, 4.5.3
pdb, 2.4.1.7, 3.2, 3.2.1.1, 3.2.7, 3.5, 7.3               distance, 4.5.6
     html, 3.2.1.6               find related chains, 4.5.1
     preparation, 7.3.11               finding dihedral angle, 4.5.8
     search, 3.2.1, 3.2.1.2, 3.2.1.3, 7.3.1                    planar angle, 4.5.7
     recent, 2.4.1.18               rama export, 4.5.10
     search, 2.5.4, 3.1.2               ramachandran plot, 4.5.9
pdbsearchfield, 2.4.2.13               rmsd, 4.5.2
pdbsearchhomology, 2.4.2.15               surface area, 4.5.5
pdbsearchidentity, 2.4.2.14          tutorials, 7.3
pdbsearcsequence, 2.4.2.16               analysis, 7.3.4
peptide, 3.3               contact area, 7.3.5
perspective, 2.4.3.9, 5.10.6               convert, 7.3.2
phi, 5.8.5               hydrogen bond, 7.3.6
picking, 5               icmpocketfinder, 7.3.7
picture, 2.4.1.14, 3.1.14, 5.15.2, 6.6.3               search, 7.3.1
     tips, 3.1.14               superimpose, 7.3.3
planar, 4.5.7, 5.8.5     superposition, 4.4
     angle, 4.5          select, 4.4.1
     angle, 5.9.2          sites by apf, 4.4.6
plane, 5.3.10, 5.13, 5.13.1, 5.14          superimpose 3D, 4.4.3
plot, 3.7, 3.7.8               grid, 4.4.5
     function, 2.4.9, 2.4.9.1               multiple proteins, 4.4.4
     preferences, 3.7.8proximity, 5.3.3, 5.3.4
pls, 7.4psi, 5.8.5
png, 2.4.1.14, 5.15, 5.15.2, 6.6.3publication quality images, 5.3.2
pocket, 3.1.8, 4.2, 4.2.1, 4.2.2, 7.3.7pubmed, 3.2.1.7
     surface, 4.2.1purple box, 2.4.3.23
     peptide, 3.1.8qs hydrogen bond, 4.2.3
     properties, 3.1.8qsar, 7.4
pocketome, 3.2, 3.2.2quality, 2.4.1.15, 3.7.5
portait, 3.7.6quick, 3.1.14
postscript, 3.7.6     image, 5.15.2
powerpoint, 7.2     start move structure, 3.1.3
ppt, 6.12, 6.14          read pdb, 3.1.2
preferences, 3.7          representation, 3.1.6
presentatio, 6.6.5          selection, 3.1.5
presentation, 6.7, 6.12               level, 3.6.3
presentations, 6          what is selected, 3.6.4
print, 5.7     dispalay.distance, 5.9.1
printer.resolution, 3.7.6     start color, 3.1.7
project, 2.4.1.5quit, 2.4.1.19
     close, 2.4.1.13rainbow, 3.7.5, 5.8.15
     rename, 2.4.1.9ramachandran plot, 4.5, 4.5.10
properties, 5.8.2random forest, 7.4
protect, 6.6.7range, 5.10.7.2
protein, 4.4.6ratio.selection, 3.7.5
     structure, 4read, 2.4.1.3, 2.4.1.17, 3.4
          analysis, 4.5     pdb, 3.1.2
               closed cavities, 4.5.4rear, 5.3.10, 5.13.1
     pdb codes, 2.4.1.18scale, 3.7.5
receptor, 4.2.1, 4.2.2screenshot, 5.16, 5.16.2
recover, 2.4.2.11     movie, 5.16.2
redo, 2.4.2.10script, 3.3, 6.6.4, 6.6.5
regression, 7.4search chembl, 3.2.3
rename project, 2.4.1.9     drugbank, 3.2.8
representation, 2.4.3.19     in workspace, 2.4.2.4
residue, 3.7.7     pdb, 3.2.1
     alternative orientaiton, 7.3.11          chemical, 3.2.1
     range, 3.6.18          ligand code, 3.2.7
     content, 2.4.4     pocketome, 3.2.2
residues, 4.2.1, 4.2.2     pubchem, 3.2.9
resize, 5.3.9.1, 5.15.3     surechembl, 3.2.4
     mesh, 5.3.9.1     tab field, 3.2.1.3
resolution, 3.2.1.3          pdb chemical, 3.2.1.1
restore, 2.4.2.11, 5.3.10, 5.13.1               sequence, 3.2.1.2
     recent backup, 2.4.2.11     uniprot, 3.2.6
ribbon, 2.5.1, 3.7.9, 5.1.3     in.workspace, 2.4.2.4
     preferences, 3.7.9secondary.structure, 2.4.4, 5.1.3
     style, 3.7.9select, 3.6.12, 3.6.13
     breaks, 5.1.3     all, 3.6.14
     cylinders, 5.1.3     amino acid, 3.6.13
     smooth, 5.1.3     molecule, 3.6.12
     worm, 5.1.3     neighbors, 3.6.15
ribbonColorStyle, 3.7.9          graphic, 3.6.16
right, 3.1.12     object, 3.6.11
     click, 3.1.12     residue, 3.6.13, 3.6.18
rmsd, 4.5, 4.5.2          by number, 3.6.18
rock, 2.4.3.15, 5.10.7, 5.10.7.1, 6          number, 3.6.18
     speed, 5.10.7.2     atom, 3.1.5, 3.6.3
root mean square deviation, 4.5.2     graphical, 3.1.5, 3.6.3
rotate, 2.4.3.15, 3.1.3, 5, 5.10.7, 5.10.7.1, 5.12, 5.12.1, 5.12.2, 6     object, 3.1.5, 3.6.3
     easy, 2.4.3.12     purple.box, 2.4.3.23
     speed, 5.10.7.2     residue, 3.1.5, 3.6.3
rotation, 5.12.1     workspace, 3.1.5, 3.6.3
ruler, 5.8.15selectall, 2.4.2.3
salt bridge, 7.3.6selecting.neighbors, 3.6.16
save, 3.5, 5.3.11, 5.10.7.4selection, 3.6.4, 3.6.5, 3.6.21, 5.3.4
     file, 3.5     clear, 2.4.2.7
     object, 3.1.9     neighbors, 2.4.2.8
     pdb, 3.5     alignment, 3.6.19
     project icb, 3.1.10     all, 2.4.2.3
     slide, 6.4     alter, 3.6.7
     image, 2.4.1.15, 3.1.14     atom, 2.4.2.5
     object, 3.1.9     basic, 3.6.2
     password, 2.4.1.11     change, 3.6.7
     picture, 2.4.1.15     clear, 2.4.2.7
     project, 2.4.1.8, 2.4.1.9, 2.4.1.10, 3.1.10     filter, 2.4.2.5, 3.6.8
saving, 2.4.1.8     graphical, 3.6.16
     project, 2.4.1.8     invert, 2.4.2.6
     mode, 2.4.3.4spec, 2.5.2
     near atoms, 2.4.2.8speed, 5.10.7.2
     neighbors, 2.4.2.5, 2.4.2.8, 3.6.15, 3.6.17stereo, 3.7.6, 5.6
     object, 3.6.11     hardware, 2.4.3.7
     other, 3.6.19     side-by-side, 2.4.3.6
     properties, 2.4.2.5stick, 3.7.5
     residue, 2.4.2.5stl, 5.7
     sphere, 3.6.15stop, 5.10.7.3
     spherical, 2.4.2.8store, 2.4.3.19, 5.10.7.4
     superposition, 4.4.1     current view, 2.4.3.19
     table, 3.6.19structure, 4.3.3, 7.3
     tools, 3.6.1, 3.6.2, 3.6.7, 3.6.8     analysis, 7.3.4
     whole, 3.6.11     representation, 5.1
     workspace, 3.6.9, 3.6.17style, 3.7.5
selectioninvert, 2.4.2.6superimpose, 2.4.8, 4.4.2, 4.4.6, 7.3.3
selections, 3.6     3D, 4.4.3
selectneighbors workspace, 3.6.17     Calpha, 4.4.3
sequence, 2.4.4, 3.2, 3.2.1.2, 3.2.5, 3.2.6, 3.3, 7.3     arrange.grid, 4.4.5
     pattern, 3.2.1.2     backbone, 4.4.3
shading, 5.3.12     heavy atoms, 4.4.3
shadow, 5.10.2     multiple, 4.4.4
shell preferences, 3.7.10superposition, 7.3.3
shift, 5.8.3surface, 2.5.1, 3.7.5, 4.2.1, 4.2.2, 5.1.6, 5.3, 5.3.3, 5.3.4
shine, 2.5.2, 3.7.5     area, 4.5
shineStyle, 3.7.3     area, 4.5.5
show, 6.3.1surfaces, 4.2, 5.3.1, 5.3.2, 5.10.5
side by side stereo, 2.4.3.6symmetry, 4.3.1, 4.3.3, 7.3.8, 7.3.9
sigmaLevel, 4.3.6, 4.3.7system preferences, 3.7.11
sites, 4.4.6tab pdb, 2.5.4
size, 4.2.3.1table, 3.3
sketch accents, 5.10.3     join, 2.4.10.5
     accents, 2.4.3.14, 5.10.3     merge, 2.4.10.5
skin, 2.5.1, 5.1.4     rows, 2.4.10.7
slab, 5.3.10, 5.13.1     sort, 2.4.10.4
slice, 5.13tag, 3.6.21
slide, 5.10.7.4, 6.2, 6.3.1, 6.6.1tags, 3.6.21
     effects, 6.5text, 3.7.7, 6.6, 6.6.1, 6.6.6
     movie, 5.16.1texture, 2.5.6
          file, 6.2threshold, 3.7.5
     navigation, 6.3.2tier, 3.1.13
     show, 6.3tools 3D, 2.4.6
     blend, 6.5     analysis, 2.4.7
     edit, 6.4.1     append rows, 2.4.10.7
     effect, 6.5     extras, 2.4.9
     smooth, 6.5          plot function, 2.4.9.1
     transition, 6.5     superimpose, 2.4.8
slides, 5.16.1, 6, 6.1, 6.3     table, 2.4.10
smooth, 5.3.9.3          Learn, 2.4.10.1
solid, 5.3.9.3          clustering, 2.4.10.3
sort table, 2.4.10.4          merge, 2.4.10.5
torsion, 5.12.6workspace, 3.1.4
     angles, 5.12, 5.12.6     panel, 3.1.4
trace, 5.1.10     selection, 3.6.9
transitions, 6     navigation, 3.6.10
translate, 3.1.3, 5, 5.12write, 3.1.14, 3.5
translation, 5.12.3     image, 2.4.1.15
transparent, 5.3.9.3     images, 5.15
     background, 5.15.3     pdb, 3.5
tut analyze alternative orientations, 7.3.11     image, 2.4.1.15
          occupancy, 7.3.10     object, 3.1.9
          symmetry, 7.3.9     picture, 2.4.1.15
tut3e, 7.3.12     project, 2.4.1.8, 3.1.10
tutorial molecular documents, 7.2     ray, 2.4.5
tutorials, 7xi, 5.8.5
unclip, 5.3.10, 5.13.1xstick, 5.1.2
undisplay, 3.1.4, 5.1.7zoom, 3.1.3, 5, 5.12, 5.12.4
     origin, 5.8.11 
undo, 2.4.2.9, 3.7 
uniprot, 3.2.6 
unit, 4.3.3 
unusual peptide, 3.3 
     activeicm, 6.12 
uundisplay-all, 2.4.3.1 
van der waal, 5.8.14 
variable, 3.7.7 
video, 5.16, 5.16.1, 5.16.2 
view, 2.4.3.19, 6.3.1 
     animate view, 2.4.3.15 
     center, 2.4.3.20 
     color background, 2.4.3.18 
     fog, 2.4.3.5 
     macroshape, 2.4.3.22 
     menu, 2.4.3 
     mesh clip, 5.13.1 
     perspective, 2.4.3.9 
     selection level, 2.4.3.3 
          mode, 2.4.3.4 
     shadow, 2.4.3.13 
     sketch accents, 2.4.3.14 
     slide show, 6.3.1 
     tools, 2.4.3 
     undisplay all, 2.4.3.1 
virus, 4.3.3 
wavefront, 2.5.6, 5.3.11 
web, 7.2 
     browser, 2.4.1.12 
window, 3.1.13 
windows, 3.1.13.1 
wire, 2.5.1, 3.7.5, 5.1.1 
wireBondSeparation, 3.7.1 

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