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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, 3.4.5     font Scale, 4.7.7
     object, 6.3.8     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, 5.4               Style, 4.7.1
4D docking, 4.2.2     hbondAngleSharpness, 4.7.1
ActiveICM, 3.3.1.11     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, 3.3.1.6     light, 4.7.3
CPK, 3.4.1     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, 3.3.1.14     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, 4.7.3Output Directory, 4.7.2
GUI.auto Save, 4.7.4PDB, 4.2.1.6, 5.1.2, 5.4
               Interval, 4.7.4     Directory, 4.7.2
     enumeration Memory Limit, 4.7.11          Style, 4.7.2
     max Nof Recent Files, 4.7.11     Search, 3.3.2.12, 3.3.2.13, 3.3.2.14, 3.3.2.15, 3.3.2.16
          Sequence Length, 4.7.4          Field, 3.3.2.13
     splash Screen Delay, 4.7.11          Homology, 3.3.2.15
               Image, 4.7.11          Identity, 3.3.2.14
     table Row Mark Colors, 4.7.4          Sequence, 3.3.2.16
     workspace Folder Style, 4.7.4     convert, 5.1.2
     workspaceTabStyle, 4.7.4PFAM, 3.3.1.6
HTTP.proxy, 4.7.11PLOT.Yratio, 4.7.8
     support Cookies, 4.7.11     color, 4.7.8
     user Agent, 4.7.11     date, 4.7.8
How To Guide, 3     draw Tics, 4.7.8
Html, 4.2.1.6     font, 4.7.8
Http Read Style, 4.7.11     fontSize, 4.7.8
Hydrogen.bond, 4.7.5     labelFont, 4.7.8
ICM Browser How To, 3.1     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, 3.3.1.14, 4.1.14
     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, 5.3.2
     stereoText, 4.7.6RNA, 4.3
Icm Prompt, 4.7.10Real Format, 4.7.10
Inx Directory, 4.7.2     Label Shift, 4.7.7
JPEG, 3.3.1.14          Style, 4.7.7
KMZ, 3.3.1.6SEQUENCE.site Colors, 4.7.4
Log Directory, 4.7.2SITE.label Style, 4.7.7
MD, 8, 8.1, 8.2, 8.3, 8.4     labelOffset, 4.7.7
MOVIE.frame Grab Mode, 4.7.4     wrap Comment, 4.7.7
Map Atom Margin, 4.7.10SLIDE.ignore Background Color, 4.7.4
     Sigma Level, 4.7.10          Fog, 4.7.4
     File Size Mb, 4.7.11Select Min Grad, 4.7.10
Mnconf, 4.7.10Show Res Code In Selection, 4.7.7
Movie.fade Nof Frames, 4.7.4SureChEMBL, 4.2.4
     quality, 4.7.4Swissprot, 3.3.1.6
          Auto, 4.7.4     Dat, 4.7.2
USER.email, 4.7.11ball, 4.7.5
     friends, 4.7.11     and stick, 3.4.1
     full Name, 4.7.11basicsel, 4.6.2
     organization, 4.7.11binding properties, 6.3.1
     phone, 4.7.11blast, 4.2.5
Var Label Style, 4.7.7     search, 4.2.5
Water Radius, 4.7.10bond, 5.2.3, 5.2.3.1, 5.2.3.2
Wire Style, 4.7.1bonding, 6.1.8
XPDB Directory, 4.7.2     preferences, 4.7.1
Xstick, 3.4.1box, 4.7.7
a-bright, 3.4.2build, 6.10.6.1
active, 7.7buttons, 7.14
activeICM, 7.8bye, 3.3.1.18
activeicm, 7.7, 7.12, 7.14, 7.14.1     alpha, 6.1.10
     advanced, 7.14     trace, 6.1.10
     background images, 7.15ca-trace, 6.1.10
     control, 7.13cache, 7.14.1
activeicmjs, 7.16cation, 5.2.5
album, 6.15.3center, 3.3.3.19, 4.1.3, 6.12, 6.12.5
align, 4.1.11change selection, 4.6.7
alpha, 3.4.2     speed range, 6.10.6.2
     channel, 4.7.6charge, 6.8.2
ambient, 3.4.2check box, 7.6.6
amino acid, 4.3chembl, 4.2.3, 4.2.4
anaglyph, 6.6chemical spreadsheet, 4.2.3
angle, 6.8.5, 6.9, 6.12.6     substructure, 4.2.1.1
animate, 3.3.3.14, 6.10.6chi, 6.8.5
     view, 6.10.6clash, 4.7.5
animation, 6.10.6.1, 6.10.6.2, 6.10.6.3, 6.10.6.4clear display and planes, 3.3.3.2
     store, 6.10.6.4     selection, 4.6.6
animations, 7     planes, 3.3.3.2
annotate, 4.6.21click, 4.1.12, 6.11, 6.12
antialias, 3.3.1.14, 3.3.3.10clip, 6.3.9, 6.13.1
     lines, 3.3.3.16clipboard, 6.15.3
     lines, 3.3.3.16clipping planes, 6
apf, 5.5     tool, 6.13
arrange, 4.1.13.1     tools, 6.13
     window, 4.1.13.1clone, 3.3.1.2
as2_graph, 4.6.5close, 6.3.3, 6.3.4
assign, 6.1.3collada, 3.4.6, 6.3.6
atom, 4.7.5color, 6.3.2, 6.3.3, 6.3.4, 6.3.8.4, 6.4, 6.4.1, 6.8.2, 6.8.3
atomLabelStyle, 4.7.7     background, 6.4.2
atomic property fields, 5.5     by, 6.4
author, 4.2.1.3     surface by proximity, 6.3.3
     play slide, 7.13               selection, 6.3.4
backbone, 6.1.10     background, 3.3.3.17, 6.4.2
background, 6.4.2, 6.4.3     distance, 6.8.10
     images activeicm, 7.15     mesh, 6.3.8.3
     image, 6.4.3coloring, 6.4.1
backup, 3.3.2.11combo display style, 4.7.9
compound, 4.2.1.3     distance, 6.8.10, 6.9.1
compress, 4.7.6     hydrogen, 6.1.7
connect, 6.3.8.1, 6.12, 6.12.7          polar, 6.1.7
     object, 6.12.7     meshes, 6.3.5
construct, 3.3.1.1, 6.10.6.1          and display.macroshape, 3.4.6
     molecule, 3.3.1.1     origin, 6.8.12
     object, 3.3.1.1     representations, 3.4.1
contact surface, 6.3.2     ribbon, 6.1.3
contacts, 6.3.3, 6.3.4     skin, 6.1.4
convert, 5.1.2     surface, 6.1.6, 6.3.1
converting pdb, 5.1.2     surfaces, 3.4.6
cpk, 6.1.5     wire, 6.1.1
crash, 3.3.2.11     xstick, 6.1.2
creat, 7.6.1distance, 6.8.10, 6.9
     new objects, 4.3     label, 4.7.7
cross section, 6.13distances, 3.4.3
current.slide, 7.13document, 7.6.4, 7.6.5
custom, 6.12     navigation, 7.6.7
     label, 6.8.8documents, 6.15.3
     rotation, 6.12.2     envelope, 3.4.1
default, 4.1.13     surface, 4.7.5
delete, 3.3.2.1, 4.6.6, 7.6.8dotted line, 6.1.3
     all, 3.3.2.2drag, 4.1.11, 4.7.7, 6.8.3, 7.6.4
     label, 6.8.9     residue label, 3.3.3.15
     all, 3.3.2.2draganddrop, 4.1.11
     angle.label, 6.9.4drop, 4.1.11, 7.6.4
     distance.label, 6.9.4drug bank, 4.2, 4.2.8
     label, 6.8.9dsPocket, 4.1.8
     selection, 3.3.2.1easy rotate, 3.3.3.12
depth, 6.3.11, 6.10.4edit, 5.2.3.1
dialog, 7.6.5     ligand tools, 3.3.2.17
diffuse, 3.4.2     menu, 3.3.2
dihedral, 6.8.5     molecular document, 7.6.1
directories preferences, 4.7.2     selection, 3.3.2.5
directory, 4.7     slide, 7.4.1
display, 4.1.4, 4.1.13.1, 4.7, 5.2.3, 5.2.3.1, 5.2.3.2, 6.14editpdbsearch, 3.3.2.12
     chemical, 6.8.11electron density map, 3.3.1.6
     delete distances, 6.9.4electrostatic surface, 6.3
     dihedral, 6.9.3electrostatics, 6.3.1
     distance2, 6.9.1elegant sketch, 6.10.3
          angles, 6.9embed browser, 7.11
     formal charge, 6.1.9     powerpoint03, 7.8
     hydrogen, 6.1.7     powerpoint07, 7.9
     mesh, 6.3.5     powerpoint10, 7.10
     meshes, 6.3.7     activeicm, 7.13
     planar angle, 6.9.2          script, 7.13
     tab, 3.4.1     browser, 7.7, 7.11
     CPK, 6.1.5     firefox, 7.7, 7.11
     angle, 6.9.2     internet.explorer, 7.7, 7.11
     dihedral.angle, 6.9.3     microsoft, 7.7
exit, 3.3.1.18h-bond, 5.2.3, 5.2.3.1, 5.2.3.2
export pdb, 4.5hardware stereo, 3.3.3.7
extra windows, 6.2hbond, 5.2
extract, 4.4.2header, 4.2.1.6
     icb, 3.3.1.5help, 2
     object icb, 4.4.2     videos, 2
     icb, 3.3.1.5high, 3.3.1.14
file, 3.3.1.3     quality, 3.3.3.11
     close, 3.3.1.12historeceptomics, 4.2.10
     compatible, 3.3.1.9hitlist, 8.4
     export, 3.3.1.11homology, 4.2.1.2, 4.2.5
     high quality image, 6.15.1     to activeicm, 3.2
     load, 3.3.1.6               create molecular documents, 3.2.3
     menu, 3.3.1                    slides, 3.2.2
     password, 3.3.1.10               getting started, 3.2.1
     preferences, 3.3.1.15               ppt, 3.2.4
     quick image, 3.3.1.13               web, 3.2.5
     icb, 4.1.10          icm browser convert display pocket, 3.1.4
     recent, 3.3.1.16                    distances angles, 3.1.9
     bak, 3.3.2.11                    get started, 3.1.1
filter selection, 4.6.8                    graphical display, 3.1.2
fog, 3.3.3.5, 6, 6.10.1                         effects, 3.1.5
font, 4.7, 4.7.7, 5.2.3.1, 6.8.2, 6.8.3                    images, 3.1.7
     preferences, 4.7.7                    labels annotation, 3.1.6
formal charge, 6.1.9                    selections, 3.1.3
front, 6.3.9, 6.13.1                    superimpose, 3.1.8
full scene antialias, 3.3.3.10          search, 4.2
     screen, 3.3.3.8          use gui, 4.1
general preferences, 4.7.5html, 3.3.1.11, 4.3, 7.6.1, 7.6.7
generalselecttools, 4.6.1hydrogen, 5.2.3, 5.2.3.1, 5.2.3.2, 6.1.8
getting started, 4     bond, 5.2, 6.1.8
glasses, 6.6          label edit, 5.2.3.1
google, 3.3.1.6               move, 5.2.3.2
     objects, 6.3.6     bonds, 5.2.4
     3D, 3.4.6, 6.3.6hyperlink, 7.6.1, 7.6.2
graphical display tutorial, 9.1iSee, 3.3.1.5, 3.3.1.11, 4.1.10, 6.15.3, 9.2
               2D3D labels, 9.1.4icb, 4.4.2, 4.5
               annotation, 9.1.2     object, 5.1
               color representation, 9.1.1icmjs, 7.16
               labels, 9.1.3identity, 4.2.1.2
graphics, 4.1image, 4.1.14, 4.7, 4.7.5, 6.15.3, 7.6.3
     controls, 6     advanced, 6.15.3
     effects, 6.10     preferences, 4.7.6
     panel, 6.2     multiple, 3.3.1.6
     preferences, 4.7.3     quality, 3.3.3.11
grob, 4.7.5, 6.3     quick, 3.3.1.13, 6.15.2
gui, 4.1.1, 4.7.4images, 6.15
     menus, 3.3insert, 7.6.4
     preferences, 4.7.4     image, 7.6.3
     tabs, 3.4     script, 7.6.4
interrupt, 6.10.6.3line, 4.7.5
     animation, 6.10.6.3lineWidth, 4.7.3
introduction icm browser, 1links, 4.6.20
isee, 7.6.5list, 4.6.18
javascript, 7.16load, 3.3.1.3, 3.3.1.16
jpg, 6.15     nmr model, 4.2.1.4
keyboard mouse, 6.11     protein structure, 5.1.1
kmz, 3.4.6, 6.3.6lock, 6.3.9, 6.13.1
label, 4.7.7logout, 3.3.1.18
     atoms, 6.8.2macros, 7.14
     color, 6.8.7macroshape, 6.3
     move, 6.8.4make, 6.10.6.1
     residues, 6.8.3     animation, 6.10.6.1
     sites, 6.8.6     molecular document, 7.6
     variables, 6.8.5     selection, 4.6
     2D, 3.4.3     molecule, 3.3.1.1
     3D, 3.4.3, 6.8.1     object, 3.3.1.1
     atom, 6.8.1making molecular slides, 7.1
     atoms, 6.8.2     html, 7.6
     color, 6.8.7map, 4.7.7
     custom, 6.8.8materials, 3.4.6
     delete, 6.8.1, 6.8.9maxColorPotential, 4.7.10
     distance, 6.8.10membrane, 8.3
     drag, 3.3.3.15menu, 7.6.5
     move, 3.3.3.15, 6.8.4     windows, 3.3.4
     residue, 6.8.1mesh, 5.2.1, 5.2.2, 6.3, 6.3.8.1, 6.3.8.2, 6.3.8.4, 6.3.9, 6.3.10, 6.3.11, 6.13.1
     residues, 6.8.3     clip, 6.3.9
     site, 6.8.1     color lighting, 6.3.8.4
     sites, 6.8.6     options, 6.3.8
     variable, 6.8.1     representation, 6.3.8.3
     variables, 6.8.5     save, 6.3.10
labeling, 6.8.1     options, 6.3.8
labels, 6.8meshes, 6.3.2, 6.10.4
     distances, 6.8.10     surfaces grobs, 6.3
     tab, 3.4.3     tab, 3.4.6
landscape, 4.7.6mmff type, 6.8.2
layer, 6.14mnSolutions, 4.7.10
layers, 6.14molecular animations slides, 7
ligand, 5.2.2     documents, 9.2
     code, 4.2.1.3, 4.2.7     dynamics, 8, 8.1, 8.2, 8.3, 8.4
     editor preferences, 3.3.2.18          membrane, 8.3
     pocket, 5.2.4          restraints, 8.2
     receptor display, 5.2          run, 8.1
     surface, 5.2.2          vls, 8.4
     pocket, 4.1.8     graphics, 6
ligand_pocket_interactions, 5.2.4molskin, 6.3.2
ligedit tab, 3.4.5mouse, 4.1.3, 6.11, 6.12
light, 3.4.2move, 3.3.3.18, 4.1.11, 4.1.13, 5.2.3.2, 6.3.8.1, 6.3.8.2, 6.12, 6.12.7
     tab, 3.4.2     mesh, 6.3.8.2
lighting, 6.3.8.4, 6.5     slide, 7.4.2
     tools, 6     cation, 5.2.5
     rotate, 6.11     pi, 5.2.5
     slab, 6.11picking, 6
     translate, 6.11picture, 3.3.1.13, 4.1.14, 6.15.2, 7.6.3
     z-rotation, 6.11     tips, 4.1.14
     zoom, 6.11pipi, 5.2.5
mtl, 6.7planar, 6.8.5
multi panel, 6.2     angle, 6.9.2
     windows, 6.2plane, 6.3.9, 6.13, 6.13.1, 6.14
multiple receptor, 4.2.2plot, 4.7, 4.7.8
navigate workspace, 4.6.10     preferences, 4.7.8
neural network Torsion Profile Neural Network Prediction Engine, 6.12.6.1png, 3.3.1.13, 6.15, 6.15.2, 7.6.3
     icm session, 3.3.1.2pocket, 4.1.8, 5.2, 5.2.1, 5.2.2
nmr model, 4.2.1.4     properties, 5.5
nntorsion, 6.12.6.1     surface, 5.2.1
non-contiguous selection, 4.6.18     peptide, 4.1.8
obj, 6.7     properties, 4.1.8
object, 4.1.11, 4.5pocketome, 4.2, 4.2.2, 5.5
objects, 5.1.2portait, 4.7.6
occlusion, 6.3.11, 6.10.4postscript, 4.7.6
     shading, 6.3.11ppt, 7.12, 7.14
          effect, 6.10.4preferences, 4.7
occupancy, 6.1.3presentation, 7.6.5, 7.7, 7.12
     display, 4.2.1.5presentations, 7
older version, 3.3.1.9print, 6.7
omega, 6.8.5printer.resolution, 4.7.6
open, 3.3.1.3, 4.4profile, 4.2.10
     file, 4.4project, 3.3.1.5
     password, 4.4.1     close, 3.3.1.12
     with password, 3.3.1.4     rename, 3.3.1.8
     password, 3.3.1.4, 4.4.1properties, 6.8.2
orange, 4.6.5protect, 7.6.8
     selection, 4.6.5protein structure, 5
origin, 6.8.12          similarity, 5.4
other selection, 4.6.19     superposition, 5.3
package.activeicm, 7.13          select, 5.3.1
pdb, 3.3.1.6, 4.2, 4.2.1.1, 4.2.7, 4.5proximity, 6.3.3, 6.3.4
     dormat, 4.5psi, 6.8.5
     html, 4.2.1.6publication quality images, 6.3.2
     search, 4.2.1, 4.2.1.2, 4.2.1.3pubmed, 4.2.1.7
     recent, 3.3.1.17purple box, 3.3.3.20
     search, 3.4.4, 4.1.2qs hydrogen bond, 5.2.3
pdbsearchfield, 3.3.2.13quality, 3.3.1.14, 4.7.5
pdbsearchhomology, 3.3.2.15quick, 4.1.14
pdbsearchidentity, 3.3.2.14     image, 6.15.2
pdbsearcsequence, 3.3.2.16     start move structure, 4.1.3
peptide, 4.3          read pdb, 4.1.2
perspective, 3.3.3.9, 6.10.5          representation, 4.1.6
phi, 6.8.5          selection, 4.1.5
pi, 5.2.5               level, 4.6.3
     display.distance, 6.9.1     project icb, 4.1.10
     start color, 4.1.7     slide, 7.4
quit, 3.3.1.18     image, 3.3.1.14, 4.1.14
rainbow, 4.7.5     object, 4.1.9
range, 6.10.6.2     password, 3.3.1.10
ratio.selection, 4.7.5     picture, 3.3.1.14
read, 3.3.1.3, 3.3.1.16, 4.4     project, 3.3.1.7, 3.3.1.8, 3.3.1.9, 4.1.10
     pdb, 4.1.2saving, 3.3.1.7
rear, 6.3.9, 6.13.1     project, 3.3.1.7
recent files, 3.3.1.16scale, 4.7.5
     pdb codes, 3.3.1.17scan_pockets, 5.5
receptor, 5.2.1, 5.2.2screening, 8.4
recover, 3.3.2.11script, 4.3, 7.6.4, 7.6.5
redo, 3.3.2.10search, 5.4
rename project, 3.3.1.8     chembl, 4.2.3
representation, 3.3.3.18     drugbank, 4.2.8
residue, 4.7.7     in workspace, 3.3.2.4
     range, 4.6.18     pdb, 4.2.1
residues, 5.2.1, 5.2.2          chemical, 4.2.1
resize, 6.3.8.1, 6.15.3          ligand code, 4.2.7
     mesh, 6.3.8.1     pocketome, 4.2.2
resolution, 4.2.1.3     pubchem, 4.2.9
restore, 3.3.2.11, 6.3.9, 6.13.1     surechembl, 4.2.4
     recent backup, 3.3.2.11     tab field, 4.2.1.3
restraints, 8.2          pdb chemical, 4.2.1.1
ribbon, 3.4.1, 4.7.9, 6.1.3               sequence, 4.2.1.2
     preferences, 4.7.9     uniprot, 4.2.6
     style, 4.7.9     in.workspace, 3.3.2.4
     breaks, 6.1.3secondary.structure, 6.1.3
     cylinders, 6.1.3select, 4.6.12, 4.6.13
     smooth, 6.1.3     all, 4.6.14
     worm, 6.1.3     amino acid, 4.6.13
ribbonColorStyle, 4.7.9     molecule, 4.6.12
right, 4.1.12     neighbors, 4.6.15
     click, 4.1.12          graphic, 4.6.16
ring, 5.2.5     object, 4.6.11
     stacking, 5.2.5     residue, 4.6.13, 4.6.18
rock, 3.3.3.14, 6.10.6, 6.10.6.1, 7          by number, 4.6.18
     speed, 6.10.6.2          number, 4.6.18
rotate, 3.3.3.14, 4.1.3, 6, 6.10.6, 6.10.6.1, 6.12, 6.12.1, 6.12.2, 7     atom, 4.1.5, 4.6.3
     torsion, 6.12.6.1     graphical, 4.1.5, 4.6.3
     easy, 3.3.3.12     object, 4.1.5, 4.6.3
     speed, 6.10.6.2     purple.box, 3.3.3.20
rotation, 6.12.1     residue, 4.1.5, 4.6.3
save, 4.5, 6.3.10, 6.10.6.4     workspace, 4.1.5, 4.6.3
     as PDB, 4.5selectall, 3.3.2.3
          pdb, 4.5selecting.neighbors, 4.6.16
     file, 4.5selection, 4.6.4, 4.6.5, 4.6.21, 6.3.4
     object, 4.1.9     clear, 3.3.2.7
     pdb, 4.5     neighbors, 3.3.2.8
     all, 3.3.2.3     effect, 7.5
     alter, 4.6.7     smooth, 7.5
     atom, 3.3.2.5     transition, 7.5
     basic, 4.6.2slides, 7, 7.1, 7.3
     change, 4.6.7smooth, 6.3.8.3
     clear, 3.3.2.7solid, 6.3.8.3
     filter, 3.3.2.5, 4.6.8spec, 3.4.2
     graphical, 4.6.16speed, 6.10.6.2
     invert, 3.3.2.6stacking, 5.2.5
     level, 3.3.3.3stereo, 4.7.6, 6.6
     mode, 3.3.3.4     hardware, 3.3.3.7
     near atoms, 3.3.2.8     side-by-side, 3.3.3.6
     neighbors, 3.3.2.5, 3.3.2.8, 4.6.15, 4.6.17stick, 4.7.5
     object, 4.6.11stl, 6.7
     other, 4.6.19stop, 6.10.6.3
     properties, 3.3.2.5store, 3.3.3.18, 6.10.6.4
     residue, 3.3.2.5     current view, 3.3.3.18
     sphere, 4.6.15strain, 6.12.6.1
     spherical, 3.3.2.8structure representation, 6.1
     superposition, 5.3.1style, 4.7.5
     table, 4.6.19superimpose, 5.3.2
     tools, 4.6.1, 4.6.2, 4.6.7, 4.6.8surface, 3.4.1, 4.7.5, 5.2.1, 5.2.2, 6.1.6, 6.3, 6.3.3, 6.3.4
     whole, 4.6.11surfaces, 5.2, 6.3.1, 6.3.2, 6.10.4
     workspace, 4.6.9, 4.6.17system preferences, 4.7.11
selectioninvert, 3.3.2.6tab pdb, 3.4.4
selections, 4.6table, 4.3
selectneighbors workspace, 4.6.17tag, 4.6.21
sequence, 4.2, 4.2.1.2, 4.2.5, 4.2.6, 4.3tags, 4.6.21
     pattern, 4.2.1.2text, 4.7.7, 7.6, 7.6.1, 7.6.7
shading, 6.3.11texture, 3.4.6
shell preferences, 4.7.10threshold, 4.7.5
shift, 6.8.3tier, 4.1.13
shine, 3.4.2, 4.7.5tissue, 4.2.10
shineStyle, 4.7.3torsion, 6.12.6, 6.12.6.1
show, 7.3.1     angles, 6.12, 6.12.6
side by side stereo, 3.3.3.6trace, 6.1.10
simulation, 8, 8.1, 8.2, 8.3, 8.4transitions, 7
size, 5.2.3.1translate, 4.1.3, 6, 6.12
sketch accents, 6.10.2translation, 6.12.3
     accents, 3.3.3.13, 6.10.2transparent, 6.3.8.3
skin, 3.4.1, 6.1.4     background, 6.15.3
slab, 6.3.9, 6.13.1tutorial molecular documents, 9.2
slice, 6.13tutorials, 9
slide, 6.10.6.4, 7.2, 7.3.1, 7.6.1unclip, 6.3.9, 6.13.1
     effects, 7.5undisplay, 4.1.4, 6.1.7
     movie file, 7.2undisplay-all, 3.3.3.1
     navigation, 7.3.2     origin, 6.8.12
     show, 7.3undo, 3.3.2.9, 4.7
     blend, 7.5uniprot, 4.2.6
     edit, 7.4.1unusual peptide, 4.3
variable, 4.7.7 
video, 2 
view, 3.3.3.18, 7.3.1 
     animate view, 3.3.3.14 
     center, 3.3.3.19 
     color background, 3.3.3.17 
     fog, 3.3.3.5 
     menu, 3.3.3 
     mesh clip, 6.13.1 
     perspective, 3.3.3.9 
     selection level, 3.3.3.3 
          mode, 3.3.3.4 
     sketch accents, 3.3.3.13 
     slide show, 7.3.1 
     tools, 3.3.3 
     undisplay all, 3.3.3.1 
vls, 8.4 
wavefront, 3.4.6, 6.3.10, 6.7 
web, 9.2 
     browser, 3.3.1.11 
window, 4.1.13 
windows, 4.1.13.1 
wire, 3.4.1, 4.7.5, 6.1.1 
wireBondSeparation, 4.7.1 
workspace, 4.1.4 
     panel, 4.1.4 
     selection, 4.6.9 
     navigation, 4.6.10 
write, 4.1.14, 4.5 
     image, 3.3.1.14 
     images, 6.15 
     pdb, 4.5 
     image, 3.3.1.14 
     object, 4.1.9 
     picture, 3.3.1.14 
     project, 3.3.1.7, 4.1.10 
xi, 6.8.5 
xstick, 6.1.2 
youtube, 2 
zoom, 4.1.3, 6, 6.12, 6.12.4 

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