Aug 11 2015 Feedback.
Contents
 
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Sequences & Alignments
Tutorials
 
Index

Index

2D, 4.7.8     dnaRibbonWorm, 2.7.9
3D, 4.5, 4.7.8, 7.2     dnaStickRadius, 2.7.9
     interactive ligand editor, 1.6.5     dnaWormRadius, 2.7.9
     object, 4.2.9     font Scale, 2.7.7
     print, 4.6     fontColor, 2.7.7
     printing, 4.6     fontLineSpacing, 2.7.7
     stereo, 4.5     grobLineWidth, 2.7.3
     predict local flexibility, 3.5.12     hbond Ball Period, 2.7.1
          protein health, 3.5.11               Style, 2.7.1
          tools identify ligand binding pocket, 3.5.14     hbondAngleSharpness, 2.7.1
               oda, 3.5.13     hbondMinStrength, 2.7.1
4D docking, 2.2.2     hbondStyle, 2.7.1
ActiveICM, 1.5.1.11     hbondWidth, 2.7.1
Atom Single Style, 2.7.3     hetatmZoom, 2.7.1
Beep, 2.7.11     hydrogenDisplay, 2.7.1
BlastDB Directory, 2.7.2     light, 2.7.3
     alphas, 4.7.3     lightPosition, 2.7.3
COLLADA, 1.5.1.6     mapLineWidth, 2.7.3
CPK, 1.6.1     occupancy Radius Ratio, 2.7.3
Clash Threshold, 2.7.10     occupancyDisplay, 2.7.3
DNA, 2.3, 6, 6.3.3     quality, 2.7.3
Dock Directory, 2.7.2     rainbow Bar Style, 2.7.4
Editor, 2.7.2     resLabelDrag, 2.7.7
FILTER.Z, 2.7.2     resize Keep Scale, 2.7.3
     gz, 2.7.2     ribbonRatio, 2.7.9
     uue, 2.7.2     ribbonWidth, 2.7.9
FTP.createFile, 2.7.11     ribbonWorm, 2.7.9
     keep File, 2.7.11     rocking, 2.7.4
     proxy, 2.7.11          Range, 2.7.4
Filter.zip, 2.7.2          Speed, 2.7.4
Force Auto Bond Typing, 2.7.11     selectionStyle, 2.7.3
GIF, 1.5.1.14, 4.15, 4.15.2     site Label Drag, 2.7.7
GRAPHIC.store Display, 2.7.3               Shift, 2.7.7
     NtoC Rainbow, 2.7.4     siteArrow, 2.7.7
     alignment Rainbow, 2.7.4     stereoMode, 2.7.3
     atomLabelShift, 2.7.7     stickRadius, 2.7.1
     ballStickRatio, 2.7.1     surfaceDotDensity, 2.7.3
     center Follows Clipping, 2.7.3     surfaceDotSize, 2.7.3
     clash Style, 2.7.3     surfaceProbeRadius, 2.7.3
     clashWidth, 2.7.3     transparency, 2.7.3
     clip Grobs, 2.7.3     wire Width, 2.7.1
          Skin, 2.7.3     wormRadius, 2.7.9
          Static, 2.7.3     xstick Backbone Ratio, 2.7.1
     discrete Rainbow, 2.7.4          Hydrogen Ratio, 2.7.1
     displayLineLabels, 2.7.7          Style, 2.7.1
     displayMapBox, 2.7.3          Vw Ratio, 2.7.1
     distance Label Drag, 2.7.1GROB.arrowRadius, 2.7.3
     dnaBallRadius, 2.7.9     atomSphereRadius, 2.7.3
     dnaRibbonRatio, 2.7.9     contourSigmaIncrement, 2.7.3
     dnaRibbonWidth, 2.7.9     relArrow Size, 2.7.3

GUI.auto Save, 2.7.4PDB, 2.2.1.6, 3.1.2, 3.3.3, 6.1
               Interval, 2.7.4     Directory, 2.7.2
     enumberation Memory Limit, 2.7.11          Style, 2.7.2
     max Nof Recent Files, 2.7.11     Search, 1.5.2.12, 1.5.2.13, 1.5.2.14, 1.5.2.15, 1.5.2.16
          Sequence Length, 2.7.4          Field, 1.5.2.13
     splash Screen Delay, 2.7.11          Homology, 1.5.2.15
               Image, 2.7.11          Identity, 1.5.2.14
     table Row Mark Colors, 2.7.4          Sequence, 1.5.2.16
     workspace Folder Style, 2.7.4     convert, 3.1.2
     workspaceTabStyle, 2.7.4PFAM, 1.5.1.6
HTTP.proxy, 2.7.11PLOT.Yratio, 2.7.8
     support Cookies, 2.7.11     color, 2.7.8
     user Agent, 2.7.11     date, 2.7.8
How To Guide, 1     draw Tics, 2.7.8
Html, 2.2.1.6     font, 2.7.8
Http Read Style, 2.7.11     fontSize, 2.7.8
Hydrogen.bond, 2.7.5     labelFont, 2.7.8
ICM Browser How To, 1.1     lineWidth, 2.7.8
          Pro How To, 1.2     logo, 2.7.8
IMAGE.bondLength2D, 2.7.6     markSize, 2.7.8
     color, 2.7.6     orientation, 2.7.8
     compress, 2.7.6     paper Size, 2.7.8
     gammaCorrection, 2.7.6     previewer, 2.7.8
     generateAlpha, 2.7.6     rainbowStyle, 2.7.8
     lineWidth, 2.7.6     seriesLabels, 2.7.8
     lineWidth2D, 2.7.6PNG, 1.5.1.14, 2.1.14, 4.15, 4.15.2
     orientation, 2.7.6Projects Directory, 2.7.2
     paper Size, 2.7.6Prosite Dat, 2.7.2
     previewResolution, 2.7.6     Viewer, 2.7.2
     previewer, 2.7.6Pub Chem, 2.2.7
     print, 2.7.6PubMed, 2.2.1.7
     printerDPI, 2.7.6Pubchem, 2.2.7
     scale, 2.7.6RMSD, 3.4.2
     stereoAngle, 2.7.6RNA, 2.3
     stereoBase, 2.7.6Ramachandran Plot, 3.5.9
     stereoText, 2.7.6Real Format, 2.7.10
Icm Prompt, 2.7.10     Label Shift, 2.7.7
Inx Directory, 2.7.2          Style, 2.7.7
JPEG, 1.5.1.14SEQUENCE.site Colors, 2.7.4
KMZ, 1.5.1.6SITE.label Style, 2.7.7
Log Directory, 2.7.2     labelOffset, 2.7.7
MOVIE.frame Grab Mode, 2.7.4     wrap Comment, 2.7.7
Map Atom Margin, 2.7.10SLIDE.ignore Background Color, 2.7.4
     Sigma Level, 2.7.10          Fog, 2.7.4
     File Size Mb, 2.7.11Select Min Grad, 2.7.10
Mnconf, 2.7.10Show Res Code In Selection, 2.7.7
Movie.fade Nof Frames, 2.7.4Swissprot, 1.5.1.6
     quality, 2.7.4     Dat, 2.7.2
          Auto, 2.7.4Temp Directory, 2.7.2
Output Directory, 2.7.2USER.email, 2.7.11

     full Name, 2.7.11     image, 6.6.2
     organization, 2.7.11     multiple, 6.3.7, 6.5.5
     phone, 2.7.11     options, 6.6.10
Var Label Style, 2.7.7     rename, 6.6.10
Water Radius, 2.7.10     reorder, 6.3.11
Wire Style, 2.7.1     ruler, 6.6.10
XPDB Directory, 2.7.2     save, 6.6.2
Xstick, 1.6.1     search, 6.6.12
a-bright, 1.6.2     selection, 6.6.13, 6.6.14
active, 5.7     sequence offset, 6.6.10
activeICM, 5.8     table, 6.6.10
activeicm, 5.7, 5.12, 5.14, 5.14.1     view, 6.6.10
     advanced, 5.14alignments, 6.5, 7.4
     background images, 5.15alpha, 1.6.2
     control, 5.13     channel, 2.7.6
advanced alignment selection, 6.6.14ambient, 1.6.2
album, 4.14.3amino acid, 2.3
align, 2.1.11anaglyph, 4.5
     dna protein, 6.5.4analysis, 1.5.4, 6.3
     multiple, 6.5.5angle, 3.5.7, 3.5.8, 4.7.5, 4.8, 4.11.6
     sequence structure, 6.5.3animate, 1.5.3.15, 4.9.7
     two sequences, 6.5.2     view, 4.9.7
     DNA to protein, 6.5.4animation, 4.9.7.1, 4.9.7.2, 4.9.7.3, 4.9.7.4
     sequence, 6.5, 6.5.6     store, 4.9.7.4
     two sequences, 6.3.5, 6.5.2animations, 5
alignment, 6.5.1, 6.6.7, 6.6.7.1, 6.6.16, 7.4.4annotate, 2.6.20
     annotation tutorial, 7.4.4     alignment, 6.6.6
     box shade font, 6.6.7annotation, 6.6.6
     editing, 6.6.1antialias, 1.5.1.14, 1.5.3.10
     editor, 6.6     lines, 1.5.3.17
     example, 6.3.13     lines, 1.5.3.17
     format, 6.6.11apf, 3.4.6
     gaps, 6.6.11append.rows, 1.5.10.7
     image, 6.6.2area, 3.5.3, 3.5.13, 7.3.5
     profile, 7.4.4arrange, 2.1.13.1
     reorder, 6.3.11     window, 2.1.13.1
     search, 6.6.12as2_graph, 2.6.5
     secondary, 7.4.4assign, 4.1.3
          structure, 6.6.16atom, 2.7.5
     selection, 6.6.13atomLabelStyle, 2.7.7
     view options, 6.6.10atomic property fields, 3.4.6
     color, 6.6.9author, 2.2.1.3
     comment, 6.6.6     play slide, 5.13
     consensus, 6.6.9, 6.6.14avi, 4.15, 4.15.2
     cut, 6.3.10b-factor, 3.5.12, 7.3.10
     display title, 6.6.10backbone, 4.1.10
     editor, 6.6background, 4.3.2, 4.3.3
     extract, 6.3.9     images activeicm, 5.15
     gaps, 6.6.11     image, 4.3.3
     horizontal scroll, 6.6.10backup, 1.5.2.11

     and stick, 1.6.1color, 3.5.11, 4.2.2, 4.2.3, 4.2.4, 4.2.9.4, 4.3, 4.3.1, 4.7.2, 4.7.3
basicsel, 2.6.2     alignment, 6.6.9
binding properties, 4.2.1     background, 4.3.2
bioinfo align multiple, 6.3.7     by, 4.3
          two sequences, 6.3.5     surface by proximity, 4.2.3
     links, 6.3.8               selection, 4.2.4
     menu, 1.5.4     background, 1.5.3.18, 4.3.2
     secondary structure, 6.3.2     distance, 4.7.10
     translation, 6.3.3     mesh, 4.2.9.3
biological, 3.3.3coloring, 4.3.1
biomolecule, 1.5.5, 3.3.3, 7.3.8, 7.3.12combine, 1.5.10.5
blast, 2.2.3, 6.4     display style, 2.7.9
     search, 2.2.3compatible, 1.5.1.9
blue lines, 6.2compound, 2.2.1.3
bond, 3.2.3, 3.2.3.1, 3.2.3.2compress, 2.7.6
bonding, 4.1.8connect, 4.2.9.1, 4.11, 4.11.7
     preferences, 2.7.1     object, 4.11.7
box, 2.7.7, 4.7.15, 6.6.7, 6.6.7.1construct, 1.5.1.1, 4.9.7.1
     alignment, 7.4.4     molecule, 1.5.1.1
build, 4.9.7.1     object, 1.5.1.1
buttons, 5.14contact, 3.5, 3.5.3, 7.3.5
bye, 1.5.1.18     surface, 4.2.2
     alpha, 4.1.10contacts, 4.2.3, 4.2.4
     trace, 4.1.10contour, 3.3.6, 3.3.7
ca-trace, 4.1.10convert, 3.1.2
cache, 5.14.1     local database, 1.5.1.5
calculate sequence similarity, 6.6.15     pdb, 7.3.2
cavities, 3.5     local.database, 1.5.1.5
     closed, 3.5.4converting pdb, 3.1.2
cell, 3.3.2cpk, 4.1.5
center, 1.5.3.20, 2.1.3, 4.11, 4.11.5crash, 1.5.2.11
change selection, 2.6.7creat, 5.6.1
     speed range, 4.9.7.2     new objects, 2.3
changing font in alignment editor, 6.6cross section, 4.12
charge, 1.5.3.21, 4.7.2crystal, 3.3.2
chemical substructure, 2.2.1.1crystallographic analysis, 3.3
chi, 4.7.5          biomolecule, 3.3.3
clash, 2.7.5, 4.7.14          contour map, 3.3.6
clear display and planes, 1.5.3.2          convert2grid, 3.3.7
     selection, 2.6.6          crystallographic cell, 3.3.2
     planes, 1.5.3.2          load eds, 3.3.4
click, 2.1.12, 4.10, 4.11          maps cell, 3.3.5
clip, 4.2.10, 4.12.1          symmetry packing, 3.3.1
clipboard, 4.14.3          tools, 7.3.8
clipping planes, 4     cell, 1.5.5
     tool, 4.12     neigbor, 3.3.1
     tools, 4.12     neighbors, 1.5.5
close, 4.2.3, 4.2.4crystallography, 3.3.4, 3.3.6, 3.3.7
     cavities, 3.5.14current.slide, 5.13
collada, 1.6.6, 4.2.7custom, 4.11

     rotation, 4.11.2     origin, 4.7.11
     vertical alignment block, 6.3.10     potential, 1.5.3.21
database, 6.4     representations, 1.6.1
     seach and alignment, 6.4     restraints, 4.7.13
default, 2.1.13     ribbon, 4.1.3
delete, 1.5.2.1, 2.6.6, 5.6.7     skin, 4.1.4
     alignment, 6.6.5     surface, 4.1.6, 4.2.1
     all, 1.5.2.2     surfaces, 1.6.6
     label, 4.7.9     tethers, 4.7.12
     alignment, 6.6.5     wire, 4.1.1
     all, 1.5.2.2     xstick, 4.1.2
     angle.label, 4.8.4distance, 3.5, 3.5.6, 4.7.10, 4.8
     distance.label, 4.8.4     label, 2.7.7
     label, 4.7.9distances, 1.6.3
     selection, 1.5.2.1docking, 3.5.13
density, 3.3.4, 3.3.6, 3.3.7document, 5.6.4, 5.6.5
depth, 4.2.12, 4.9.5     navigation, 5.6.6
dialog, 5.6.5documents, 4.14.3
diffuse, 1.6.2     envelope, 1.6.1
dihedral, 3.5.8, 4.7.5     surface, 2.7.5
     angle, 3.5dotted line, 4.1.3
directories preferences, 2.7.2drag, 2.1.11, 2.7.7, 4.7.3, 5.6.4, 6.5.6
directory, 2.7     and drop sequences, 6.5.6
display, 2.1.4, 2.1.13.1, 2.7, 3.2.3, 3.2.3.1, 3.2.3.2, 4.7.14, 4.13     residue label, 1.5.3.16
     delete distances, 4.8.4draganddrop, 2.1.11
     dihedral, 4.8.3drop, 2.1.11, 5.6.4, 6.5.6
     distance restraints, 4.7.13drug bank, 2.2, 2.2.6
     distance2, 4.8.1dsPocket, 2.1.8
          angles, 4.8easy rotate, 1.5.3.12
     formal charge, 4.1.9edit, 3.2.3.1
     gradient, 4.7.16     alignment, 6.6.1
     hydrogen, 4.1.7     ligand tools, 1.5.2.17
     mesh, 4.2.5     menu, 1.5.2
     meshes, 4.2.8     molecular document, 5.6.1
     planar angle, 4.8.2     selection, 1.5.2.5
     tab, 1.6.1     slide, 5.4.1
     tether, 4.7.12editpdbsearch, 1.5.2.12
     toggle, 4.7.15eds, 3.3.4, 3.3.6, 3.3.7
     CPK, 4.1.5electron, 3.3.4, 3.3.6, 3.3.7
     angle, 4.8.2     denisty map, 3.3.5
     dihedral.angle, 4.8.3     densitry map.contour, 1.5.5
     distace, 4.7.10          map, 1.5.1.6, 1.5.5, 3.3.4, 3.3.6
     distance, 4.7.13, 4.8.1electrostatic potential, 1.5.3.21
     electrostatic, 1.5.3.21     surface, 4.2
     energy.gradient, 4.7.16electrostatics, 4.2.1
     hydrogen, 4.1.7elegant sketch, 4.9.4
          polar, 4.1.7embed browser, 5.11
     macroshape, 4.2.6     powerpoint03, 5.8
     meshes, 4.2.5     powerpoint07, 5.9
          and display.macroshape, 1.6.6     powerpoint10, 5.10

          script, 5.13               color representation, 7.1.1
     browser, 5.7, 5.11               labels, 7.1.3
     firefox, 5.7, 5.11graphics, 2.1
     internet.explorer, 5.7, 5.11     controls, 4
     microsoft, 5.7     effects, 4.9
     powerpoint, 5.7, 5.8, 5.9, 5.10     preferences, 2.7.3
energy, 3.5.11, 4.7.14     shadow, 1.5.3.13, 4.9.2
exit, 1.5.1.18green arrows, 6.6.16
export, 3.5.10     lines, 6.2
extract, 2.4.2, 6.1grob, 2.7.5, 3.3.4, 3.3.6, 3.3.7, 4.2
     icb, 1.5.1.4gui, 2.1.1, 2.7.4
     object icb, 2.4.2     menus, 1.5
     sub alignment, 6.3.9     preferences, 2.7.4
     icb, 1.5.1.4     tabs, 1.6
fasta, 6.1.5h-bond, 3.2.3, 3.2.3.1, 3.2.3.2
file, 1.5.1.2hardware stereo, 1.5.3.7
     close, 1.5.1.12hbond, 3.2, 7.3.6
     compatible, 1.5.1.9header, 2.2.1.6
     export, 1.5.1.11health, 3.5.11
     high quality image, 4.14.1hidden block format, 6.6.11
     load, 1.5.1.6          width, 6.6.11
     menu, 1.5.1high, 1.5.1.14
     password, 1.5.1.10     quality, 1.5.3.11
     preferences, 1.5.1.15homology, 2.2.1.2, 2.2.3
     quick image, 1.5.1.13     to activeicm, 1.3
     icb, 2.1.10               create molecular documents, 1.3.3
     recent, 1.5.1.16                    slides, 1.3.2
     bak, 1.5.2.11               getting started, 1.3.1
filter selection, 2.6.8               ppt, 1.3.4
flexibility, 3.5.12               web, 1.3.5
fog, 1.5.3.5, 4, 4.9.1          icm browser convert display pocket, 1.1.4
font, 2.7, 2.7.7, 3.2.3.1, 4.7.2, 4.7.3, 6.6.7, 6.6.7.1                    distances angles, 1.1.9
     preferences, 2.7.7                    get started, 1.1.1
     size, 6.6                    graphical display, 1.1.2
formal charge, 4.1.9                         effects, 1.1.5
frame, 6.3.3                    images, 1.1.7
front, 4.2.10, 4.12.1                    labels annotation, 1.1.6
full scene antialias, 1.5.3.10                    pro crystallographic tools, 1.2.6
     screen, 1.5.3.8                         get started, 1.2.1
general preferences, 2.7.5                         graphics, 1.2.2
generalselecttools, 2.6.1                         plots, 1.2.8
generator, 3.3.3                         sequence analysis, 1.2.7
getting started, 2                         structure analysis, 1.2.3
glasses, 4.5                         superimpose, 1.2.5
google, 1.5.1.6                         surfaces, 1.2.4
     objects, 4.2.7                    selections, 1.1.3
     3D, 1.6.6, 4.2.7                    superimpose, 1.1.8
graphical display tutorial, 7.1          search, 2.2
               2D3D labels, 7.1.4          use gui, 2.1
               annotation, 7.1.2html, 1.5.1.11, 2.3, 5.6.1, 5.6.6

     bond, 3.2, 4.1.8, 7.3.6     custom, 4.7.8
          label edit, 3.2.3.1     delete, 4.7.1, 4.7.9
               move, 3.2.3.2     distance, 4.7.10
hyperlink, 5.6.1, 5.6.2     drag, 1.5.3.16
iSee, 1.5.1.4, 1.5.1.11, 2.1.10, 4.14.3, 7.2     move, 1.5.3.16, 4.7.4
icb, 2.4.2, 2.5     residue, 4.7.1
     chemist howto chemical search, 1.4.3     residues, 4.7.3
               cluster, 1.4.5     site, 4.7.1
               combi library, 1.4.7     sites, 4.7.6
               ph4, 1.4.4     variable, 4.7.1
               plots, 1.4.8     variables, 4.7.5
               sketch, 1.4.1labeling, 4.7.1
               spreadsheets, 1.4.2labels, 4.7
               stereoisomers tautomers, 1.4.6     distances, 4.7.10
          tutorials, 1.4     tab, 1.6.3
     object, 3.1, 7.3.2landscape, 2.7.6
icmFastAlignment, 6.4layer, 4.13
icmPocketFinder, 3.5.14layers, 4.13
icmpocketfinder, 7.3.7ligand, 3.2.2
identity, 2.2.1.2     code, 2.2.1.3, 2.2.5
image, 2.1.14, 2.7, 2.7.5, 4.14.3, 5.6.3     editor preferences, 1.5.2.18
     advanced, 4.14.3     receptor display, 3.2
     preferences, 2.7.6     surface, 3.2.2
     multiple, 1.5.1.6     pocket, 2.1.8
     quality, 1.5.3.11     receptor.contact, 3.5.3
     quick, 1.5.1.13, 4.14.2ligedit tab, 1.6.5
images, 4.14light, 1.6.2
insert, 5.6.4     tab, 1.6.2
     image, 5.6.3lighting, 4.2.9.4, 4.4
     script, 5.6.4line, 2.7.5
interaction, 3.5.3lineWidth, 2.7.3
interactive, 7.2link, 6.3.8
interrupt, 4.9.7.3     structure to alignment, 7.4
     animation, 4.9.7.3links, 2.6.19
isee, 5.6.5load, 1.5.1.2, 1.5.1.16, 3.3.4, 3.3.6, 3.3.7, 6.1
jpg, 4.14     example alignment, 6.3.13
keyboard mouse, 4.10     nmr model, 2.2.1.4
kmz, 1.6.6, 4.2.7     protein structure, 3.1.1
label, 2.7.7     sequence, 6.1
     atoms, 4.7.2          extract pdb, 6.1.3
     color, 4.7.7          from file, 6.1.4
     move, 4.7.4          paste, 6.1.2
     residues, 4.7.3          swissprot, 6.1.1
     sites, 4.7.6lock, 4.2.10, 4.12.1
     variables, 4.7.5logout, 1.5.1.18
     2D, 1.6.3macros, 5.14
     3D, 1.6.3, 4.7.1macroshape, 1.5.3.22, 4.2, 4.2.6
     atom, 4.7.1make, 4.9.7.1
     atoms, 4.7.2     alignment, 6.5.1
     color, 4.7.7     animation, 4.9.7.1

     selection, 2.6multiple receptor, 2.2.2
     molecule, 1.5.1.1navigate workspace, 2.6.10
     object, 1.5.1.1new, 6.1
making molecular slides, 5.1nmr model, 2.2.1.4
     html, 5.6object, 2.1.11, 2.5, 7.3
map, 2.7.7, 3.3.4, 3.3.6, 3.3.7objects, 3.1.2
     cel, 3.3.5occlusion, 4.2.12, 4.9.5
materials, 1.6.6     shading, 4.2.12
maxColorPotential, 2.7.10          effect, 4.9.5
menu, 5.6.5occupancy, 4.1.3, 7.3.10
     chemistry, 1.5.14     display, 2.2.1.5
     docking, 1.5.15oda, 3.5.13
     homology, 1.5.13older version, 1.5.1.9
     molmechanics, 1.5.16omega, 4.7.5
     tools chemical search, 1.5.11open, 1.5.1.2, 2.4
          molecular editor, 1.5.12     file, 2.4
     windows, 1.5.17     password, 2.4.1
mesh, 3.2.1, 3.2.2, 3.3.4, 3.3.6, 3.3.7, 4.2, 4.2.9.1, 4.2.9.2, 4.2.9.4, 4.2.10, 4.2.11, 4.2.12, 4.12.1     with password, 1.5.1.3
     clip, 4.2.10     movie, 4.15, 4.15.2
     color lighting, 4.2.9.4     password, 1.5.1.3, 2.4.1
     options, 4.2.9optimal, 3.5.13
     representation, 4.2.9.3orange, 2.6.5
     save, 4.2.11     selection, 2.6.5
     options, 4.2.9origin, 4.7.11
meshes, 4.2.2, 4.9.5other selection, 2.6.18
     surfaces grobs, 4.2overlay, 7.3.3
     tab, 1.6.6package.activeicm, 5.13
mmff type, 4.7.2packing, 3.3.1
mnSolutions, 2.7.10pdb, 1.5.1.6, 2.2, 2.2.1.1, 2.2.5, 2.5, 7.3
molecular animations slides, 5     html, 2.2.1.6
     documents, 7.2     preparation, 7.3.11
     graphics, 4     search, 2.2.1, 2.2.1.2, 2.2.1.3, 7.3.1
molskin, 4.2.2     recent, 1.5.1.17
mouse, 2.1.3, 4.10, 4.11     search, 1.6.4, 2.1.2
mov, 4.15, 4.15.2pdbsearchfield, 1.5.2.13
move, 1.5.3.19, 2.1.11, 2.1.13, 3.2.3.2, 4.2.9.1, 4.2.9.2, 4.11, 4.11.7pdbsearchhomology, 1.5.2.15
     mesh, 4.2.9.2pdbsearchidentity, 1.5.2.14
     slide, 5.4.2pdbsearcsequence, 1.5.2.16
     structure, 4.11peptide, 2.3
     tools, 4percentage similarity, 6.6.15, 7.4.4
     rotate, 4.10perspective, 1.5.3.9, 4.9.6
     slab, 4.10phi, 4.7.5
     translate, 4.10phylogenetic, 6.6.8
     z-rotation, 4.10phylogeny, 6.6.8
     zoom, 4.10picking, 4
movie, 4.15.1picture, 1.5.1.13, 2.1.14, 4.14.2, 5.6.3
     making, 4.15, 4.15.2     tips, 2.1.14
     open, 4.15, 4.15.2planar, 3.5.7, 4.7.5
mpeg, 4.15, 4.15.1, 4.15.2     angle, 3.5
mpg, 4.15, 4.15.2     angle, 4.8.2

plot, 2.7, 2.7.8          select, 3.4.1
     function, 1.5.9, 1.5.9.1          sites by apf, 3.4.6
     preferences, 2.7.8          superimpose 3D, 3.4.3
png, 1.5.1.13, 4.14, 4.14.2, 5.6.3               grid, 3.4.5
pocket, 2.1.8, 3.2, 3.2.1, 3.2.2, 3.5.14, 7.3.7               multiple proteins, 3.4.4
     surface, 3.2.1protein-protein, 3.5.13
     peptide, 2.1.8proximity, 4.2.3, 4.2.4
     properties, 2.1.8psi, 4.7.5
pocketome, 2.2, 2.2.2publication quality images, 4.2.2
portait, 2.7.6pubmed, 2.2.1.7
postscript, 2.7.6purple box, 1.5.3.23
powerpoint, 7.2qs hydrogen bond, 3.2.3
ppt, 5.12, 5.14quality, 1.5.1.14, 2.7.5
predict, 6.3.2quick, 2.1.14
preferences, 2.7     image, 4.14.2
presentatio, 5.6.5     start move structure, 2.1.3
presentation, 5.7, 5.12          read pdb, 2.1.2
presentations, 5          representation, 2.1.6
print, 4.6          selection, 2.1.5
     alignment, 6.6.4               level, 2.6.3
     alignment, 6.6.4          what is selected, 2.6.4
printer.resolution, 2.7.6     dispalay.distance, 4.8.1
project, 1.5.1.4     start color, 2.1.7
     close, 1.5.1.12quit, 1.5.1.18
     rename, 1.5.1.8rainbow, 2.7.5, 4.7.15
properties, 4.7.2ramachandran plot, 3.5, 3.5.10
protect, 5.6.7range, 4.9.7.2
protein, 3.4.6, 6ratio.selection, 2.7.5
     health, 3.5.11read, 1.5.1.2, 1.5.1.16, 2.4, 6.1
     structure, 3     pdb, 2.1.2
          analysis, 3.5rear, 4.2.10, 4.12.1
               closed cavities, 3.5.4recent files, 1.5.1.16
               contact areas, 3.5.3     pdb codes, 1.5.1.17
               distance, 3.5.6receptor, 3.2.1, 3.2.2
               find related chains, 3.5.1recover, 1.5.2.11
               finding dihedral angle, 3.5.8     cylinders, 6.6.16
                    planar angle, 3.5.7     lines, 6.2
               rama export, 3.5.10redo, 1.5.2.10
               ramachandran plot, 3.5.9rename project, 1.5.1.8
               rmsd, 3.5.2representation, 1.5.3.19
               surface area, 3.5.5residue, 2.7.7
          tutorials, 7.3     alternative orientaiton, 7.3.11
               analysis, 7.3.4     content, 6.3.1
               contact area, 7.3.5     content, 1.5.4, 6.3, 6.3.1
               convert, 7.3.2residues, 3.2.1, 3.2.2
               hydrogen bond, 7.3.6resize, 4.2.9.1, 4.14.3
               icmpocketfinder, 7.3.7     mesh, 4.2.9.1
               search, 7.3.1resolution, 2.2.1.3
               superimpose, 7.3.3restore, 1.5.2.11, 4.2.10, 4.12.1
     superposition, 3.4     recent backup, 1.5.2.11

     preferences, 2.7.9secondary.sctructure, 6.3.2
     style, 2.7.9     structure, 1.5.4, 4.1.3, 6.3
     breaks, 4.1.3select, 2.6.12, 2.6.13
     cylinders, 4.1.3     all, 2.6.14
     smooth, 4.1.3     amino acid, 2.6.13
     worm, 4.1.3     molecule, 2.6.12
ribbonColorStyle, 2.7.9     neighbors, 2.6.15
right, 2.1.12          graphic, 2.6.16
     click, 2.1.12     object, 2.6.11
rmsd, 3.5, 3.5.2     residue, 2.6.13
rock, 1.5.3.15, 4.9.7, 4.9.7.1, 5     atom, 2.1.5, 2.6.3
     speed, 4.9.7.2     graphical, 2.1.5, 2.6.3
root mean square deviation, 3.5.2     object, 2.1.5, 2.6.3
rotate, 1.5.3.15, 2.1.3, 4, 4.9.7, 4.9.7.1, 4.11, 4.11.1, 4.11.2, 5     purple.box, 1.5.3.23
     easy, 1.5.3.12     residue, 2.1.5, 2.6.3
     speed, 4.9.7.2     workspace, 2.1.5, 2.6.3
rotation, 4.11.1selectall, 1.5.2.3
ruler, 4.7.15selecting.neighbors, 2.6.16
salt bridge, 7.3.6selection, 2.6.4, 2.6.5, 2.6.20, 4.2.4
save, 2.5, 4.2.11, 4.9.7.4, 6.1.5     clear, 1.5.2.7
     alignment, 6.6.3     neighbors, 1.5.2.8
     file, 2.5     alignment, 2.6.18
     object, 2.1.9     all, 1.5.2.3
     pdb, 2.5     alter, 2.6.7
     project icb, 2.1.10     atom, 1.5.2.5
     sequence, 6.1.5     basic, 2.6.2
     slide, 5.4     change, 2.6.7
     image, 1.5.1.14, 2.1.14     clear, 1.5.2.7
     object, 2.1.9     filter, 1.5.2.5, 2.6.8
     password, 1.5.1.10     graphical, 2.6.16
     picture, 1.5.1.14     invert, 1.5.2.6
     project, 1.5.1.7, 1.5.1.8, 1.5.1.9, 2.1.10     level, 1.5.3.3
saving, 1.5.1.7     mode, 1.5.3.4
     project, 1.5.1.7     near atoms, 1.5.2.8
scale, 2.7.5     neighbors, 1.5.2.5, 1.5.2.8, 2.6.15, 2.6.17
screenshot, 4.15, 4.15.2     object, 2.6.11
     movie, 4.15.2     other, 2.6.18
script, 2.3, 5.6.4, 5.6.5     properties, 1.5.2.5
search drugbank, 2.2.6     residue, 1.5.2.5
     in workspace, 1.5.2.4     sphere, 2.6.15
     pdb, 2.2.1     spherical, 1.5.2.8
          chemical, 2.2.1     superposition, 3.4.1
          ligand code, 2.2.5     table, 2.6.18
     pocketome, 2.2.2     tools, 2.6.1, 2.6.2, 2.6.7, 2.6.8
     pubchem, 2.2.7     whole, 2.6.11
     tab field, 2.2.1.3     workspace, 2.6.9, 2.6.17
          pdb chemical, 2.2.1.1selectioninvert, 1.5.2.6
               sequence, 2.2.1.2selections, 2.6
     uniprot, 2.2.4     links, 6.3.8
     in.workspace, 1.5.2.4selectneighbors workspace, 2.6.17

     analysis, 6.3sort table, 1.5.10.4
     identity, 6.6.15spec, 1.6.2
     pattern, 2.2.1.2speed, 4.9.7.2
     reordering, 6.6.8squence.amino acid, 6.3.4
     secondary structure, 6.2stereo, 2.7.6, 4.5
     similarity, 6.6.15     hardware, 1.5.3.7
     structure, 6.3.6     side-by-side, 1.5.3.6
     type, 6.3.4stick, 2.7.5
     DNA, 6.3.4stl, 4.6
     alignment, 6.3.5, 6.5.2, 6.5.6stop, 4.9.7.3
     nucleotide, 6.3.4store, 1.5.3.19, 4.9.7.4
     protein, 6.3.4     current view, 1.5.3.19
     search, 6.4strain, 3.5.11
     structure.alignment, 6.3.6, 6.5.3structure, 3.3.3, 7.3
sequences, 6     analysis, 7.3.4
     unique, 6.3.12     representation, 4.1
     extract, 6.3.12style, 2.7.5
     unique, 6.3.12superimpose, 1.5.8, 3.4.2, 3.4.6, 7.3.3
shade, 6.6.7, 6.6.7.1     3D, 3.4.3
     alignment, 7.4.4     Calpha, 3.4.3
shading, 4.2.12     arrange.grid, 3.4.5
shadow, 4.9.2     backbone, 3.4.3
shell preferences, 2.7.10     heavy atoms, 3.4.3
shift, 4.7.3     multiple, 3.4.4
shine, 1.6.2, 2.7.5superposition, 7.3.3
shineStyle, 2.7.3surface, 1.6.1, 2.7.5, 3.2.1, 3.2.2, 4.1.6, 4.2, 4.2.3, 4.2.4
show, 5.3.1     area, 3.5
side by side stereo, 1.5.3.6     area, 3.5.5
sigmaLevel, 3.3.6, 3.3.7surfaces, 3.2, 4.2.1, 4.2.2, 4.9.5
sites, 3.4.6swissprot, 6.1
size, 3.2.3.1symmetry, 3.3.1, 3.3.3, 7.3.8, 7.3.9
sketch accents, 4.9.3system preferences, 2.7.11
     accents, 1.5.3.14, 4.9.3tab pdb, 1.6.4
skin, 1.6.1, 4.1.4table, 2.3
slab, 4.2.10, 4.12.1     join, 1.5.10.5
slice, 4.12     merge, 1.5.10.5
slide, 4.9.7.4, 5.2, 5.3.1, 5.6.1     rows, 1.5.10.7
     effects, 5.5     sort, 1.5.10.4
     movie, 4.15.1tag, 2.6.20
          file, 5.2tags, 2.6.20
     navigation, 5.3.2temperature, 3.5.12
     show, 5.3text, 2.7.7, 5.6, 5.6.1, 5.6.6
     blend, 5.5texture, 1.6.6
     edit, 5.4.1threshold, 2.7.5
     effect, 5.5tier, 2.1.13
     smooth, 5.5tools 3D, 1.5.6
     transition, 5.5     analysis, 1.5.7
slides, 4.15.1, 5, 5.1, 5.3     append rows, 1.5.10.7
smooth, 4.2.9.3     extras, 1.5.9
solid, 4.2.9.3          plot function, 1.5.9.1

     table, 1.5.10     sketch accents, 1.5.3.14
          Learn, 1.5.10.1     slide show, 5.3.1
          clustering, 1.5.10.3     tools, 1.5.3
          merge, 1.5.10.5     undisplay all, 1.5.3.1
          predict, 1.5.10.2virus, 3.3.3
torsion, 4.11.6wavefront, 1.6.6, 4.2.11
     angles, 4.11, 4.11.6web, 7.2
trace, 4.1.10     browser, 1.5.1.11
transitions, 5window, 2.1.13
translate, 2.1.3, 4, 4.11windows, 2.1.13.1
translation, 4.11.3, 6.3.3wire, 1.6.1, 2.7.5, 4.1.1
transparent, 4.2.9.3wireBondSeparation, 2.7.1
     background, 4.14.3workspace, 2.1.4
tree, 6.6.8     panel, 2.1.4
     branch swapping, 6.6.8     selection, 2.6.9
tut analyze alternative orientations, 7.3.11     navigation, 2.6.10
          occupancy, 7.3.10write, 2.1.14, 2.5
          symmetry, 7.3.9     alignment, 6.6.3
tut3e, 7.3.12     image, 1.5.1.14
tutorial molecular documents, 7.2     images, 4.14
     sequence alignment, 7.4     pdb, 2.5
               link, 7.4.2     image, 1.5.1.14
               load sequence, 7.4.1     object, 2.1.9
               sequence conservation, 7.4.3     picture, 1.5.1.14
tutorials, 7     project, 1.5.1.7, 2.1.10
unclip, 4.2.10, 4.12.1     ray, 1.5.5
undisplay, 2.1.4, 4.1.7xi, 4.7.5
     box shade font, 6.6.7.1xstick, 4.1.2
     origin, 4.7.11zoom, 2.1.3, 4, 4.11, 4.11.4
undo, 1.5.2.9, 2.7 
uniprot, 2.2.4 
unit, 3.3.3 
unusual peptide, 2.3 
     activeicm, 5.12 
uundisplay-all, 1.5.3.1 
van der waal, 4.7.14 
variable, 2.7.7 
video, 4.15, 4.15.1, 4.15.2 
view, 1.5.3.19, 5.3.1 
     animate view, 1.5.3.15 
     center, 1.5.3.20 
     color background, 1.5.3.18 
     fog, 1.5.3.5 
     macroshape, 1.5.3.22 
     menu, 1.5.3 
     mesh clip, 4.12.1 
     perspective, 1.5.3.9 
     selection level, 1.5.3.3 
          mode, 1.5.3.4 
     shadow, 1.5.3.13 

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