Sep 13 2018 Feedback.
Contents
 
Help Videos
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Sequences & Alignments
Tutorials
 
Index

Index

2D, 5.8.8     dnaRibbonRatio, 3.7.9
3D, 5.6, 5.8.8, 8.2     dnaRibbonWidth, 3.7.9
     interactive ligand editor, 2.6.5     dnaRibbonWorm, 3.7.9
     object, 5.3.9     dnaStickRadius, 3.7.9
     print, 5.7     dnaWormRadius, 3.7.9
     printing, 5.7     font Scale, 3.7.7
     stereo, 5.6     fontColor, 3.7.7
     predict local flexibility, 4.5.12     fontLineSpacing, 3.7.7
          protein health, 4.5.11     grobLineWidth, 3.7.3
          tools identify ligand binding pocket, 4.5.14     hbond Ball Period, 3.7.1
               oda, 4.5.13               Style, 3.7.1
4D docking, 3.2.2     hbondAngleSharpness, 3.7.1
ActiveICM, 2.5.1.12     hbondMinStrength, 3.7.1
Atom Single Style, 3.7.3     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, 2.5.1.7     light, 3.7.3
CPK, 2.6.1     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, 7, 7.3.3     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, 2.5.1.15, 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, 7.1
               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, 2.5.2.12, 2.5.2.13, 2.5.2.14, 2.5.2.15, 2.5.2.16
          Sequence Length, 3.7.4          Field, 2.5.2.13
     splash Screen Delay, 3.7.11          Homology, 2.5.2.15
               Image, 3.7.11          Identity, 2.5.2.14
     table Row Mark Colors, 3.7.4          Sequence, 2.5.2.16
     workspace Folder Style, 3.7.4     convert, 4.1.2
     workspaceTabStyle, 3.7.4PFAM, 2.5.1.7
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, 2.5.1.15, 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, 3.7.6RMSD, 4.4.2
     stereoAngle, 3.7.6RNA, 3.3
     stereoBase, 3.7.6Ramachandran Plot, 4.5.9
     stereoText, 3.7.6Real Format, 3.7.10
Icm Prompt, 3.7.10     Label Shift, 3.7.7
Inx Directory, 3.7.2          Style, 3.7.7
JPEG, 2.5.1.15SEQUENCE.site Colors, 3.7.4
KMZ, 2.5.1.7SITE.label Style, 3.7.7
Log Directory, 3.7.2     labelOffset, 3.7.7
MOVIE.frame Grab Mode, 3.7.4     wrap Comment, 3.7.7
Map Atom Margin, 3.7.10SLIDE.ignore Background Color, 3.7.4
     Sigma Level, 3.7.10          Fog, 3.7.4
     File Size Mb, 3.7.11Select Min Grad, 3.7.10
Mnconf, 3.7.10Show Res Code In Selection, 3.7.7
Movie.fade Nof Frames, 3.7.4SureChEMBL, 3.2.4
     quality, 3.7.4Swissprot, 2.5.1.7
Temp Directory, 3.7.2     cut, 7.3.11
USER.email, 3.7.11     display title, 7.7.10
     friends, 3.7.11     editor, 7.7
     full Name, 3.7.11     extract, 7.3.10
     organization, 3.7.11     gaps, 7.7.11
     phone, 3.7.11     horizontal scroll, 7.7.10
Var Label Style, 3.7.7     image, 7.7.2
Water Radius, 3.7.10     multiple, 7.3.7, 7.6.5
Wire Style, 3.7.1     options, 7.7.10
XPDB Directory, 3.7.2     rename, 7.7.10
Xstick, 2.6.1     reorder, 7.3.12
a-bright, 2.6.2     ruler, 7.7.10
active, 6.7     save, 7.7.2
activeICM, 6.8     search, 7.7.12
activeicm, 6.7, 6.12, 6.14, 6.14.1     selection, 7.7.13, 7.7.14
     advanced, 6.14     sequence offset, 7.7.10
     background images, 6.15     table, 7.7.10
     control, 6.13     view, 7.7.10
activeicmjs, 6.16alignments, 7.6, 8.4
advanced alignment selection, 7.7.14alpha, 2.6.2
album, 5.15.3     channel, 3.7.6
align, 3.1.11ambient, 2.6.2
     dna protein, 7.6.4amino acid, 3.3
     multiple, 7.6.5anaglyph, 5.6
     sequence structure, 7.6.3analysis, 2.5.4, 7.3
     two sequences, 7.6.2angle, 4.5.7, 4.5.8, 5.8.5, 5.9, 5.12.6
     DNA to protein, 7.6.4animate, 2.5.3.15, 5.10.7
     sequence, 7.6, 7.6.6     view, 5.10.7
     two sequences, 7.3.5, 7.6.2animation, 5.10.7.1, 5.10.7.2, 5.10.7.3, 5.10.7.4
alignment, 7.3.8, 7.6.1, 7.7.7, 7.7.7.1, 7.7.16, 7.8, 8.4.4     store, 5.10.7.4
     annotation tutorial, 8.4.4animations, 6
     box shade font, 7.7.7annotate, 3.6.21
     editing, 7.7.1     alignment, 7.7.6
     editor, 7.7annotation, 7.7.6
     example, 7.3.14antialias, 2.5.1.15, 2.5.3.10
     format, 7.7.11     lines, 2.5.3.17
     gaps, 7.7.11     lines, 2.5.3.17
     image, 7.7.2apf, 4.4.6
     profile, 8.4.4append.rows, 2.5.10.7
     reorder, 7.3.12area, 4.5.3, 4.5.13, 8.3.5
     search, 7.7.12arrange, 3.1.13.1
     secondary, 8.4.4     window, 3.1.13.1
          structure, 7.7.16as2_graph, 3.6.5
     selection, 7.7.13assign, 5.1.3
     strength, 7.3.8atom, 3.7.5
          profile, 7.3.8atomLabelStyle, 3.7.7
     view options, 7.7.10atomic property fields, 4.4.6
     color, 7.7.9author, 3.2.1.3
     comment, 7.7.6     play slide, 6.13
     consensus, 7.7.9, 7.7.14avi, 5.16, 5.16.2
backbone, 5.1.10click, 3.1.12, 5.11, 5.12
background, 5.4.2, 5.4.3clip, 5.3.10, 5.13.1
     images activeicm, 6.15clipboard, 5.15.3
     image, 5.4.3clipping planes, 5
backup, 2.5.2.11     tool, 5.13
ball, 3.7.5     tools, 5.13
     and stick, 2.6.1clone, 2.5.1.2
basicsel, 3.6.2close, 5.3.3, 5.3.4
binding properties, 5.3.1     cavities, 4.5.14
bioinfo align multiple, 7.3.7collada, 2.6.6, 5.3.7
          two sequences, 7.3.5color, 4.5.11, 5.3.2, 5.3.3, 5.3.4, 5.3.9.4, 5.4, 5.4.1, 5.8.2, 5.8.3, 7.8
     links, 7.3.9     alignment, 7.7.9
     menu, 2.5.4     background, 5.4.2
     secondary structure, 7.3.2     by, 5.4
     translation, 7.3.3          alignment, 7.8
biological, 4.3.3     surface by proximity, 5.3.3
biomolecule, 2.5.5, 4.3.3, 8.3.8, 8.3.12               selection, 5.3.4
blast, 3.2.5, 7.4     background, 2.5.3.18, 5.4.2
     search, 3.2.5     distance, 5.8.10
blue lines, 7.2     mesh, 5.3.9.3
bond, 4.2.3, 4.2.3.1, 4.2.3.2coloring, 5.4.1
bonding, 5.1.8combine, 2.5.10.5
     preferences, 3.7.1     display style, 3.7.9
box, 3.7.7, 5.8.15, 7.7.7, 7.7.7.1compatible, 2.5.1.10
     alignment, 8.4.4compound, 3.2.1.3
build, 5.10.7.1compress, 3.7.6
buttons, 6.14connect, 5.3.9.1, 5.12, 5.12.7
bye, 2.5.1.19     object, 5.12.7
     alpha, 5.1.10construct, 2.5.1.1, 5.10.7.1
     trace, 5.1.10     molecule, 2.5.1.1
ca-trace, 5.1.10     object, 2.5.1.1
cache, 6.14.1contact, 4.5, 4.5.3, 8.3.5
calculate sequence similarity, 7.7.15     surface, 5.3.2
cavities, 4.5contacts, 5.3.3, 5.3.4
     closed, 4.5.4contour, 4.3.6, 4.3.7
cell, 4.3.2convert, 4.1.2
center, 2.5.3.20, 3.1.3, 5.12, 5.12.5     local database, 2.5.1.6
change selection, 3.6.7     pdb, 8.3.2
     speed range, 5.10.7.2     local.database, 2.5.1.6
changing font in alignment editor, 7.7converting pdb, 4.1.2
charge, 2.5.3.21, 5.8.2cpk, 5.1.5
check box, 6.6.6crash, 2.5.2.11
chembl, 3.2.3, 3.2.4creat, 6.6.1
chemical spreadsheet, 3.2.3     new objects, 3.3
     substructure, 3.2.1.1cross section, 5.13
chi, 5.8.5crystal, 4.3.2
clash, 3.7.5, 5.8.14crystallographic analysis, 4.3
clear display and planes, 2.5.3.2          biomolecule, 4.3.3
     selection, 3.6.6          contour map, 4.3.6
     planes, 2.5.3.2          convert2grid, 4.3.7
          load eds, 4.3.4     angle, 5.9.2
          maps cell, 4.3.5     dihedral.angle, 5.9.3
          symmetry packing, 4.3.1     distace, 5.8.10
          tools, 8.3.8     distance, 5.8.13, 5.9.1
     cell, 2.5.5     electrostatic, 2.5.3.21
     neigbor, 4.3.1     energy.gradient, 5.8.16
     neighbors, 2.5.5     hydrogen, 5.1.7
crystallography, 4.3.4, 4.3.6, 4.3.7          polar, 5.1.7
current.slide, 6.13     macroshape, 5.3.6
custom, 5.12     meshes, 5.3.5
     label, 5.8.8          and display.macroshape, 2.6.6
     rotation, 5.12.2     origin, 5.8.11
     vertical alignment block, 7.3.11     potential, 2.5.3.21
database, 7.4     representations, 2.6.1
     seach and alignment, 7.4     restraints, 5.8.13
default, 3.1.13     ribbon, 5.1.3
delete, 2.5.2.1, 3.6.6, 6.6.8     skin, 5.1.4
     alignment, 7.7.5     surface, 5.1.6, 5.3.1
     all, 2.5.2.2     surfaces, 2.6.6
     label, 5.8.9     tethers, 5.8.12
     alignment, 7.7.5     wire, 5.1.1
     all, 2.5.2.2     xstick, 5.1.2
     angle.label, 5.9.4distance, 4.5, 4.5.6, 5.8.10, 5.9
     distance.label, 5.9.4     label, 3.7.7
     label, 5.8.9distances, 2.6.3
     selection, 2.5.2.1docking, 4.5.13
density, 4.3.4, 4.3.6, 4.3.7document, 6.6.4, 6.6.5
depth, 5.3.12, 5.10.5     navigation, 6.6.7
dialog, 6.6.5documents, 5.15.3
diffuse, 2.6.2     envelope, 2.6.1
dihedral, 4.5.8, 5.8.5     surface, 3.7.5
     angle, 4.5dotted line, 5.1.3
directories preferences, 3.7.2drag, 3.1.11, 3.7.7, 5.8.3, 6.6.4, 7.6.6
directory, 3.7     and drop sequences, 7.6.6
display, 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     residue label, 2.5.3.16
     delete distances, 5.9.4draganddrop, 3.1.11
     dihedral, 5.9.3drop, 3.1.11, 6.6.4, 7.6.6
     distance restraints, 5.8.13drug bank, 3.2, 3.2.8
     distance2, 5.9.1dsPocket, 3.1.8
          angles, 5.9easy rotate, 2.5.3.12
     formal charge, 5.1.9edit, 4.2.3.1
     gradient, 5.8.16     alignment, 7.7.1
     hydrogen, 5.1.7     ligand tools, 2.5.2.17
     mesh, 5.3.5     menu, 2.5.2
     meshes, 5.3.8     molecular document, 6.6.1
     planar angle, 5.9.2     selection, 2.5.2.5
     tab, 2.6.1     slide, 6.4.1
     tether, 5.8.12editpdbsearch, 2.5.2.12
     toggle, 5.8.15eds, 4.3.4, 4.3.6, 4.3.7
     CPK, 5.1.5electron, 4.3.4, 4.3.6, 4.3.7
     densitry map.contour, 2.5.5     screen, 2.5.3.8
          map, 2.5.1.7, 2.5.5, 4.3.4, 4.3.6general preferences, 3.7.5
electrostatic potential, 2.5.3.21generalselecttools, 3.6.1
     surface, 5.3generator, 4.3.3
electrostatics, 5.3.1getting started, 3
elegant sketch, 5.10.4glasses, 5.6
embed browser, 6.11google, 2.5.1.7
     powerpoint03, 6.8     objects, 5.3.7
     powerpoint07, 6.9     3D, 2.6.6, 5.3.7
     powerpoint10, 6.10graphical display tutorial, 8.1
     activeicm, 6.13               2D3D labels, 8.1.4
          script, 6.13               annotation, 8.1.2
     browser, 6.7, 6.11               color representation, 8.1.1
     firefox, 6.7, 6.11               labels, 8.1.3
     internet.explorer, 6.7, 6.11graphics, 3.1
     microsoft, 6.7     controls, 5
     powerpoint, 6.7, 6.8, 6.9, 6.10     effects, 5.10
energy, 4.5.11, 5.8.14     panel, 5.2
exit, 2.5.1.19     preferences, 3.7.3
export, 4.5.10     shadow, 2.5.3.13, 5.10.2
extra windows, 5.2green arrows, 7.7.16
extract, 3.4.2, 7.1     lines, 7.2
     icb, 2.5.1.5grob, 3.7.5, 4.3.4, 4.3.6, 4.3.7, 5.3
     object icb, 3.4.2gui, 3.1.1, 3.7.4
     sub alignment, 7.3.10     menus, 2.5
     icb, 2.5.1.5     preferences, 3.7.4
fasta, 7.1.5     tabs, 2.6
file, 2.5.1.3h-bond, 4.2.3, 4.2.3.1, 4.2.3.2
     close, 2.5.1.13hardware stereo, 2.5.3.7
     compatible, 2.5.1.10hbond, 4.2, 8.3.6
     export, 2.5.1.12header, 3.2.1.6
     high quality image, 5.15.1health, 4.5.11
     load, 2.5.1.7help, 1
     menu, 2.5.1     videos, 1
     password, 2.5.1.11hidden block format, 7.7.11
     preferences, 2.5.1.16          width, 7.7.11
     quick image, 2.5.1.14high, 2.5.1.15
     icb, 3.1.10     quality, 2.5.3.11
     recent, 2.5.1.17homology, 3.2.1.2, 3.2.5
     bak, 2.5.2.11     to activeicm, 2.3
filter selection, 3.6.8               create molecular documents, 2.3.3
flexibility, 4.5.12                    slides, 2.3.2
fog, 2.5.3.5, 5, 5.10.1               getting started, 2.3.1
font, 3.7, 3.7.7, 4.2.3.1, 5.8.2, 5.8.3, 7.7.7, 7.7.7.1               ppt, 2.3.4
     preferences, 3.7.7               web, 2.3.5
     size, 7.7          icm browser convert display pocket, 2.1.4
formal charge, 5.1.9                    distances angles, 2.1.9
frame, 7.3.3                    get started, 2.1.1
front, 5.3.10, 5.13.1                    graphical display, 2.1.2
full scene antialias, 2.5.3.10                         effects, 2.1.5
                    labels annotation, 2.1.6     animation, 5.10.7.3
                    pro crystallographic tools, 2.2.6isee, 6.6.5
                         get started, 2.2.1javascript, 6.16
                         graphics, 2.2.2jpg, 5.15
                         plots, 2.2.8keyboard mouse, 5.11
                         sequence analysis, 2.2.7kmz, 2.6.6, 5.3.7
                         structure analysis, 2.2.3label, 3.7.7
                         superimpose, 2.2.5     atoms, 5.8.2
                         surfaces, 2.2.4     color, 5.8.7
                    selections, 2.1.3     move, 5.8.4
                    superimpose, 2.1.8     residues, 5.8.3
          search, 3.2     sites, 5.8.6
          use gui, 3.1     variables, 5.8.5
html, 2.5.1.12, 3.3, 6.6.1, 6.6.7     2D, 2.6.3
hydrogen, 4.2.3, 4.2.3.1, 4.2.3.2, 5.1.8, 8.3.6     3D, 2.6.3, 5.8.1
     bond, 4.2, 5.1.8, 8.3.6     atom, 5.8.1
          label edit, 4.2.3.1     atoms, 5.8.2
               move, 4.2.3.2     color, 5.8.7
     bonds, 4.2.4     custom, 5.8.8
hyperlink, 6.6.1, 6.6.2     delete, 5.8.1, 5.8.9
iSee, 2.5.1.5, 2.5.1.12, 3.1.10, 5.15.3, 8.2     distance, 5.8.10
icb, 3.4.2, 3.5     drag, 2.5.3.16
     chemist howto chemical search, 2.4.3     move, 2.5.3.16, 5.8.4
               cluster, 2.4.5     residue, 5.8.1
               combi library, 2.4.7     residues, 5.8.3
               ph4, 2.4.4     site, 5.8.1
               plots, 2.4.8     sites, 5.8.6
               sketch, 2.4.1     variable, 5.8.1
               spreadsheets, 2.4.2     variables, 5.8.5
               stereoisomers tautomers, 2.4.6labeling, 5.8.1
          tutorials, 2.4labels, 5.8
     object, 4.1, 8.3.2     distances, 5.8.10
icmFastAlignment, 7.4     tab, 2.6.3
icmPocketFinder, 4.5.14landscape, 3.7.6
icmjs, 6.16layer, 5.14
icmpocketfinder, 8.3.7layers, 5.14
identity, 3.2.1.2ligand, 4.2.2
image, 3.1.14, 3.7, 3.7.5, 5.15.3, 6.6.3     code, 3.2.1.3, 3.2.7
     advanced, 5.15.3     editor preferences, 2.5.2.18
     preferences, 3.7.6     pocket, 4.2.4
     multiple, 2.5.1.7     receptor display, 4.2
     quality, 2.5.3.11     surface, 4.2.2
     quick, 2.5.1.14, 5.15.2     pocket, 3.1.8
images, 5.15     receptor.contact, 4.5.3
insert, 6.6.4ligand_pocket_interactions, 4.2.4
     image, 6.6.3ligedit tab, 2.6.5
     script, 6.6.4light, 2.6.2
interaction, 4.5.3     tab, 2.6.2
interactive, 8.2lighting, 5.3.9.4, 5.5
interrupt, 5.10.7.3line, 3.7.5
link, 7.3.9molecular animations slides, 6
     structure to alignment, 8.4     documents, 8.2
links, 3.6.20     graphics, 5
list, 3.6.18molskin, 5.3.2
load, 2.5.1.3, 2.5.1.17, 4.3.4, 4.3.6, 4.3.7, 7.1mouse, 3.1.3, 5.11, 5.12
     example alignment, 7.3.14mov, 5.16, 5.16.2
     nmr model, 3.2.1.4move, 2.5.3.19, 3.1.11, 3.1.13, 4.2.3.2, 5.3.9.1, 5.3.9.2, 5.12, 5.12.7
     protein structure, 4.1.1     mesh, 5.3.9.2
     sequence, 7.1     slide, 6.4.2
          extract pdb, 7.1.3     structure, 5.12
          from file, 7.1.4     tools, 5
          paste, 7.1.2     rotate, 5.11
          swissprot, 7.1.1     slab, 5.11
lock, 5.3.10, 5.13.1     translate, 5.11
logout, 2.5.1.19     z-rotation, 5.11
macros, 6.14     zoom, 5.11
macroshape, 2.5.3.22, 5.3, 5.3.6movie, 5.16.1
make, 5.10.7.1     making, 5.16, 5.16.2
     alignment, 7.6.1     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, 2.5.1.1     windows, 5.2
     object, 2.5.1.1multiple receptor, 3.2.2
making molecular slides, 6.1navigate workspace, 3.6.10
     html, 6.6new, 7.1
map, 3.7.7, 4.3.4, 4.3.6, 4.3.7     icm session, 2.5.1.2
     cel, 4.3.5nmr model, 3.2.1.4
materials, 2.6.6non-contiguous selection, 3.6.18
maxColorPotential, 3.7.10object, 3.1.11, 3.5, 8.3
menu, 6.6.5objects, 4.1.2
     chemistry, 2.5.14occlusion, 5.3.12, 5.10.5
     docking, 2.5.15     shading, 5.3.12
     homology, 2.5.13          effect, 5.10.5
     molmechanics, 2.5.16occupancy, 5.1.3, 8.3.10
     tools chemical search, 2.5.11     display, 3.2.1.5
          molecular editor, 2.5.12oda, 4.5.13
     windows, 2.5.17older version, 2.5.1.10
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, 5.13.1omega, 5.8.5
     clip, 5.3.10open, 2.5.1.3, 3.4
     color lighting, 5.3.9.4     file, 3.4
     options, 5.3.9     password, 3.4.1
     representation, 5.3.9.3     with password, 2.5.1.4
     save, 5.3.11     movie, 5.16, 5.16.2
     options, 5.3.9     password, 2.5.1.4, 3.4.1
meshes, 5.3.2, 5.10.5optimal, 4.5.13
     surfaces grobs, 5.3orange, 3.6.5
     tab, 2.6.6     selection, 3.6.5
mmff type, 5.8.2origin, 5.8.11
mnSolutions, 3.7.10other selection, 3.6.19
package.activeicm, 6.13     rename, 2.5.1.9
packing, 4.3.1properties, 5.8.2
pdb, 2.5.1.7, 3.2, 3.2.1.1, 3.2.7, 3.5, 8.3protect, 6.6.8
     html, 3.2.1.6protein, 4.4.6, 7
     preparation, 8.3.11     health, 4.5.11
     search, 3.2.1, 3.2.1.2, 3.2.1.3, 8.3.1     structure, 4
     recent, 2.5.1.18          analysis, 4.5
     search, 2.6.4, 3.1.2               closed cavities, 4.5.4
pdbsearchfield, 2.5.2.13               contact areas, 4.5.3
pdbsearchhomology, 2.5.2.15               distance, 4.5.6
pdbsearchidentity, 2.5.2.14               find related chains, 4.5.1
pdbsearcsequence, 2.5.2.16               finding dihedral angle, 4.5.8
peptide, 3.3                    planar angle, 4.5.7
percentage similarity, 7.7.15, 8.4.4               rama export, 4.5.10
perspective, 2.5.3.9, 5.10.6               ramachandran plot, 4.5.9
phi, 5.8.5               rmsd, 4.5.2
phylogenetic, 7.7.8               surface area, 4.5.5
phylogeny, 7.7.8          tutorials, 8.3
picking, 5               analysis, 8.3.4
picture, 2.5.1.14, 3.1.14, 5.15.2, 6.6.3               contact area, 8.3.5
     tips, 3.1.14               convert, 8.3.2
planar, 4.5.7, 5.8.5               hydrogen bond, 8.3.6
     angle, 4.5               icmpocketfinder, 8.3.7
     angle, 5.9.2               search, 8.3.1
plane, 5.3.10, 5.13, 5.13.1, 5.14               superimpose, 8.3.3
plot, 3.7, 3.7.8     superposition, 4.4
     function, 2.5.9, 2.5.9.1          select, 4.4.1
     preferences, 3.7.8          sites by apf, 4.4.6
png, 2.5.1.14, 5.15, 5.15.2, 6.6.3          superimpose 3D, 4.4.3
pocket, 3.1.8, 4.2, 4.2.1, 4.2.2, 4.5.14, 8.3.7               grid, 4.4.5
     surface, 4.2.1               multiple proteins, 4.4.4
     peptide, 3.1.8protein-protein, 4.5.13
     properties, 3.1.8proximity, 5.3.3, 5.3.4
pocketome, 3.2, 3.2.2psi, 5.8.5
portait, 3.7.6publication quality images, 5.3.2
postscript, 3.7.6pubmed, 3.2.1.7
powerpoint, 8.2purple box, 2.5.3.23
ppt, 6.12, 6.14qs hydrogen bond, 4.2.3
predict, 7.3.2quality, 2.5.1.15, 3.7.5
preferences, 3.7quick, 3.1.14
presentatio, 6.6.5     image, 5.15.2
presentation, 6.7, 6.12     start move structure, 3.1.3
presentations, 6          read pdb, 3.1.2
print, 5.7          representation, 3.1.6
     alignment, 7.7.4          selection, 3.1.5
     alignment, 7.7.4               level, 3.6.3
printer.resolution, 3.7.6          what is selected, 3.6.4
profile, 7.3.8     dispalay.distance, 5.9.1
project, 2.5.1.5     start color, 3.1.7
     close, 2.5.1.13quit, 2.5.1.19
ramachandran plot, 4.5, 4.5.10     pdb, 3.5
range, 5.10.7.2     project icb, 3.1.10
ratio.selection, 3.7.5     sequence, 7.1.5
read, 2.5.1.3, 2.5.1.17, 3.4, 7.1     slide, 6.4
     pdb, 3.1.2     image, 2.5.1.15, 3.1.14
rear, 5.3.10, 5.13.1     object, 3.1.9
recent files, 2.5.1.17     password, 2.5.1.11
     pdb codes, 2.5.1.18     picture, 2.5.1.15
receptor, 4.2.1, 4.2.2     project, 2.5.1.8, 2.5.1.9, 2.5.1.10, 3.1.10
recover, 2.5.2.11saving, 2.5.1.8
     cylinders, 7.7.16     project, 2.5.1.8
     lines, 7.2scale, 3.7.5
redo, 2.5.2.10screenshot, 5.16, 5.16.2
rename project, 2.5.1.9     movie, 5.16.2
representation, 2.5.3.19script, 3.3, 6.6.4, 6.6.5
residue, 3.7.7search chembl, 3.2.3
     alternative orientaiton, 8.3.11     drugbank, 3.2.8
     content, 7.3.1     in workspace, 2.5.2.4
     range, 3.6.18     pdb, 3.2.1
     content, 2.5.4, 7.3, 7.3.1          chemical, 3.2.1
residues, 4.2.1, 4.2.2          ligand code, 3.2.7
resize, 5.3.9.1, 5.15.3     pocketome, 3.2.2
     mesh, 5.3.9.1     pubchem, 3.2.9
resolution, 3.2.1.3     surechembl, 3.2.4
restore, 2.5.2.11, 5.3.10, 5.13.1     tab field, 3.2.1.3
     recent backup, 2.5.2.11          pdb chemical, 3.2.1.1
ribbon, 2.6.1, 3.7.9, 5.1.3               sequence, 3.2.1.2
     preferences, 3.7.9     uniprot, 3.2.6
     style, 3.7.9     in.workspace, 2.5.2.4
     breaks, 5.1.3secondary.sctructure, 7.3.2
     cylinders, 5.1.3     structure, 2.5.4, 5.1.3, 7.3
     smooth, 5.1.3select, 3.6.12, 3.6.13
     worm, 5.1.3     all, 3.6.14
ribbonColorStyle, 3.7.9     amino acid, 3.6.13
right, 3.1.12     molecule, 3.6.12
     click, 3.1.12     neighbors, 3.6.15
rmsd, 4.5, 4.5.2          graphic, 3.6.16
rock, 2.5.3.15, 5.10.7, 5.10.7.1, 6     object, 3.6.11
     speed, 5.10.7.2     residue, 3.6.13, 3.6.18
root mean square deviation, 4.5.2          by number, 3.6.18
rotate, 2.5.3.15, 3.1.3, 5, 5.10.7, 5.10.7.1, 5.12, 5.12.1, 5.12.2, 6          number, 3.6.18
     easy, 2.5.3.12     atom, 3.1.5, 3.6.3
     speed, 5.10.7.2     graphical, 3.1.5, 3.6.3
rotation, 5.12.1     object, 3.1.5, 3.6.3
ruler, 5.8.15     purple.box, 2.5.3.23
salt bridge, 8.3.6     residue, 3.1.5, 3.6.3
save, 3.5, 5.3.11, 5.10.7.4, 7.1.5     workspace, 3.1.5, 3.6.3
     alignment, 7.7.3selectall, 2.5.2.3
     file, 3.5selecting.neighbors, 3.6.16
     object, 3.1.9selection, 3.6.4, 3.6.5, 3.6.21, 5.3.4
     neighbors, 2.5.2.8     unique, 7.3.13
     alignment, 3.6.19shade, 7.7.7, 7.7.7.1
     all, 2.5.2.3     alignment, 8.4.4
     alter, 3.6.7shading, 5.3.12
     atom, 2.5.2.5shadow, 5.10.2
     basic, 3.6.2shell preferences, 3.7.10
     change, 3.6.7shift, 5.8.3
     clear, 2.5.2.7shine, 2.6.2, 3.7.5
     filter, 2.5.2.5, 3.6.8shineStyle, 3.7.3
     graphical, 3.6.16show, 6.3.1
     invert, 2.5.2.6side by side stereo, 2.5.3.6
     level, 2.5.3.3sigmaLevel, 4.3.6, 4.3.7
     mode, 2.5.3.4sites, 4.4.6
     near atoms, 2.5.2.8size, 4.2.3.1
     neighbors, 2.5.2.5, 2.5.2.8, 3.6.15, 3.6.17sketch accents, 5.10.3
     object, 3.6.11     accents, 2.5.3.14, 5.10.3
     other, 3.6.19skin, 2.6.1, 5.1.4
     properties, 2.5.2.5slab, 5.3.10, 5.13.1
     residue, 2.5.2.5slice, 5.13
     sphere, 3.6.15slide, 5.10.7.4, 6.2, 6.3.1, 6.6.1
     spherical, 2.5.2.8     effects, 6.5
     superposition, 4.4.1     movie, 5.16.1
     table, 3.6.19          file, 6.2
     tools, 3.6.1, 3.6.2, 3.6.7, 3.6.8     navigation, 6.3.2
     whole, 3.6.11     show, 6.3
     workspace, 3.6.9, 3.6.17     blend, 6.5
selectioninvert, 2.5.2.6     edit, 6.4.1
selections, 3.6     effect, 6.5
     links, 7.3.9     smooth, 6.5
selectneighbors workspace, 3.6.17     transition, 6.5
sequence, 2.5.4, 3.2, 3.2.1.2, 3.2.5, 3.2.6, 3.3, 7, 7.1, 7.1.5, 7.2, 7.3, 7.3.7, 7.6.1, 7.6.5, 8.3, 8.4, 8.4.4slides, 5.16.1, 6, 6.1, 6.3
     analysis, 7.3smooth, 5.3.9.3
     editor, 7.5solid, 5.3.9.3
     identity, 7.7.15sort table, 2.5.10.4
     pattern, 3.2.1.2spec, 2.6.2
     reordering, 7.7.8speed, 5.10.7.2
     secondary structure, 7.2squence.amino acid, 7.3.4
     similarity, 7.7.15stereo, 3.7.6, 5.6
     sites, 7.5     hardware, 2.5.3.7
     structure, 7.3.6     side-by-side, 2.5.3.6
     type, 7.3.4stick, 3.7.5
     DNA, 7.3.4stl, 5.7
     alignment, 7.3.5, 7.6.2, 7.6.6stop, 5.10.7.3
     nucleotide, 7.3.4store, 2.5.3.19, 5.10.7.4
     protein, 7.3.4     current view, 2.5.3.19
     search, 7.4strain, 4.5.11
     structure.alignment, 7.3.6, 7.6.3structure, 4.3.3, 8.3
sequences, 7     analysis, 8.3.4
     unique, 7.3.13     representation, 5.1
     extract, 7.3.13style, 3.7.5
     3D, 4.4.3          symmetry, 8.3.9
     Calpha, 4.4.3tut3e, 8.3.12
     arrange.grid, 4.4.5tutorial molecular documents, 8.2
     backbone, 4.4.3     sequence alignment, 8.4
     heavy atoms, 4.4.3               link, 8.4.2
     multiple, 4.4.4               load sequence, 8.4.1
superposition, 8.3.3               sequence conservation, 8.4.3
surface, 2.6.1, 3.7.5, 4.2.1, 4.2.2, 5.1.6, 5.3, 5.3.3, 5.3.4tutorials, 8
     area, 4.5unclip, 5.3.10, 5.13.1
     area, 4.5.5undisplay, 3.1.4, 5.1.7
surfaces, 4.2, 5.3.1, 5.3.2, 5.10.5     box shade font, 7.7.7.1
swissprot, 7.1, 7.5     origin, 5.8.11
symmetry, 4.3.1, 4.3.3, 8.3.8, 8.3.9undo, 2.5.2.9, 3.7
system preferences, 3.7.11uniprot, 3.2.6, 7.5
tab pdb, 2.6.4unit, 4.3.3
table, 3.3unusual peptide, 3.3
     join, 2.5.10.5     activeicm, 6.12
     merge, 2.5.10.5uundisplay-all, 2.5.3.1
     rows, 2.5.10.7van der waal, 5.8.14
     sort, 2.5.10.4variable, 3.7.7
tag, 3.6.21video, 1, 5.16, 5.16.1, 5.16.2
tags, 3.6.21view, 2.5.3.19, 6.3.1
temperature, 4.5.12     animate view, 2.5.3.15
text, 3.7.7, 6.6, 6.6.1, 6.6.7     center, 2.5.3.20
texture, 2.6.6     color background, 2.5.3.18
threshold, 3.7.5     fog, 2.5.3.5
tier, 3.1.13     macroshape, 2.5.3.22
tools 3D, 2.5.6     menu, 2.5.3
     analysis, 2.5.7     mesh clip, 5.13.1
     append rows, 2.5.10.7     perspective, 2.5.3.9
     extras, 2.5.9     selection level, 2.5.3.3
          plot function, 2.5.9.1          mode, 2.5.3.4
     superimpose, 2.5.8     shadow, 2.5.3.13
     table, 2.5.10     sketch accents, 2.5.3.14
          Learn, 2.5.10.1     slide show, 6.3.1
          clustering, 2.5.10.3     tools, 2.5.3
          merge, 2.5.10.5     undisplay all, 2.5.3.1
          predict, 2.5.10.2virus, 4.3.3
torsion, 5.12.6wavefront, 2.6.6, 5.3.11
     angles, 5.12, 5.12.6web, 8.2
trace, 5.1.10     browser, 2.5.1.12
transitions, 6window, 3.1.13
translate, 3.1.3, 5, 5.12windows, 3.1.13.1
translation, 5.12.3, 7.3.3wire, 2.6.1, 3.7.5, 5.1.1
transparent, 5.3.9.3wireBondSeparation, 3.7.1
     background, 5.15.3workspace, 3.1.4
tree, 7.7.8     panel, 3.1.4
     branch swapping, 7.7.8     selection, 3.6.9
tut analyze alternative orientations, 8.3.11     navigation, 3.6.10
          occupancy, 8.3.10write, 3.1.14, 3.5
     image, 2.5.1.15 
     images, 5.15 
     pdb, 3.5 
     image, 2.5.1.15 
     object, 3.1.9 
     picture, 2.5.1.15 
     project, 2.5.1.8, 3.1.10 
     ray, 2.5.5 
xi, 5.8.5 
xstick, 5.1.2 
youtube, 1 
zoom, 3.1.3, 5, 5.12, 5.12.4 

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