help/html/colourSchemes/index.html

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  22 <head>
  23 <title>Colour Schemes</title>
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  33 </head>
  34 <body>
  35   <p>
  36     <strong>Colour schemes</strong>
  37   </p>
  38   <p>Jalview allows the user to set a colour scheme for the
  39     whole alignment view or for each group defined on regions within it.</p>
  40   <p>To change the colour for a view, simply select a new colour scheme from
  41     the &quot;Colour&quot; menu.</p>
  42   <p>To change the colour of a group, right click on any residue
  43     within a group and use the popup menu to define the group colour.</p>
  44   <p>At the top of the &quot;Colour&quot; menu you'll see a tick box
  45     &quot;Apply Colour to all groups&quot;. This is ticked by
  46     default so that a chosen colour scheme will be applied to all
  47     existing groups. If you wish to maintain the colour scheme for
  48     defined groups, make sure you deselect this option before selecting
  49     a new scheme in the Colour menu.</p>
  50   <p>
  51     The <strong>&quot;Colour&#8594;<a
  52       href="../colourSchemes/textcolour.html">Colour Text...</a>&quot;
  53     </strong> entry opens a dialog box to set a different text colour for light
  54     and dark background, and the intensity threshold for transition
  55     between them.
  56   </p>
  57   <p>The default colour schemes are summarised in the table below:
  58   <div align="center">
  59     <p>&nbsp;</p>
  60     <p>
  61       <strong>Protein Colour Schemes</strong>
  62     </p>
  63     <table border="1">
  64       <tr>
  65         <td>
  66           <table border="1">
  67             <tr>
  68               <td nowrap></td>
  69               <td>A</td>
  70               <td>R</td>
  71               <td>N</td>
  72               <td>D</td>
  73               <td>C</td>
  74               <td>Q</td>
  75               <td>E</td>
  76               <td>G</td>
  77               <td>H</td>
  78               <td>I</td>
  79               <td>L</td>
  80               <td>K</td>
  81               <td>M</td>
  82               <td>F</td>
  83               <td>P</td>
  84               <td>S</td>
  85               <td>T</td>
  86               <td>W</td>
  87               <td>Y</td>
  88               <td>V</td>
  89               <td>B</td>
  90               <td>X</td>
  91               <td>Z</td>
  92             </tr>
  93             <tr>
  94               <td height="24">Clustal</td>
  95               <td bgcolor="#80a0f0"></td>
  96               <td bgcolor="#f01505"></td>
  97               <td bgcolor="#00ff00"></td>
  98               <td bgcolor="#c048c0"></td>
  99               <td bgcolor="#f08080"></td>
 100               <td bgcolor="#00ff00"></td>
 101               <td bgcolor="#c048c0"></td>
 102               <td bgcolor="#f09048"></td>
 103               <td bgcolor="#15a4a4"></td>
 104               <td bgcolor="#80a0f0"></td>
 105               <td bgcolor="#80a0f0"></td>
 106               <td bgcolor="#f01505"></td>
 107               <td bgcolor="#80a0f0"></td>
 108               <td bgcolor="#80a0f0"></td>
 109               <td bgcolor="#ffff00"></td>
 110               <td bgcolor="#00ff00"></td>
 111               <td bgcolor="#00ff00"></td>
 112               <td bgcolor="#80a0f0"></td>
 113               <td bgcolor="#15a4a4"></td>
 114               <td bgcolor="#80a0f0"></td>
 115               <td></td>
 116               <td></td>
 117               <td></td>
 118             </tr>
 119             <tr>
 120               <td height="24">Zappo</td>
 121               <td bgcolor="#ffafaf"></td>
 122               <td bgcolor="#6464ff"></td>
 123               <td bgcolor="#00ff00"></td>
 124               <td bgcolor="#ff0000"></td>
 125               <td bgcolor="#ffff00"></td>
 126               <td bgcolor="#00ff00"></td>
 127               <td bgcolor="#ff0000"></td>
 128               <td bgcolor="#ff00ff"></td>
 129               <td bgcolor="#6464ff"></td>
 130               <td bgcolor="#ffafaf"></td>
 131               <td bgcolor="#ffafaf"></td>
 132               <td bgcolor="#6464ff"></td>
 133               <td bgcolor="#ffafaf"></td>
 134               <td bgcolor="#ffc800"></td>
 135               <td bgcolor="#ff00ff"></td>
 136               <td bgcolor="#00ff00"></td>
 137               <td bgcolor="#00ff00"></td>
 138               <td bgcolor="#ffc800"></td>
 139               <td bgcolor="#ffc800"></td>
 140               <td bgcolor="#ffafaf"></td>
 141               <td></td>
 142               <td></td>
 143               <td></td>
 144             </tr>
 145             <tr>
 146               <td>Taylor</td>
 147               <td bgcolor="#ccff00"></td>
 148               <td bgcolor="#0000ff"></td>
 149               <td bgcolor="#cc00ff"></td>
 150               <td bgcolor="#ff0000"></td>
 151               <td bgcolor="#ffff00"></td>
 152               <td bgcolor="#ff00cc"></td>
 153               <td bgcolor="#ff0066"></td>
 154               <td bgcolor="#ff9900"></td>
 155               <td bgcolor="#0066ff"></td>
 156               <td bgcolor="#66ff00"></td>
 157               <td bgcolor="#33ff00"></td>
 158               <td bgcolor="#6600ff"></td>
 159               <td bgcolor="#00ff00"></td>
 160               <td bgcolor="#00ff66"></td>
 161               <td bgcolor="#ffcc00"></td>
 162               <td bgcolor="#ff3300"></td>
 163               <td bgcolor="#ff6600"></td>
 164               <td bgcolor="#00ccff"></td>
 165               <td bgcolor="#00ffcc"></td>
 166               <td bgcolor="#99ff00"></td>
 167               <td></td>
 168               <td></td>
 169               <td></td>
 170             </tr>
 171             <tr>
 172               <td>Hydrophobicity</td>
 173               <td bgcolor="#ad0052"></td>
 174               <td bgcolor="#0000ff"></td>
 175               <td bgcolor="#0c00f3"></td>
 176               <td bgcolor="#0c00f3"></td>
 177               <td bgcolor="#c2003d"></td>
 178               <td bgcolor="#0c00f3"></td>
 179               <td bgcolor="#0c00f3"></td>
 180               <td bgcolor="#6a0095"></td>
 181               <td bgcolor="#1500ea"></td>
 182               <td bgcolor="#ff0000"></td>
 183               <td bgcolor="#ea0015"></td>
 184               <td bgcolor="#0000ff"></td>
 185               <td bgcolor="#b0004f"></td>
 186               <td bgcolor="#cb0034"></td>
 187               <td bgcolor="#4600b9"></td>
 188               <td bgcolor="#5e00a1"></td>
 189               <td bgcolor="#61009e"></td>
 190               <td bgcolor="#5b00a4"></td>
 191               <td bgcolor="#4f00b0"></td>
 192               <td bgcolor="#f60009"></td>
 193               <td bgcolor="#0c00f3"></td>
 194               <td bgcolor="#680097"></td>
 195               <td bgcolor="#0c00f3"></td>
 196             </tr>
 197             <tr>
 198               <td>Helix Propensity</td>
 199               <td bgcolor="#e718e7"></td>
 200               <td bgcolor="#6f906f"></td>
 201               <td bgcolor="#1be41b"></td>
 202               <td bgcolor="#778877"></td>
 203               <td bgcolor="#23dc23"></td>
 204               <td bgcolor="#926d92"></td>
 205               <td bgcolor="#ff00ff"></td>
 206               <td bgcolor="#00ff00"></td>
 207               <td bgcolor="#758a75"></td>
 208               <td bgcolor="#8a758a"></td>
 209               <td bgcolor="#ae51ae"></td>
 210               <td bgcolor="#a05fa0"></td>
 211               <td bgcolor="#ef10ef"></td>
 212               <td bgcolor="#986798"></td>
 213               <td bgcolor="#00ff00"></td>
 214               <td bgcolor="#36c936"></td>
 215               <td bgcolor="#47b847"></td>
 216               <td bgcolor="#8a758a"></td>
 217               <td bgcolor="#21de21"></td>
 218               <td bgcolor="#857a85"></td>
 219               <td bgcolor="#49b649"></td>
 220               <td bgcolor="#758a75"></td>
 221               <td bgcolor="#c936c9"></td>
 222             </tr>
 223             <tr>
 224               <td nowrap>Strand Propensity</td>
 225               <td bgcolor="#5858a7"></td>
 226               <td bgcolor="#6b6b94"></td>
 227               <td bgcolor="#64649b"></td>
 228               <td bgcolor="#2121de"></td>
 229               <td bgcolor="#9d9d62"></td>
 230               <td bgcolor="#8c8c73"></td>
 231               <td bgcolor="#0000ff"></td>
 232               <td bgcolor="#4949b6"></td>
 233               <td bgcolor="#60609f"></td>
 234               <td bgcolor="#ecec13"></td>
 235               <td bgcolor="#b2b24d"></td>
 236               <td bgcolor="#4747b8"></td>
 237               <td bgcolor="#82827d"></td>
 238               <td bgcolor="#c2c23d"></td>
 239               <td bgcolor="#2323dc"></td>
 240               <td bgcolor="#4949b6"></td>
 241               <td bgcolor="#9d9d62"></td>
 242               <td bgcolor="#c0c03f"></td>
 243               <td bgcolor="#d3d32c"></td>
 244               <td bgcolor="#ffff00"></td>
 245               <td bgcolor="#4343bc"></td>
 246               <td bgcolor="#797986"></td>
 247               <td bgcolor="#4747b8"></td>
 248             </tr>
 249             <tr>
 250               <td>Turn Propensity</td>
 251               <td bgcolor="#2cd3d3"></td>
 252               <td bgcolor="#708f8f"></td>
 253               <td bgcolor="#ff0000"></td>
 254               <td bgcolor="#e81717"></td>
 255               <td bgcolor="#a85757"></td>
 256               <td bgcolor="#3fc0c0"></td>
 257               <td bgcolor="#778888"></td>
 258               <td bgcolor="#ff0000"></td>
 259               <td bgcolor="#708f8f"></td>
 260               <td bgcolor="#00ffff"></td>
 261               <td bgcolor="#1ce3e3"></td>
 262               <td bgcolor="#7e8181"></td>
 263               <td bgcolor="#1ee1e1"></td>
 264               <td bgcolor="#1ee1e1"></td>
 265               <td bgcolor="#f60909"></td>
 266               <td bgcolor="#e11e1e"></td>
 267               <td bgcolor="#738c8c"></td>
 268               <td bgcolor="#738c8c"></td>
 269               <td bgcolor="#9d6262"></td>
 270               <td bgcolor="#07f8f8"></td>
 271               <td bgcolor="#f30c0c"></td>
 272               <td bgcolor="#7c8383"></td>
 273               <td bgcolor="#5ba4a4"></td>
 274             </tr>
 275             <tr>
 276               <td>Buried Index</td>
 277               <td bgcolor="#00a35c"></td>
 278               <td bgcolor="#00fc03"></td>
 279               <td bgcolor="#00eb14"></td>
 280               <td bgcolor="#00eb14"></td>
 281               <td bgcolor="#0000ff"></td>
 282               <td bgcolor="#00f10e"></td>
 283               <td bgcolor="#00f10e"></td>
 284               <td bgcolor="#009d62"></td>
 285               <td bgcolor="#00d52a"></td>
 286               <td bgcolor="#0054ab"></td>
 287               <td bgcolor="#007b84"></td>
 288               <td bgcolor="#00ff00"></td>
 289               <td bgcolor="#009768"></td>
 290               <td bgcolor="#008778"></td>
 291               <td bgcolor="#00e01f"></td>
 292               <td bgcolor="#00d52a"></td>
 293               <td bgcolor="#00db24"></td>
 294               <td bgcolor="#00a857"></td>
 295               <td bgcolor="#00e619"></td>
 296               <td bgcolor="#005fa0"></td>
 297               <td bgcolor="#00eb14"></td>
 298               <td bgcolor="#00b649"></td>
 299               <td bgcolor="#00f10e"></td>
 300             </tr>
 301           </table>
 302         </td>
 303       </tr>
 304     </table>
 305     <p>&nbsp;</p>
 306     <p>
 307       <strong>Nucleotide Colour Schemes</strong>
 308     </p>
 309     <table border="1">
 310       <tr>
 311         <td>
 312           <table border="1">
 313             <tr>
 314               <td nowrap></td>
 315               <td>A</td>
 316               <!--Adenine-->
 317               <td>C</td>
 318               <!--Cytosine-->
 319               <td>G</td>
 320               <!--Guanine-->
 321               <td>T</td>
 322               <!--Thymine-->
 323               <td>U</td>
 324               <!--Uracil-->
 325               <td>I</td>
 326               <!--Inosine-->
 327               <td>X</td>
 328               <!--Xanthine-->
 329               <td>R</td>
 330               <!--Unknown Purine-->
 331               <td>Y</td>
 332               <!--Unknown Pyrimidine-->
 333               <td>N</td>
 334               <!--Unknown-->
 335               <td>W</td>
 336               <!--Weak nucleotide (A or T)-->
 337               <td>S</td>
 338               <!--Strong nucleotide (G or C)-->
 339               <td>M</td>
 340               <!--Amino (A or C)-->
 341               <td>K</td>
 342               <!--Keto (G or T)-->
 343               <td>B</td>
 344               <!--Not A (G or C or T)-->
 345               <td>H</td>
 346               <!--Not G (A or C or T)-->
 347               <td>D</td>
 348               <!--Not C (A or G or T)-->
 349               <td>V</td>
 350               <!--Not T (A or G or C-->
 351             </tr>
 352             <tr>
 353               <td height="24">Nucleotide</td>
 354               <td bgcolor="#64F73F"></td>
 355               <td bgcolor="#FFB340"></td>
 356               <td bgcolor="#EB413C"></td>
 357               <td bgcolor="#3C88EE"></td>
 358               <td bgcolor="#3C88EE"></td>
 359               <td></td>
 360               <td></td>
 361               <td></td>
 362               <td></td>
 363               <td></td>
 364               <td></td>
 365               <td></td>
 366               <td></td>
 367               <td></td>
 368               <td></td>
 369               <td></td>
 370               <td></td>
 371               <td></td>
 372             </tr>
 373             <tr>
 374               <td height="24">Purine/Pyrimidine</td>
 375               <td bgcolor="#FF83FA"></td>
 376               <td bgcolor="#40E0D0"></td>
 377               <td bgcolor="#FF83FA"></td>
 378               <td bgcolor="#40E0D0"></td>
 379               <td bgcolor="#40E0D0"></td>
 380               <td></td>
 381               <td></td>
 382               <td bgcolor="#FF83FA"></td>
 383               <td bgcolor="#40E0D0"></td>
 384               <td></td>
 385               <td></td>
 386               <td></td>
 387               <td></td>
 388               <td></td>
 389               <td></td>
 390               <td></td>
 391               <td></td>
 392               <td></td>
 393             </tr>
 394           </table>
 395         </td>
 396       </tr>
 397     </table>
 398
 399
 400   </div>
 401   <p align="center">&nbsp;</p>
 402 </body>
 403 </html>