#Comments in ALscript command files start with a #
     #Commands are free format - separated by blank, tab or comma characters
     #But no blank lines.  Blank lines must have a comment character #
     #
     BLOCK_FILE 	6seqs.blc
     OUTPUT_FILE 	6seqs.ps
     PORTRAIT
     POINTSIZE 6
     DEFINE_FONT 0 Helvetica DEFAULT
     DEFINE_FONT 1 Helvetica-Bold DEFAULT
     DEFINE_FONT 2 Helvetica REL .5
     DEFINE_FONT 3 Symbol REL 1.2
     IDENT_WIDTH 6
     ADD_SEQ 0 4
     ADD_SEQ 6 3
     DEFINE_COLOUR 1 1 0 0
     DEFINE_COLOUR 2 0 0 1
     DEFINE_COLOUR 3 0 1 0
     DEFINE_COLOUR 4 0 1 1
     DEFINE_COLOUR 5 1 0 1
     DEFINE_COLOUR 6 1 .4 .4
     DEFINE_COLOUR 7 .4 .4 1
     DEFINE_COLOUR 8 .4  1 .4
     #NUMBER_SEQS
     #DO_TICKS
     NO_NUMBERS
     SETUP		#Tell the program to get on with the formatting.
     #
     RELATIVE_TO 5  1 #assumes your sequence on top
     #
     #Block 1
     FONT_REGION 113  1  273  1 1
     COLOUR_TEXT_REGION 113  1  273  1 99
     COLOUR_REGION 113  1  273  1 6
     TEXT 114 1 "PDZ TANDEM"
     #Block2
     FONT_REGION 113  3  192  3 1
     COLOUR_TEXT_REGION 113  3  192  3 99
     COLOUR_REGION 113  3  192  3 7
     TEXT 116 3 "PDZ-1"
     TEXT 150 3 "PDZ-1"
     #BLOCK3
     FONT_REGION 197  3  273  3 1
     COLOUR_REGION 197  3  273  3 8
     TEXT 210 3 "PDZ-2"
     TEXT 255 3 "PDZ-2"
     #
     #Secondary Structure
     COLOUR_TEXT_REGION  112 12 119 12 4
     STRAND  112 12 119
     COLOUR_TEXT_REGION  120 12 123 12 5
     HELIX   120 12 123
     COLOUR_TEXT_REGION  126 12 132 12 4
     STRAND  126 12 132
     COLOUR_TEXT_REGION  135 12 142 12 4
     STRAND  135 12 142
     COLOUR_TEXT_REGION  145 12 148 12 5
     HELIX   145 12 148
     COLOUR_TEXT_REGION  154 12 162 12 4
     STRAND  154 12 162
     COLOUR_TEXT_REGION  164 12 166 12 4
     STRAND  164 12 166
     COLOUR_TEXT_REGION  170 12 181 12 5
     HELIX   170 12 181
     COLOUR_TEXT_REGION  184 12 193 12 4
     STRAND  184 12 193
     COLOUR_TEXT_REGION  196 12 203 12 4
     STRAND  196 12 203
     COLOUR_TEXT_REGION  210 12 214 12 4
     STRAND  210 12 214
     COLOUR_TEXT_REGION  217 12 222 12 4
     STRAND  217 12 222
     COLOUR_TEXT_REGION  225 12 231 12 5
     HELIX   225 12 231
     COLOUR_TEXT_REGION  234 12 242 12 4
     STRAND  234 12 242
     COLOUR_TEXT_REGION  244 12 246 12 4
     STRAND  244 12 246
     COLOUR_TEXT_REGION  250 12 260 12 5
     HELIX   250 12 260
     COLOUR_TEXT_REGION  263 12 271 12 4
     STRAND  263 12 271
     #Secondary Structure Labels
     FONT_REGION 1 13 357 13 3
     TEXT 115 13 "b1"
     TEXT 121 13 "a1"
     TEXT 129 13 "b2"
     TEXT 138 13 "b3"
     TEXT 146 13 "a2"
     TEXT 158 13 "b4"
     TEXT 165 13 "b5"
     TEXT 175 13 "a3"
     TEXT 188 13 "b6"
     TEXT 199 13 "b7"
     TEXT 212 13 "b8"
     TEXT 219 13 "b9"
     TEXT 228 13 "a4"
     TEXT 238 13 "b10"
     TEXT 245 13 "b11"
     TEXT 255 13 "a5"
     TEXT 267 13 "b12"
     #
     #  Mask for conservative substitution
     #  Next line assumes your sequence is on top of the alignment
     RELATIVE_TO 0
     SUB_CHARS 1 5 357 10 SPACE "-"
     calcons  1 5 357 10
     mask SETUP
     mask ILLEGAL "-"
     #Last number on next line is % conserved for conservative sub
     mask CONSERVATION 1 5 357 10 4
     mask SCOL 1 5 357 10 2
     mask RESET
     #  Mask for conserved
     mask SETUP
     mask ILLEGAL "-"
     #Last number on next line is #/total seqs for conserved
     mask  ID 1 5 357 10 5
     mask SCOL 1 5 357 10 3
     mask RESET
     #  Mask for total identity
     mask CONSERVATION 1 5 357 10 10
     mask SCOL 1 5 357 10 1
     mask CCOL 1 5 357 10 99
     mask FONT 1 5 357 10 1
     mask RESET
     # End of Alscript input file