--- /dev/null
+#
+# This is the alscript command file used to create the figure
+# published in: Roach P. L. et al (1995), Nature (June)
+#
+# The figure shows Isopenicillin N synthase with homologues
+# secondary structure and other information. It makes use
+# of many features of alscript 2.0
+#
+# Comments in the file all start with the # sign
+#
+#
+# define the alignment block file
+BLOCK_FILE ipns.blc
+# define the output file name
+OUTPUT_FILE ipns.ps
+# select portrait mode - longest paper side is vertical
+PORTRAIT
+# select point size for characters - this can be any number.
+POINTSIZE 6.5
+#
+# Define fonts that we will use in the alignment. You give each font
+# a unique number. The names of the fonts are standard PostScript
+# font names.
+#
+# This one means call Helvetica at the Default pointsize, font 0
+DEFINE_FONT 0 Helvetica DEFAULT
+# This means call Helvetica-Oblique at 70% of the default point size, font 1
+DEFINE_FONT 1 Helvetica-Oblique REL 0.70
+DEFINE_FONT 2 Helvetica-Bold DEFAULT
+define_font 5 Symbol REL 1.2
+define_font 6 Helvetica REL 0.7
+#
+# Colour definitions
+#
+# Define the colours that we will use in the alignment. Each colour is given
+# a number by which it is referred to later. The three numbers following
+# each colour are red,green,blue intensities.
+#
+# e.g. this defines colour number 1 to be red (1,0,0).
+DEFINE_COLOUR 1 1 0 0
+#DEFINE_COLOUR 2 0.8 1 0.8
+DEFINE_COLOUR 2 1 1 0
+DEFINE_COLOUR 3 0 0 1
+DEFINE_COLOUR 4 1 1 1
+DEFINE_COLOUR 5 1 1 1
+DEFINE_COLOUR 6 1 0.5 0
+DEFINE_COLOUR 7 1 0 1
+DEFINE_COLOUR 8 0 0 0
+DEFINE_COLOUR 9 1 1 1
+define_colour 10 0 1 0
+define_colour 11 0 0 0
+#
+# The add_seq command adds extra space to the alignment you have read in.
+#
+#
+# Here we are adding space for four more lines after sequence number 8.
+add_seq 8 4
+#
+# This means don't number the sequences
+no_numbers
+#
+# Alter the width of the space for identifiers at the lhs of the plot. This
+# must be set by trial and error - 10 is the default.
+ident_width 6
+#
+# Only print sequence identifiers on the first line of a multi-line/page
+# alignment plot.
+id_only_on_first_line
+#
+# This is some fiddling to reduce the default vertical spacing between
+# sequence lines. We did this to improve the appearance of the alignment
+# in a single column of Nature. Other features of the display can
+# be modified in a similar way - e.g. x_space_factor.
+y_space_factor 0.05
+#
+# commands above the SETUP are about the overall layout etc. Commands
+# after, are giving specific boxing/shading/colouring etc.
+#
+SETUP
+#
+# Calcluate conservation values for the complete alignment. Conservation
+# values range from 0-10 where 10 is an identity. Values above 5 show
+# increasing similarities in physico-chemical properties. Having calculated
+# conservation values, we can then colour the plot to highlight conserved
+# positions.
+#
+calcons 1 1 424 8
+#
+# set mask for conserved position better than 5
+#
+# this clears the MASK array of all previous settings
+mask SETUP
+# this masks all columns of the alignment for which the conservation
+# is > 5.
+mask CONSERVATION ALL 5
+#
+# Now we box the masked positions and colour the
+# text backgrounds yellow (colour 2). Note that this operation could
+# be restricted to a subset of the alignment rather than the whole thing.
+mask BOX 1 1 424 8
+#
+# The SCOL command colours the backgrounds of the character. The CCOL
+# command colours the character itself.
+mask SCOL 1 1 424 8 2
+#
+# This resets the MASK commands ready for another operation. If you don't
+# reset, then subsequent mask commands are ADDED to the existing mask
+#
+mask RESET
+#
+#now do thw same for identities, only this time in red
+#with white lettering
+mask CONSERVATION ALL 10
+mask SCOL 1 1 424 8 1
+mask CCOL 1 1 424 8 99
+mask FONT 1 1 424 8 2
+mask RESET
+#
+# sub_id allows the identifier to be modified. At present it is not possible
+# to mix fonts within an ID, but the ID_FONT command can be used to modify the
+# font used for individual IDs.
+sub_id 1 "ACCO"
+sub_id 2 "F3OH"
+sub_id 3 "H6H "
+sub_id 4 "FOLS"
+sub_id 5 "GC20"
+sub_id 6 "DAOCS"
+sub_id 7 "DAOC/DACS "
+sub_id 8 "IPNS"
+#
+# These are the secondary structure definitions. They were entered by
+# hand from an analysis of the IPNS structure.
+#
+# Secondary structure
+#
+# Set Numbering relative to IPNS
+#
+# The x values (sequence position) of any commands that follow a
+# relative_to command will be translated into absolute alignment position.
+# This takes account of gaps in the alignment.
+relative_to 8
+#
+# Set the font for the line that will say alpha1, beta2 etc to Symbol font.
+# Region commands operate on a region of the alignment - they usually expect
+# four numbers to define the region - the numbers are x,y,x1,y1 where y and y1
+# are the sequences and x and x1 are the residue positions.
+font_region 1 11 331 11 5
+#
+#colour all secondary structures black (colour 11)
+#
+colour_text_region 1 10 331 10 11
+#
+# Now draw all the helices and strands and label and colour them.
+#
+# For example, Tell ALSCRIPT to draw a strand from 11 to 13 of sequence 10
+strand 11 10 13
+# Now write the text b1 (will be a Greek b because of the
+# font_region command above).
+ text 12 11 "b1"
+helix 15 10 18
+ text 16 11 "a1"
+helix 22 10 37
+ text 30 11 "a2"
+strand 41 10 45
+ text 43 11 "b2"
+helix 51 10 64
+ text 57 11 "a3"
+helix 67 10 73
+ text 70 11 "a4"
+strand 89 10 91
+ text 90 11 "b3"
+strand 101 10 105
+ text 103 11 "b4"
+helix 115 10 118
+ text 116 11 "a5"
+helix 138 10 163
+ text 151 11 "a6"
+helix 172 10 174
+ text 173 11 "a7"
+#
+#barrel strand 1
+strand 183 10 189
+# set the colour to green for this strand.
+ colour_text_region 183 10 189 10 10
+ text 186 11 "b5"
+#
+helix 197 10 199
+ text 198 11 "a8"
+strand 201 10 202
+ text 201 11 "b6"
+strand 208 10 209
+ text 208 11 "b7"
+#
+#barrel strands 2-6
+strand 210 10 214
+ text 212 11 "b8"
+ colour_text_region 210 10 214 10 10
+strand 220 10 225
+ text 222 11 "b9"
+ colour_text_region 220 10 225 10 10
+strand 231 10 235
+ text 233 11 "b10"
+ colour_text_region 231 10 235 10 10
+strand 238 10 241
+ text 239 11 "b11"
+ colour_text_region 238 10 241 10 10
+strand 249 10 253
+ text 250 11 "b12"
+ colour_text_region 249 10 253 10 10
+#
+helix 255 10 260
+ text 257 11 "a9"
+#
+#
+#barrel strands 7-8
+strand 270 10 273
+ text 271 11 "b13"
+ colour_text_region 270 10 273 10 10
+strand 279 10 286
+ text 282 11 "b14"
+ colour_text_region 279 10 286 10 10
+#
+#
+#
+strand 293 10 294
+ text 293 11 "b15"
+strand 311 10 312
+ text 311 11 "b16"
+helix 313 10 323
+ text 317 11 "a10"
+#
+#Now add arrows for the residues within 8A of the Mn
+#
+# The TEXT command normally just writes out the specified text
+# at the specified position. However, special TEXT objects
+# exist. These all start with the @ symbol.
+#
+colour_text_region 214 12 214 12 1
+#
+# This draws a filled up arrow at position 214,12.
+text 214 12 "@fuparrow"
+colour_text_region 216 12 216 12 1
+text 216 12 "@fuparrow"
+colour_text_region 270 12 270 12 1
+text 270 12 "@fuparrow"
+colour_text_region 330 12 330 12 1
+text 330 12 "@fuparrow"
+#
+text 41 12 "@fuparrow"
+text 252 12 "@fuparrow"
+text 221 12 "@fuparrow"
+text 187 12 "@fuparrow"
+text 285 12 "@fuparrow"
+text 223 12 "@fuparrow"
+text 272 12 "@fuparrow"
+text 218 12 "@fuparrow"
+text 231 12 "@fuparrow"
+#
+#
+# Now set the sequence numbering back to alignment positions.
+relative_to 0
+#
+#
+# From here to the end of the file was created by the alsnum program
+# alsnum creates text commands for numbering a plot relative to a
+# specific sequence, rather than the alignment numbers that are
+# normally shown. Please see the ALSCRIPT manual for further details.
+#
+#
+# Text commands created for numbering
+# Sequence Number: 8
+# Starting Number: 1
+# Interval: 10
+# Position: 9
+TEXT 53 9 "10"
+TEXT 65 9 "20"
+TEXT 78 9 "30"
+TEXT 88 9 "40"
+TEXT 101 9 "50"
+TEXT 111 9 "60"
+TEXT 121 9 "70"
+TEXT 131 9 "80"
+TEXT 141 9 "90"
+TEXT 151 9 "100"
+TEXT 161 9 "110"
+TEXT 171 9 "120"
+TEXT 181 9 "130"
+TEXT 191 9 "140"
+TEXT 201 9 "150"
+TEXT 211 9 "160"
+TEXT 221 9 "170"
+TEXT 231 9 "180"
+TEXT 241 9 "190"
+TEXT 251 9 "200"
+TEXT 261 9 "210"
+TEXT 271 9 "220"
+TEXT 281 9 "230"
+TEXT 297 9 "240"
+TEXT 307 9 "250"
+TEXT 317 9 "260"
+TEXT 327 9 "270"
+TEXT 343 9 "280"
+TEXT 353 9 "290"
+TEXT 363 9 "300"
+TEXT 378 9 "310"
+TEXT 388 9 "320"
+TEXT 398 9 "330"
git://source.jalview.org / jpred.git / blobdiff