# # 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"