--- /dev/null
+# Illustration of ALSCRIPT Command File
+#
+# Illustrates some of the MASK commands
+#
+# example 1 # Comment lines begin with the # symbol
+#
+#
+# (A) Input and output files:
+#
+BLOCK_FILE example1.blc # Define the block file to format
+OUTPUT_FILE example4.ps # Where to put the result
+#
+MAX_SIDE 11 # Fiddle with margins...
+Y_OFFSET 50 # This is just to fill the page with the
+X_OFFSET 80 # Alignment. Defaults normally work OK
+#
+# (B) Page Layout and overall spacing:
+#
+ADD_SEQ 38 1 # Make space after sequence 38
+ADD_SEQ 39 3 # Make space after sequence 39
+ADD_SEQ 69 1
+PORTRAIT # Portrait paper orientation
+POINTSIZE 10 # 10 point default pointsize
+#NUMBER_SEQS 1 # Set to 1 for numbers at left of plot
+IDENT_WIDTH 8
+#
+# (C) Font definitions:
+#
+DEFINE_FONT 0 Helvetica DEFAULT # Set font 0 to be Helvetica at default pointsize
+DEFINE_FONT 1 Helvetica REL 0.75 # Set font 1 to be 0.75 times default Helvetica
+DEFINE_FONT 3 Helvetica-Bold DEFAULT
+DEFINE_FONT 4 Times-Bold DEFAULT
+DEFINE_FONT 5 Helvetica-BoldOblique DEFAULT
+DEFINE_FONT 6 Times-Roman DEFAULT
+SETUP # Tell the program to get on with the formatting
+#
+# some formatting commands
+#
+SURROUND_CHARS LIV ALL # Surround all L and Y characters
+FONT_CHARS IV ALL 5 # Use font 5 for all I and V characters
+FONT_CHARS ASN ALL 1 # Show A and S and N characters in small caps
+FONT_CHARS KR ALL 4 # Show K and R in Times-Bold
+BOX_REGION 14 1 16 38 # Rectangular box of residues 14-16
+SHADE_CHARS + ALL 0.0 # Shade all + characters black
+SURROUND_CHARS 56+789 1 40 27 40 # Box numbers and + on line 40
+LINE TOP 2 40 8 # Draw horizontal lines to
+LINE BOTTOM 2 40 8 # Join up surrounded numbers
+TEXT 2 42 "Helix Pattern"
+TEXT 12 42 "Glycine Loop" # Add text annotations
+TEXT 21 42 "Helix Pattern"
+SUB_ID 49 "Helix Predictions"
+SUB_ID 58 "Sheet Predictions" # Change the identifiers for prediction histograms
+SUB_ID 68 "Turn Predictions"
+#INVERSE_CHARS DE ALL
+#SHADE_CHARS D ALL 0.5
+#SHADE_CHARS E ALL 0.0
+#
+# (D) Some formatting commands: to illustrate the use of MASK
+#
+mask SETUP #setup the mask
+sub_chars 1 1 27 38 SPACE . #substitute spaces for dots
+mask ILLEGAL "." #. is not to be used in frequency calculation
+mask FRE 1 1 27 38 # do the frequency calculation
+mask BOX 1 1 27 38 # use the resulting mask to create boxing lines
+mask SHADE 1 1 27 38 0.2 # shade
+mask INVERSE 1 1 27 38 # inverse - could also alter the font
+sub_chars 1 1 27 38 . SPACE # switch the dots back to spaces
+#
+# (E) Now make the prediction histograms nicer.
+#
+SURROUND_CHARS H 1 44 27 53
+SHADE_CHARS H 1 44 27 53 0.5 # Shade the Helix predictions 0.5 grey
+SUB_CHARS 1 44 27 53 H SPACE # Substitute " " for "H"
+#
+SURROUND_CHARS E 1 54 27 63 # Surround the Beta Predictions
+SHADE_CHARS E 1 54 27 63 0.7 # Shade the Beta Predictions
+SUB_CHARS 1 54 27 63 E SPACE # Substitute the E for space in the beta predictions
+#
+SURROUND_CHARS T 1 64 27 73 # Surround the Turn Predictions
+SHADE_CHARS T 1 64 27 73 0.9 # Shade the Turn Predictions
+SUB_CHARS 1 64 27 73 T SPACE # Substitute the T for space in the turn predictions
+#
+SUB_ID 75 "Summary Prediction" # Annotate and shade the summary prediction
+SHADE_CHARS HY 1 75 27 75 0.5
+SHADE_CHARS T 1 75 27 75 0.9
+#
+#
+# Now change the identifier codes
+#
+ID_FONT ALL 6
+SUB_ID 1 "Annexin I H4"
+SUB_ID 2 "Annexin I M4"
+SUB_ID 3 "Annexin I R4"
+SUB_ID 4 "Annexin V R4"
+SUB_ID 5 "Annexin V H4"
+SUB_ID 6 "Annexin V C4"
+SUB_ID 7 "Annexin II H4"
+SUB_ID 8 "Annexin II B4"
+SUB_ID 9 "Annexin II M4"
+SUB_ID 10 "Annexin IV P4"
+SUB_ID 11 "Annexin IV B4"
+SUB_ID 12 "Annexin IV H4"
+SUB_ID 13 "Annexin VI H4"
+SUB_ID 14 "Annexin VI M4"
+SUB_ID 15 "Annexin VI H8"
+SUB_ID 16 "Annexin VI M8"
+SUB_ID 17 "Annexin V BH4"
+SUB_ID 18 "Annexin VII 4"
+SUB_ID 19 "Annexin III H4"
+SUB_ID 20 "Annexin III R4"
+SUB_ID 21 "Annexin II M3"
+SUB_ID 22 "Annexin II H3"
+SUB_ID 23 "Annexin II B3"
+SUB_ID 24 "Annexin I H3"
+SUB_ID 25 "Annexin I M3"
+SUB_ID 26 "Annexin I R3"
+SUB_ID 27 "Annexin V C3"
+SUB_ID 28 "Annexin V H3"
+SUB_ID 29 "Annexin V R3"
+SUB_ID 30 "Annexin VI H3"
+SUB_ID 31 "Annexin VI M3"
+SUB_ID 32 "Annexin IV H3"
+SUB_ID 33 "Annexin IV B3"
+SUB_ID 34 "Annexin IV P3"
+SUB_ID 35 "Annexin V BH3"
+SUB_ID 36 "Annexin III H3"
+SUB_ID 37 "Annexin III R3"
+SUB_ID 38 "Annexin VII 3"
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