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STEP 2 COMMANDS

All these are optional formatting commands.

IMPORTANT PLEASE READ THIS NOTE:

For those commands that accept region definitions (e.g. SURROUND_CHARS) it is easiest to think of the region being defined in terms of X and Y coordinates, where X is the sequence residue coordinate and Y is the sequence number coordinate. Thus 3 7 means the 3rd residue in sequence 7. 3 7 12 42 means the rectangular box bounded by residue 3 of sequence 7 and residue 12 of sequence 42.

SURROUND_CHARS <string> ALL

Draw lines round, but not between the characters that are in the string. e.g.

SURROUND_CHARS GP ALL

will draw lines round all G and P characters in the alignment, but not between adjacent G and P characters.

SURROUND_CHARS <string> <int> <int> <int> <int>

Similar command, but the surrounding is restricted to the region defined by the four integers.

e.g.

SURROUND_CHARS ILVW 3 12 7 32

would surround ILVW characters that occur in the region defined from residue positions 3-7 of sequences 12 to 32.

SHADE_CHARS <string> ALL <float>

Shade all characters in the <string> by the grey value given by <float>. e.g.

SHADE_CHARS GP ALL 0.5

would shade all G and P characters in the alignment by the grey value 0.5.

SHADE_CHARS <string> <int> <int> <int> <int> <float>

restricts the shading to the region defined by the four integers. Thus

SHADE_CHARS ILVW 3 12 7 32 0.7

would shade I L V and W characters from residues 3-7 of sequences 12-32 inclusive with a grey value of 0.7.

FONT_CHARS <string> ALL <int>

e.g.

FONT_CHARS GP ALL 7

would use font 7 to write out all G and P characters. Font 7 MUST have been defined using the DEFINE_FONTcommands above.

FONT_CHARS <string> <int> <int> <int> <int> <int>

Similar to previous command, but restricts the effect to the region defined by the first four integers. The font must have been defined by the DEFINE_FONT command.

e.g.

FONT_CHARS ILVW 3 45 9 70 7

Would set the font to 7 for I L V and W characters for residues 3-9 of sequences 45-70 inclusive. The font must have been defined by the DEFINE_FONT command.

FONT_REGION <int> <int> <int> <int> <int>

Define the font to use throughout the region specified by the first four integers.

e.g.

FONT_REGION 3 12 20 40 10

Use font 10 for residues from residues 3-20 of sequences 12-40. The font must have been defined using the DEFINE_FONTcommand.

FONT_RESIDUE <int> <int> <int>

Set the font for use with a single residue position - most useful when used with the TEXT command.

e.g.

FONT_RESIDUE 3 7 2

Use font 2 for residue 3 of sequence 7. Font 2 must have been defined using the DEFINE_FONT command.

LINE <string> <int> <int> <int>

There are four commands of this type for drawing horizontal or vertical lines on the alignment.

LINE LEFT <int> <int> <int>

Draw a line to the left of the character positions indicated.

e.g.

LINE LEFT 3 12 24

Draw a vertical line starting at residue 3 of sequence 12 and ending at residue 3 of sequence 24.

LINE TOP 3 12 24

Draw a horizontal line above the character positions from residue 3 of sequence 12 to residue 24 of sequence 12.

Similar commands are:

LINE BOTTOM <int> <int> <int> Draw a line at bottom of character position.

LINE RIGHT <int> <int> <int> Draw a line at right of character position.

BOX_REGION <int> <int> <int> <int>

Draw a box around the region indicated by the four integers.

e.g.

BOX_REGION 2 5 30 7

Would box from residue 2 of sequence 5 to residue 30 of sequence 7.

SHADE_REGION <int> <int> <int> <int> <float>

Shade the region indicated by the integers with the grey value shown by the float. e.g.

SHADE_REGION 30 40 35 46 0.2

Would shade from residue 30-35 of sequences 40-46 with a grey value of 0.2.

SHADE_RES <int> <int> <float>

Shade just one amino acid with the grey value.

e.g.

SHADE_RES 3 4 0.7

Shades residue 3 of sequence 7. (Note: this can also be achieved with the

SHADE_REGION command, but requires 2 extra numbers)

TEXT <int> <int> <qstring>

Place the text string at the location indicated.

e.g.

TEXT 30 70 "Active Site His"

would put the text Active Site His starting at position 30 of sequence 70. (Use FONT_RESIDUE or FONT_REGION commands to set the font of the text). Text added with the TEXT command will not be split across page breaks, so you may in some circumstances need to fiddle a little with the location/pointsize for the text to get the desired result.

ID_FONT ALL <int>

Set the font for all identifier codes to the font number shown by <int>. e.g.

ID_FONT ALL 3

Would set all the identifier codes to font 3.

ID_FONT <int> <int>

Set the font for a specific identifier to font number. e.g.

ID_FONT 12 4

Use font 4 for the identifer of sequence 12, default font for all other identifiers.

SUB_CHARS ALL <char> <char>

Substitute the characters indicated.

e.g.

SUB_CHARS ALL + *

would change all occurences of + to * in the alignment.

SUB_CHARS <int> <int> <int> <int> <char> <char>

restrict the substitution to the region shown.

e.g.

SUB_CHARS 1 1 7 8 %*

would substitute * for %from residue 1-7 of sequences 1-8. NOTE: To substitute for or with the space character use the word SPACE. e.g. to change all space characters to -.

SUB_CHARS ALL SPACE -

SUB_ID <int> <qstring>

Replace the numbered identifier by the string. e.g.

SUB_ID 34 "Predicted Secondary Structure"

would replace whatever the identifier of sequence 34 was, by the text shown. This is useful when used in conjunction with the ADD_SEQ command shown under the STEP 1 commands.

INVERSE_CHARS <string> ALL/Range (similar syntax to FONT_CHARS but no font number)

Print the selected characters in white. This clearly will only work if you first use the SHADE_CHARScommand to shade the characters with something other than white.

CCOL_CHARS <string> ALL <int>

Colour all characters in the <string> by the colour defined by <int>.

e.g.

CCOL_CHARS GP ALL 12

would colour all G and P characters in the alignment by the colour 12. This colour MUST have been defined by the DEFINE_COLOUR command.

CCOL_CHARS <string> <int> <int> <int> <int> <int>

restricts the colouring to the region defined by the four integers. Thus

CCOL_CHARS ILVW 3 12 7 32 7

would colour I L V and W characters from residues 3-7 of sequences 12-32 inclusive with the colour 7.

SCOL_CHARS: This has identical syntax to SCOL_CHARS, but colours the background of the character, rather than the letter itself.

COLOUR_REGION <int> <int> <int> <int> <int>

COLOR_REGIONColour the region indicated by the integers with the colour number given as the last number.

e.g.

COLOUR_REGION 30 40 35 46 2

Would colour from residue 30-35 of sequences 40-46 with the colour 2.

COLOUR_RES <int> <int> <int>

Colour just one amino acid with the defined colour.

e.g.

COLOUR_RES 3 4 7

Colours residue 3 of sequence 7. (Note: this can also be achieved with the COLOUR_REGION command, but requires 2 extra numbers)



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gjb@bioch.ox.ac.uk