1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
|
This is a file of default parameters for use with BOXSHADE
there are several sections, one for GENERAL parameters and one for each
output device.
The parameters may be edited freely, they reflect the input expected
from the keyboard if BOXSHADE is run interactively. The purpose of each
parameter is documented briefly within the respective line.
When editing, one has to regard:
- one parameter per line (background/foreground shading = one parameter)
- parameters of a section (labeled :SECTION) start in the first line
after the label
- there may be no empty (or comment) lines between the parameters of a
section. These lines are allowed only between sections
- only the leftmost part of every parameter line is looked at. Comments
are allowed starting at row 10
- don't change the section header
:GENERAL
1 input type (1: PRETTY)
1 output device (1: ANSI Terminal)
N consensus to single sequence?
60 sequence chars per line
Y sequence names to be printed?
N sequence numbers to be printed?
1 No of empty lines between blocks
Y special shading for similar residues
N special shading for conserved residues
N consensus output
LU consensus display pattern
N split output to multiple files
N default numbering (starting at 1)
0.5 default threshold fraction
:HTML
WB normal residues
BW identical residues
1B similar residues
B2 globally conserved residues
:POSTSCRIPT
WB normal residues
BW identical residues
1B similar residues
B2 globally conserved residues
10 character size (in Pts.)
n landscape mode
:CRT
LD normal residues
BL identical residues
LR similar residues
BW globally conserved residues
:RTF
WK normal residues
WR identical residues
WB similar residues
WM globally conserved residues
10 character size (in pts)
:ANSI
N normal residues
R identical residues
B similar residues
E globally conserved residues
:ASCII
L normal residues
- identical residues
l similar residues
. globally conserved residues
:HPGL
0F1N normal residues (bgnd/fgnd)
2F1N identical residues
3F1N similar residues
2F4N globally conserved residues
8 character size (in Pts.)
N landscape mode
:LJ250
B normal residues
R identical residues
L similar residues
M globally conserved residues
:FIG
WB normal residues
BW identical residues
1B similar residues
BY globally conserved residues
12 0=Tms,12=Cour,16=Helv,28=Palat
10 character size (in Pts.)
:ReGIS
WB normal residues
BW identical residues
LW similar residues
BY globally conserved residues
:VT
N normal residues
R identical residues
B similar residues
E globally conserved residues
:PICTFILE
WB normal residues
BW identical residues
1B similar residues
B2 globally conserved residues
10 character size (in Pts.)
T shade only ?
n landscape mode
|