Subsections


molmol.macro_apply

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Synopsis

Execute Molmol macros.

Defaults

molmol.macro_apply(data_type=None, style=`classic', colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None)

Keyword arguments

data_type: The data type to map to the structure.

style: The style of the macro.

colour_start_name: The name of the starting colour of the linear colour gradient. This can be either one of the X11 or one of the Molmol colour names listed in the description. If this is set, then the starting colour RGB colour array cannot be given.

colour_start_rgb: The starting colour of the linear colour gradient. This is an RGB colour array with values ranging from 0 to 1. If this is set, then the starting colour name cannot be given.

colour_end_name: The name of the ending colour of the linear colour gradient. This can be either one of the X11 or one of the Molmol colour names listed in the description. If this is set, then the ending colour RGB colour array cannot be given.

colour_end_rgb: The ending colour of the linear colour gradient. This is an RGB colour array with values ranging from 0 to 1. If this is set, then the ending colour name cannot be given.

colour_list: The colour list to search for the colour names. This can be either `molmol' or `x11'.

Description

This allows spin specific values to be mapped to a structure through Molmol macros. Currently only the `classic' style, which is described below, is available.

Colour

The values are coloured based on a linear colour gradient which is specified through starting and ending colours. These can either be a string to identify one of the RGB (red, green, blue) colour arrays listed in the tables below, or you can give the RGB vector itself. For example, `white' and [1.0, 1.0, 1.0] both select the same colour. Leaving both colours unset will select the default colour gradient which for each type of analysis is described below.

When supplying the colours as strings, two lists of colours can be selected from which to match the strings. These are the default Molmol colour list and the X11 colour list, both of which are described in the tables below. The default behaviour is to first search the Molmol list and then the X11 colour list, raising an error if neither contain the name. To explicitly select these lists, set the colour list to either `molmol' or `x11'.

Model-free classic style

Creator: Edward d'Auvergne

Argument string: "classic"

Description: The classic style draws the backbone of a protein in a cylindrical bond style. Rather than colouring the amino acids to which the NH bond belongs, the three covalent bonds of the peptide bond from Ca to Ca in which the NH bond is located are coloured. Deselected residues are shown as black lines.

Supported data types:

Please see Table 17.22 on page [*].


Table 17.22: The model-free classic style for mapping model spin specific data onto 3D molecular structures using either PyMOL or Molmol.
\begin{table*}\begin{scriptsize}
\begin{center}\begin{tabularx}{\textwidth}{ll...
...\\
\bottomrule
\\ [-5pt]
\end{tabularx}\end{center}\end{scriptsize}\end{table*}


Molmol RGB colour arrays

The following table is a list of colours used in Molmol and their corresponding RGB colour values ranging from 0 to 1.

Please see Table 17.23 on page [*].


Table 17.23: Molmol colour names and corresponding RGB colour values (from 0 to 1)
Name Red Green Blue
'black' 0.000 0.000 0.000
'navy' 0.000 0.000 0.502
'blue' 0.000 0.000 1.000
'dark green' 0.000 0.392 0.000
'green' 0.000 1.000 0.000
'cyan' 0.000 1.000 1.000
'turquoise' 0.251 0.878 0.816
'royal blue' 0.255 0.412 0.882
'aquamarine' 0.498 1.000 0.831
'sky green' 0.529 0.808 0.922
'dark violet' 0.580 0.000 0.827
'pale green' 0.596 0.984 0.596
'purple' 0.627 0.125 0.941
'brown' 0.647 0.165 0.165
'light blue' 0.678 0.847 0.902
'grey' 0.745 0.745 0.745
'light grey' 0.827 0.827 0.827
'violet' 0.933 0.510 0.933
'light coral' 0.941 0.502 0.502
'khaki' 0.941 0.902 0.549
'beige' 0.961 0.961 0.863
'red' 1.000 0.000 0.000
'magenta' 1.000 0.000 1.000
'deep pink' 1.000 0.078 0.576
'orange red' 1.000 0.271 0.000
'hot pink' 1.000 0.412 0.706
'coral' 1.000 0.498 0.314
'dark orange' 1.000 0.549 0.000
'orange' 1.000 0.647 0.000
'pink' 1.000 0.753 0.796
'gold' 1.000 0.843 0.000
'yellow' 1.000 1.000 0.000
'light yellow' 1.000 1.000 0.878
'ivory' 1.000 1.000 0.941
'white' 1.000 1.000 1.000

X11 RGB colour arrays

The following table is the list of X11 colour names and their corresponding RGB colour values ranging from 0 to 255.

Please see Table 17.24 on page [*].

Table 17.24: X11 colour names and corresponding RGB colour values
Name Red Green Blue
snow 255 250 250
ghost white 248 248 255
white smoke 245 245 245
gainsboro 220 220 220
floral white 255 250 240
old lace 253 245 230
linen 250 240 230
antique white 250 235 215
papaya whip 255 239 213
blanched almond 255 235 205
bisque 255 228 196
peach puff 255 218 185
navajo white 255 222 173
moccasin 255 228 181
cornsilk 255 248 220
ivory 255 255 240
lemon chiffon 255 250 205
seashell 255 245 238
honeydew 240 255 240
mint cream 245 255 250
azure 240 255 255
alice blue 240 248 255
lavender 230 230 250
lavender blush 255 240 245
misty rose 255 228 225
white 255 255 255
black 0 0 0
dark slate grey 47 79 79
dim grey 105 105 105
slate grey 112 128 144
light slate grey 119 136 153
grey 190 190 190
light grey 211 211 211
midnight blue 25 25 112
navy 0 0 128
cornflower blue 100 149 237
dark slate blue 72 61 139
slate blue 106 90 205
medium slate blue 123 104 238
light slate blue 132 112 255
medium blue 0 0 205
royal blue 65 105 225
blue 0 0 255
dodger blue 30 144 255
deep sky blue 0 191 255
sky blue 135 206 235
light sky blue 135 206 250
steel blue 70 130 180
light steel blue 176 196 222
light blue 173 216 230
powder blue 176 224 230
pale turquoise 175 238 238
dark turquoise 0 206 209
medium turquoise 72 209 204
turquoise 64 224 208
cyan 0 255 255
light cyan 224 255 255
cadet blue 95 158 160
medium aquamarine 102 205 170
aquamarine 127 255 212
dark green 0 100 0
dark olive green 85 107 47
dark sea green 143 188 143
sea green 46 139 87
medium sea green 60 179 113
light sea green 32 178 170
pale green 152 251 152
spring green 0 255 127
lawn green 124 252 0
green 0 255 0
chartreuse 127 255 0
medium spring green 0 250 154
green yellow 173 255 47
lime green 50 205 50
yellow green 154 205 50
forest green 34 139 34
olive drab 107 142 35
dark khaki 189 183 107
khaki 240 230 140
pale goldenrod 238 232 170
light goldenrod yellow 250 250 210
light yellow 255 255 224
yellow 255 255 0
gold 255 215 0
light goldenrod 238 221 130
goldenrod 218 165 32
dark goldenrod 184 134 11
rosy brown 188 143 143
indian red 205 92 92
saddle brown 139 69 19
sienna 160 82 45
peru 205 133 63
burlywood 222 184 135
beige 245 245 220
wheat 245 222 179
sandy brown 244 164 96
tan 210 180 140
chocolate 210 105 30
firebrick 178 34 34
brown 165 42 42
dark salmon 233 150 122
salmon 250 128 114
light salmon 255 160 122
orange 255 165 0
dark orange 255 140 0
coral 255 127 80
light coral 240 128 128
tomato 255 99 71
orange red 255 69 0
red 255 0 0
hot pink 255 105 180
deep pink 255 20 147
pink 255 192 203
light pink 255 182 193
pale violet red 219 112 147
maroon 176 48 96
medium violet red 199 21 133
violet red 208 32 144
magenta 255 0 255
violet 238 130 238
plum 221 160 221
orchid 218 112 214
medium orchid 186 85 211
dark orchid 153 50 204
dark violet 148 0 211
blue violet 138 43 226
purple 160 32 240
medium purple 147 112 219
thistle 216 191 216
snow 1 255 250 250
snow 2 238 233 233
snow 3 205 201 201
snow 4 139 137 137
seashell 1 255 245 238
seashell 2 238 229 222
seashell 3 205 197 191
seashell 4 139 134 130
antique white 1 255 239 219
antique white 2 238 223 204
antique white 3 205 192 176
antique white 4 139 131 120
bisque 1 255 228 196
bisque 2 238 213 183
bisque 3 205 183 158
bisque 4 139 125 107
peach puff 1 255 218 185
peach puff 2 238 203 173
peach puff 3 205 175 149
peach puff 4 139 119 101
navajo white 1 255 222 173
navajo white 2 238 207 161
navajo white 3 205 179 139
navajo white 4 139 121 94
lemon chiffon 1 255 250 205
lemon chiffon 2 238 233 191
lemon chiffon 3 205 201 165
lemon chiffon 4 139 137 112
cornsilk 1 255 248 220
cornsilk 2 238 232 205
cornsilk 3 205 200 177
cornsilk 4 139 136 120
ivory 1 255 255 240
ivory 2 238 238 224
ivory 3 205 205 193
ivory 4 139 139 131
honeydew 1 240 255 240
honeydew 2 224 238 224
honeydew 3 193 205 193
honeydew 4 131 139 131
lavender blush 1 255 240 245
lavender blush 2 238 224 229
lavender blush 3 205 193 197
lavender blush 4 139 131 134
misty rose 1 255 228 225
misty rose 2 238 213 210
misty rose 3 205 183 181
misty rose 4 139 125 123
azure 1 240 255 255
azure 2 224 238 238
azure 3 193 205 205
azure 4 131 139 139
slate blue 1 131 111 255
slate blue 2 122 103 238
slate blue 3 105 89 205
slate blue 4 71 60 139
royal blue 1 72 118 255
royal blue 2 67 110 238
royal blue 3 58 95 205
royal blue 4 39 64 139
blue 1 0 0 255
blue 2 0 0 238
blue 3 0 0 205
blue 4 0 0 139
dodger blue 1 30 144 255
dodger blue 2 28 134 238
dodger blue 3 24 116 205
dodger blue 4 16 78 139
steel blue 1 99 184 255
steel blue 2 92 172 238
steel blue 3 79 148 205
steel blue 4 54 100 139
deep sky blue 1 0 191 255
deep sky blue 2 0 178 238
deep sky blue 3 0 154 205
deep sky blue 4 0 104 139
sky blue 1 135 206 255
sky blue 2 126 192 238
sky blue 3 108 166 205
sky blue 4 74 112 139
light sky blue 1 176 226 255
light sky blue 2 164 211 238
light sky blue 3 141 182 205
light sky blue 4 96 123 139
slate grey 1 198 226 255
slate grey 2 185 211 238
slate grey 3 159 182 205
slate grey 4 108 123 139
light steel blue 1 202 225 255
light steel blue 2 188 210 238
light steel blue 3 162 181 205
light steel blue 4 110 123 139
light blue 1 191 239 255
light blue 2 178 223 238
light blue 3 154 192 205
light blue 4 104 131 139
light cyan 1 224 255 255
light cyan 2 209 238 238
light cyan 3 180 205 205
light cyan 4 122 139 139
pale turquoise 1 187 255 255
pale turquoise 2 174 238 238
pale turquoise 3 150 205 205
pale turquoise 4 102 139 139
cadet blue 1 152 245 255
cadet blue 2 142 229 238
cadet blue 3 122 197 205
cadet blue 4 83 134 139
turquoise 1 0 245 255
turquoise 2 0 229 238
turquoise 3 0 197 205
turquoise 4 0 134 139
cyan 1 0 255 255
cyan 2 0 238 238
cyan 3 0 205 205
cyan 4 0 139 139
dark slate grey 1 151 255 255
dark slate grey 2 141 238 238
dark slate grey 3 121 205 205
dark slate grey 4 82 139 139
aquamarine 1 127 255 212
aquamarine 2 118 238 198
aquamarine 3 102 205 170
aquamarine 4 69 139 116
dark sea green 1 193 255 193
dark sea green 2 180 238 180
dark sea green 3 155 205 155
dark sea green 4 105 139 105
sea green 1 84 255 159
sea green 2 78 238 148
sea green 3 67 205 128
sea green 4 46 139 87
pale green 1 154 255 154
pale green 2 144 238 144
pale green 3 124 205 124
pale green 4 84 139 84
spring green 1 0 255 127
spring green 2 0 238 118
spring green 3 0 205 102
spring green 4 0 139 69
green 1 0 255 0
green 2 0 238 0
green 3 0 205 0
green 4 0 139 0
chartreuse 1 127 255 0
chartreuse 2 118 238 0
chartreuse 3 102 205 0
chartreuse 4 69 139 0
olive drab 1 192 255 62
olive drab 2 179 238 58
olive drab 3 154 205 50
olive drab 4 105 139 34
dark olive green 1 202 255 112
dark olive green 2 188 238 104
dark olive green 3 162 205 90
dark olive green 4 110 139 61
khaki 1 255 246 143
khaki 2 238 230 133
khaki 3 205 198 115
khaki 4 139 134 78
light goldenrod 1 255 236 139
light goldenrod 2 238 220 130
light goldenrod 3 205 190 112
light goldenrod 4 139 129 76
light yellow 1 255 255 224
light yellow 2 238 238 209
light yellow 3 205 205 180
light yellow 4 139 139 122
yellow 1 255 255 0
yellow 2 238 238 0
yellow 3 205 205 0
yellow 4 139 139 0
gold 1 255 215 0
gold 2 238 201 0
gold 3 205 173 0
gold 4 139 117 0
goldenrod 1 255 193 37
goldenrod 2 238 180 34
goldenrod 3 205 155 29
goldenrod 4 139 105 20
dark goldenrod 1 255 185 15
dark goldenrod 2 238 173 14
dark goldenrod 3 205 149 12
dark goldenrod 4 139 101 8
rosy brown 1 255 193 193
rosy brown 2 238 180 180
rosy brown 3 205 155 155
rosy brown 4 139 105 105
indian red 1 255 106 106
indian red 2 238 99 99
indian red 3 205 85 85
indian red 4 139 58 58
sienna 1 255 130 71
sienna 2 238 121 66
sienna 3 205 104 57
sienna 4 139 71 38
burlywood 1 255 211 155
burlywood 2 238 197 145
burlywood 3 205 170 125
burlywood 4 139 115 85
wheat 1 255 231 186
wheat 2 238 216 174
wheat 3 205 186 150
wheat 4 139 126 102
tan 1 255 165 79
tan 2 238 154 73
tan 3 205 133 63
tan 4 139 90 43
chocolate 1 255 127 36
chocolate 2 238 118 33
chocolate 3 205 102 29
chocolate 4 139 69 19
firebrick 1 255 48 48
firebrick 2 238 44 44
firebrick 3 205 38 38
firebrick 4 139 26 26
brown 1 255 64 64
brown 2 238 59 59
brown 3 205 51 51
brown 4 139 35 35
salmon 1 255 140 105
salmon 2 238 130 98
salmon 3 205 112 84
salmon 4 139 76 57
light salmon 1 255 160 122
light salmon 2 238 149 114
light salmon 3 205 129 98
light salmon 4 139 87 66
orange 1 255 165 0
orange 2 238 154 0
orange 3 205 133 0
orange 4 139 90 0
dark orange 1 255 127 0
dark orange 2 238 118 0
dark orange 3 205 102 0
dark orange 4 139 69 0
coral 1 255 114 86
coral 2 238 106 80
coral 3 205 91 69
coral 4 139 62 47
tomato 1 255 99 71
tomato 2 238 92 66
tomato 3 205 79 57
tomato 4 139 54 38
orange red 1 255 69 0
orange red 2 238 64 0
orange red 3 205 55 0
orange red 4 139 37 0
red 1 255 0 0
red 2 238 0 0
red 3 205 0 0
red 4 139 0 0
deep pink 1 255 20 147
deep pink 2 238 18 137
deep pink 3 205 16 118
deep pink 4 139 10 80
hot pink 1 255 110 180
hot pink 2 238 106 167
hot pink 3 205 96 144
hot pink 4 139 58 98
pink 1 255 181 197
pink 2 238 169 184
pink 3 205 145 158
pink 4 139 99 108
light pink 1 255 174 185
light pink 2 238 162 173
light pink 3 205 140 149
light pink 4 139 95 101
pale violet red 1 255 130 171
pale violet red 2 238 121 159
pale violet red 3 205 104 137
pale violet red 4 139 71 93
maroon 1 255 52 179
maroon 2 238 48 167
maroon 3 205 41 144
maroon 4 139 28 98
violet red 1 255 62 150
violet red 2 238 58 140
violet red 3 205 50 120
violet red 4 139 34 82
magenta 1 255 0 255
magenta 2 238 0 238
magenta 3 205 0 205
magenta 4 139 0 139
orchid 1 255 131 250
orchid 2 238 122 233
orchid 3 205 105 201
orchid 4 139 71 137
plum 1 255 187 255
plum 2 238 174 238
plum 3 205 150 205
plum 4 139 102 139
medium orchid 1 224 102 255
medium orchid 2 209 95 238
medium orchid 3 180 82 205
medium orchid 4 122 55 139
dark orchid 1 191 62 255
dark orchid 2 178 58 238
dark orchid 3 154 50 205
dark orchid 4 104 34 139
purple 1 155 48 255
purple 2 145 44 238
purple 3 125 38 205
purple 4 85 26 139
medium purple 1 171 130 255
medium purple 2 159 121 238
medium purple 3 137 104 205
medium purple 4 93 71 139
thistle 1 255 225 255
thistle 2 238 210 238
thistle 3 205 181 205
thistle 4 139 123 139
grey 0 0 0 0
grey 1 3 3 3
grey 2 5 5 5
grey 3 8 8 8
grey 4 10 10 10
grey 5 13 13 13
grey 6 15 15 15
grey 7 18 18 18
grey 8 20 20 20
grey 9 23 23 23
grey 10 26 26 26
grey 11 28 28 28
grey 12 31 31 31
grey 13 33 33 33
grey 14 36 36 36
grey 15 38 38 38
grey 16 41 41 41
grey 17 43 43 43
grey 18 46 46 46
grey 19 48 48 48
grey 20 51 51 51
grey 21 54 54 54
grey 22 56 56 56
grey 23 59 59 59
grey 24 61 61 61
grey 25 64 64 64
grey 26 66 66 66
grey 27 69 69 69
grey 28 71 71 71
grey 29 74 74 74
grey 30 77 77 77
grey 31 79 79 79
grey 32 82 82 82
grey 33 84 84 84
grey 34 87 87 87
grey 35 89 89 89
grey 36 92 92 92
grey 37 94 94 94
grey 38 97 97 97
grey 39 99 99 99
grey 40 102 102 102
grey 41 105 105 105
grey 42 107 107 107
grey 43 110 110 110
grey 44 112 112 112
grey 45 115 115 115
grey 46 117 117 117
grey 47 120 120 120
grey 48 122 122 122
grey 49 125 125 125
grey 50 127 127 127
grey 51 130 130 130
grey 52 133 133 133
grey 53 135 135 135
grey 54 138 138 138
grey 55 140 140 140
grey 56 143 143 143
grey 57 145 145 145
grey 58 148 148 148
grey 59 150 150 150
grey 60 153 153 153
grey 61 156 156 156
grey 62 158 158 158
grey 63 161 161 161
grey 64 163 163 163
grey 65 166 166 166
grey 66 168 168 168
grey 67 171 171 171
grey 68 173 173 173
grey 69 176 176 176
grey 70 179 179 179
grey 71 181 181 181
grey 72 184 184 184
grey 73 186 186 186
grey 74 189 189 189
grey 75 191 191 191
grey 76 194 194 194
grey 77 196 196 196
grey 78 199 199 199
grey 79 201 201 201
grey 80 204 204 204
grey 81 207 207 207
grey 82 209 209 209
grey 83 212 212 212
grey 84 214 214 214
grey 85 217 217 217
grey 86 219 219 219
grey 87 222 222 222
grey 88 224 224 224
grey 89 227 227 227
grey 90 229 229 229
grey 91 232 232 232
grey 92 235 235 235
grey 93 237 237 237
grey 94 240 240 240
grey 95 242 242 242
grey 96 245 245 245
grey 97 247 247 247
grey 98 250 250 250
grey 99 252 252 252
grey 100 255 255 255
dark grey 169 169 169
dark blue 0 0 139
dark cyan 0 139 139
dark magenta 139 0 139
dark red 139 0 0
light green 144 238 144

Prompt examples

To map the order parameter values, S2, onto the structure using the classic style, type:

[numbers=none]
relax> molmol.macro_apply('s2')

[numbers=none]
relax> molmol.macro_apply(data_type='s2')

[numbers=none]
relax> molmol.macro_apply(data_type='s2', style="classic")


The relax user manual (PDF), created 2016-10-28.