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Class for interfacing with Molmol.
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Inherited from |
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Clear the Molmol command history. Description ~~~~~~~~~~~ This will clear the Molmol history from memory. |
Execute a user supplied Molmol command.
Keyword Arguments
~~~~~~~~~~~~~~~~~
command: The Molmol command to execute.
Description
~~~~~~~~~~~
This allows Molmol commands to be passed to the program. This can be useful for automation or
scripting.
Examples
~~~~~~~~
To reinitialise the Molmol instance, type:
relax> molmol.command("InitAll yes")
|
Execute Molmol macros.
Keyword Arguments
~~~~~~~~~~~~~~~~~
data_type: The data type to map to the structure.
style: The style of the macro.
colour_start: The starting colour, either an array or string, of the linear colour gradient.
colour_end: The ending colour, either an array or string, of the linear colour gradient.
colour_list: The list of colours to match the start and end strings.
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.
Examples
~~~~~~~~
To map the order parameter values, S2, onto the structure using the classic style, type:
relax> molmol.macro_apply('s2')
relax> molmol.macro_apply(data_type='s2')
relax> molmol.macro_apply(data_type='s2', style="classic")
Colour
~~~~~~
The values are coloured based on a linear colour gradient which is specified through the 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:
____________________________________________________________________________________________
| | | |
| Data type | String | Description |
|________________|_____________|___________________________________________________________|
| | | |
| S2. | 's2' | The standard model-free order parameter, equal to S2f.S2s |
| | | for the two timescale models. The default colour |
| | | gradient starts at 'yellow' and ends at 'red'. |
| | | |
| S2f. | 's2f' | The order parameter of the faster of two internal |
| | | motions. Residues which are described by model-free |
| | | models m1 to m4, the single timescale models, are |
| | | illustrated as white neon bonds. The default colour |
| | | gradient is the same as that for the S2 data type. |
| | | |
| S2s. | 's2s' | The order parameter of the slower of two internal |
| | | motions. This functions exactly as S2f except that S2s |
| | | is plotted instead. |
| | | |
| Amplitude of | 'amp_fast' | Model independent display of the amplite of fast motions. |
| fast motions. | | For residues described by model-free models m5 to m8, the |
| | | value plotted is that of S2f. However, for residues |
| | | described by models m1 to m4, what is shown is dependent |
| | | on the timescale of the motions. This is because these |
| | | single timescale models can, at times, be perfect |
| | | approximations to the more complex two timescale models. |
| | | Hence if te is less than 200 ps, S2 is plotted. Otherwise |
| | | the peptide bond is coloured white. The default colour |
| | | gradient is the same as that for S2. |
| | | |
| Amplitude of | 'amp_slow' | Model independent display of the amplite of slow motions, |
| slow motions. | | arbitrarily defined as motions slower than 200 ps. For |
| | | residues described by model-free models m5 to m8, the |
| | | order parameter S2 is plotted if ts > 200 ps. For models |
| | | m1 to m4, S2 is plotted if te > 200 ps. The default |
| | | colour gradient is the same as that for S2. |
| | | |
| te. | 'te' | The correlation time, te. The default colour gradient |
| | | starts at 'turquoise' and ends at 'blue'. |
| | | |
| tf. | 'tf' | The correlation time, tf. The default colour gradient is |
| | | the same as that of te. |
| | | |
| ts. | 'ts' | The correlation time, ts. The default colour gradient |
| | | starts at 'blue' and ends at 'black'. |
| | | |
| Timescale of | 'time_fast' | Model independent display of the timescale of fast |
| fast motions | | motions. For models m5 to m8, only the parameter tf is |
| | | plotted. For models m2 and m4, the parameter te is |
| | | plotted only if it is less than 200 ps. All other |
| | | residues are assumed to have a correlation time of zero. |
| | | The default colour gradient is the same as that of te. |
| | | |
| Timescale of | 'time_slow' | Model independent display of the timescale of slow |
| slow motions | | motions. For models m5 to m8, only the parameter ts is |
| | | plotted. For models m2 and m4, the parameter te is |
| | | plotted only if it is greater than 200 ps. All other |
| | | residues are coloured white. The default colour gradient |
| | | is the same as that of ts. |
| | | |
| Chemical | 'rex' | The chemical exchange, Rex. Residues which experience no |
| exchange | | chemical exchange are coloured white. The default colour |
| | | gradient starts at 'yellow' and finishes at 'red'. |
|________________|_____________|___________________________________________________________|
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.
_______________________________________________________________
| | | | |
| 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.
_______________________________________________________________
| | | | |
| 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 |
|_______________________________|_________|_________|_________|
|
Open and execute the Molmol macro file. Keyword Arguments ~~~~~~~~~~~~~~~~~ file: The name of the Molmol macro file. dir: The directory name. Description ~~~~~~~~~~~ This user function is for opening and running a Molmol macro located within a text file. Examples ~~~~~~~~ To execute the macro file 's2.mac' located in the directory 'molmol', type: relax> molmol.macro_run(file='s2.mac') relax> molmol.macro_run(file='s2.mac', dir='molmol') |
Create Molmol macros.
Keyword Arguments
~~~~~~~~~~~~~~~~~
data_type: The data type to map to the structure.
style: The style of the macro.
colour_start: The starting colour, either an array or string, of the linear colour gradient.
colour_end: The ending colour, either an array or string, of the linear colour gradient.
colour_list: The list of colours to match the start and end strings.
file: The name of the file.
dir: The directory name.
force: A flag which, if set to True, will cause the file to be overwritten.
Description
~~~~~~~~~~~
This allows residues specific values to be mapped to a structure through the creation of a Molmol
'*.mac' macro which can be executed in Molmol by clicking on 'File, Macro, Execute User...'.
Currently only the 'classic' style, which is described below, is available.
Examples
~~~~~~~~
To create a Molmol macro mapping the order parameter values, S2, onto the structure using
the classic style, type:
relax> molmol.macro_write('s2')
relax> molmol.macro_write(data_type='s2')
relax> molmol.macro_write(data_type='s2', style="classic", file='s2.mac', dir='molmol')
Colour
~~~~~~
The values are coloured based on a linear colour gradient which is specified through the 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:
____________________________________________________________________________________________
| | | |
| Data type | String | Description |
|________________|_____________|___________________________________________________________|
| | | |
| S2. | 's2' | The standard model-free order parameter, equal to S2f.S2s |
| | | for the two timescale models. The default colour |
| | | gradient starts at 'yellow' and ends at 'red'. |
| | | |
| S2f. | 's2f' | The order parameter of the faster of two internal |
| | | motions. Residues which are described by model-free |
| | | models m1 to m4, the single timescale models, are |
| | | illustrated as white neon bonds. The default colour |
| | | gradient is the same as that for the S2 data type. |
| | | |
| S2s. | 's2s' | The order parameter of the slower of two internal |
| | | motions. This functions exactly as S2f except that S2s |
| | | is plotted instead. |
| | | |
| Amplitude of | 'amp_fast' | Model independent display of the amplite of fast motions. |
| fast motions. | | For residues described by model-free models m5 to m8, the |
| | | value plotted is that of S2f. However, for residues |
| | | described by models m1 to m4, what is shown is dependent |
| | | on the timescale of the motions. This is because these |
| | | single timescale models can, at times, be perfect |
| | | approximations to the more complex two timescale models. |
| | | Hence if te is less than 200 ps, S2 is plotted. Otherwise |
| | | the peptide bond is coloured white. The default colour |
| | | gradient is the same as that for S2. |
| | | |
| Amplitude of | 'amp_slow' | Model independent display of the amplite of slow motions, |
| slow motions. | | arbitrarily defined as motions slower than 200 ps. For |
| | | residues described by model-free models m5 to m8, the |
| | | order parameter S2 is plotted if ts > 200 ps. For models |
| | | m1 to m4, S2 is plotted if te > 200 ps. The default |
| | | colour gradient is the same as that for S2. |
| | | |
| te. | 'te' | The correlation time, te. The default colour gradient |
| | | starts at 'turquoise' and ends at 'blue'. |
| | | |
| tf. | 'tf' | The correlation time, tf. The default colour gradient is |
| | | the same as that of te. |
| | | |
| ts. | 'ts' | The correlation time, ts. The default colour gradient |
| | | starts at 'blue' and ends at 'black'. |
| | | |
| Timescale of | 'time_fast' | Model independent display of the timescale of fast |
| fast motions | | motions. For models m5 to m8, only the parameter tf is |
| | | plotted. For models m2 and m4, the parameter te is |
| | | plotted only if it is less than 200 ps. All other |
| | | residues are assumed to have a correlation time of zero. |
| | | The default colour gradient is the same as that of te. |
| | | |
| Timescale of | 'time_slow' | Model independent display of the timescale of slow |
| slow motions | | motions. For models m5 to m8, only the parameter ts is |
| | | plotted. For models m2 and m4, the parameter te is |
| | | plotted only if it is greater than 200 ps. All other |
| | | residues are coloured white. The default colour gradient |
| | | is the same as that of ts. |
| | | |
| Chemical | 'rex' | The chemical exchange, Rex. Residues which experience no |
| exchange | | chemical exchange are coloured white. The default colour |
| | | gradient starts at 'yellow' and finishes at 'red'. |
|________________|_____________|___________________________________________________________|
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.
_______________________________________________________________
| | | | |
| 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.
_______________________________________________________________
| | | | |
| 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 |
|_______________________________|_________|_________|_________|
|
Apply the Molmol ribbon style.
Description
~~~~~~~~~~~
This applies the Molmol ribbon style which is equivalent to clicking on 'ribbon' in the Molmol side
menu. To do this, the following commands are executed:
CalcAtom 'H'
CalcAtom 'HN'
CalcSecondary
XMacStand ribbon.mac
Examples
~~~~~~~~
To apply the ribbon style to the PDB file loaded, type:
relax> molmol.ribbon()
|
Display the diffusion tensor PDB geometric object over the loaded PDB.
Keyword Arguments
~~~~~~~~~~~~~~~~~
file: The name of the PDB file containing the tensor geometric object.
Description
~~~~~~~~~~~
In executing this user function, a PDB file must have previously been loaded , a geometric object or
polygon representing the Brownian rotational diffusion tensor will be overlain with the loaded PDB
file and displayed within Molmol. The PDB file containing the geometric object must be created
using the complementary structure.create_diff_tensor_pdb user function.
To display the diffusion tensor, the multiple commands will be executed. To overlay the structure
with the diffusion tensor, everything will be selected and reoriented and moved to their original
PDB frame positions:
SelectAtom ''
SelectBond ''
SelectAngle ''
SelectDist ''
SelectPrim ''
RotateInit
MoveInit
Next the tensor PDB file is read in, selected, and the covalent bonds of the PDB CONECT records
calculated:
ReadPdb file
SelectMol '@file'
CalcBond 1 1 1
Then only the atoms and bonds of the geometric object are selected and the 'ball/stick' style
applied:
SelectAtom '0'
SelectBond '0'
SelectAtom ':TNS'
SelectBond ':TNS'
XMacStand ball_stick.mac
The appearance is finally touched up:
RadiusAtom 1
SelectAtom ':TNS@C*'
RadiusAtom 1.5
|
View the collection of molecules from the loaded PDB file. Description ~~~~~~~~~~~ This will simply launch Molmol. Examples ~~~~~~~~ relax> molmol.view() |
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