molmol.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

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.

**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.

**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.

**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:

molmol.macro_apply

Synopsis

Defaults

Keyword arguments