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1 Jmol Colors

Table: RGB Colors in Jmol
ID Name RGB1 RGB2
1 H [255,255,255] FFFFFF
2 He [217,255,255] D9FFFF
3 Li [204,128,255] CC80FF
4 Be [194,255,0] C2FF00
5 B [255,181,181] FFB5B5
6 C [144,144,144] 909090
7 N [48,80,248] 3050F8
8 O [255,13,13] FF0D0D
9 F [144,224,80] 90E050
10 Ne [179,227,245] B3E3F5
11 Na [171,92,242] AB5CF2
12 Mg [138,255,0] 8AFF00
13 Al [191,166,166] BFA6A6
14 Si [240,200,160] F0C8A0
15 P [255,128,0] FF8000
16 S [255,255,48] FFFF30
17 Cl [31,240,31] 1FF01F
18 Ar [128,209,227] 80D1E3
19 K [143,64,212] 8F40D4
20 Ca [61,255,0] 3DFF00
21 Sc [230,230,230] E6E6E6
22 Ti [191,194,199] BFC2C7
23 V [166,166,171] A6A6AB
24 Cr [138,153,199] 8A99C7
25 Mn [156,122,199] 9C7AC7
26 Fe [224,102,51] E06633
27 Co [240,144,160] F090A0
28 Ni [80,208,80] 50D050
29 Cu [200,128,51] C88033
30 Zn [125,128,176] 7D80B0
31 Ga [194,143,143] C28F8F
32 Ge [102,143,143] 668F8F
33 As [189,128,227] BD80E3
34 Se [255,161,0] FFA100
35 Br [166,41,41] A62929
36 Kr [92,184,209] 5CB8D1
37 Rb [112,46,176] 702EB0
38 Sr [0,255,0] 00FF00
39 Y [148,255,255] 94FFFF
40 Zr [148,224,224] 94E0E0
41 Nb [115,194,201] 73C2C9
42 Mo [84,181,181] 54B5B5
43 Tc [59,158,158] 3B9E9E
44 Ru [36,143,143] 248F8F
45 Rh [10,125,140] 0A7D8C
46 Pd [0,105,133] 006985
47 Ag [192,192,192] C0C0C0
48 Cd [255,217,143] FFD98F
49 In [166,117,115] A67573
50 Sn [102,128,128] 668080
51 Sb [158,99,181] 9E63B5
52 Te [212,122,0] D47A00
53 I [148,0,148] 940094
54 Xe [66,158,176] 429EB0
55 Cs [87,23,143] 57178F
56 Ba [0,201,0] 00C900
57 La [112,212,255] 70D4FF
58 Ce [255,255,199] FFFFC7
59 Pr [217,255,199] D9FFC7
60 Nd [199,255,199] C7FFC7
61 Pm [163,255,199] A3FFC7
62 Sm [143,255,199] 8FFFC7
63 Eu [97,255,199] 61FFC7
64 Gd [69,255,199] 45FFC7
65 Tb [48,255,199] 30FFC7
66 Dy [31,255,199] 1FFFC7
67 Ho [0,255,156] 00FF9C
68 Er [0,230,117] 00E675
69 Tm [0,212,82] 00D452
70 Yb [0,191,56] 00BF38
71 Lu [0,171,36] 00AB24
72 Hf [77,194,255] 4DC2FF
73 Ta [77,166,255] 4DA6FF
74 W [33,148,214] 2194D6
75 Re [38,125,171] 267DAB
76 Os [38,102,150] 266696
77 Ir [23,84,135] 175487
78 Pt [208,208,224] D0D0E0
79 Au [255,209,35] FFD123
80 Hg [184,184,208] B8B8D0
81 Tl [166,84,77] A6544D
82 Pb [87,89,97] 575961
83 Bi [158,79,181] 9E4FB5
84 Po [171,92,0] AB5C00
85 At [117,79,69] 754F45
86 Rn [66,130,150] 428296
87 Fr [66,0,102] 420066
88 Ra [0,125,0] 007D00
89 Ac [112,171,250] 70ABFA
90 Th [0,186,255] 00BAFF
91 Pa [0,161,255] 00A1FF
92 U [0,143,255] 008FFF
93 Np [0,128,255] 0080FF
94 Pu [0,107,255] 006BFF
95 Am [84,92,242] 545CF2
96 Cm [120,92,227] 785CE3
97 Bk [138,79,227] 8A4FE3
98 Cf [161,54,212] A136D4
99 Es [179,31,212] B31FD4
100 Fm [179,31,186] B31FBA
101 Md [179,13,166] B30DA6
102 No [189,13,135] BD0D87
103 Lr [199,0,102] C70066
104 Rf [204,0,89] CC0059
105 Db [209,0,79] D1004F
106 Sg [217,0,69] D90045
107 Bh [224,0,56] E00038
108 Hs [230,0,46] E6002E
109 Mt [235,0,38] EB0026

2 Simple Manual

2.1 Script Examples:

  • convert xyz to idtf: javaw.exe -Xmx512m -jar D:\dosbin\jmol\Jmol.jar -j "load D:\Temp\Download\a.xyz;rotate best; write D:\Temp\Download\a.idtf" --nodisplay --exit
  • convert cif to idtf: javaw.exe -Xmx512m -jar D:\dosbin\jmol\Jmol.jar -j "load D:\Temp\Download\a.cif {444 666 1}; display cell=555; write D:\Temp\Download\a.idtf" --nodisplay --exit

2.2 Console Commands

2.2.1 Visualize charge density, Open console in jmol

load a.cif
isosurface id1 color red cutoff  0.2 a.cube
isosurface id1 plane (atomno=1) (atomno=2) (atomno=3) color range 0 .2

2.3 Add Macros to Jmol Macro Menu (Win)

  1. Create a folder containing macros (e.g., D:\software\jmol\macros)

  2. Creat macro files in this folder, such as Init.macro,

   Title: Init
   Script:  load "" {555 555 -1}; spin off;frame 1; animation off; hover on;set bondRadiusMilliAngstroms 100; axes offset -0.2; background white;unitcell 0.05; color unitcell green;

or savecif.macro

Title: SaveCif
Script: fname= getProperty("fileName"); fext=fname.split(".")[0]; fbase=fname.replace("."+fext,"");fid=_frameid[-3][0]; fout=fbase+"_"+fid+".cif";write @fout;
  1. make symbol link using DOS
junction %USERPROFILE%/.jmol/macros D:\software\jmol\macros
  1. The macros will appear in the macro menu.

2.4 Modify shortcuts to the pop-up menu

  1. Open jmol console
  2. Run write MENU jmol.menu, and copy it to D:\software\jmol
  3. Add commands to jmol.menu
# Add Menu4Mu to popupMenu
Menu4Mu | 我的菜单 = Muinit MuJSmol 2D331 SaveCif 
MuJSmol | 转到 JSmol = script https://blog.nanomat.top/jmolfunc/Path2Url.spt
Muinit | 初始化 = load "" {555 555 -1}; spin off;frame 1; animation off; hover on;set bondRadiusMilliAngstroms 100; axes offset -0.2; background white;unitcell 0.05; color unitcell green; 
2D331 | 331 For 2D = load "" {445 665 1}
SaveCif | 导出cif = fname= getProperty("fileName"); fext=fname.split(".")[0]; fbase=fname.replace("."+fext,"");fid=_frameid[-3][0]; 
# End of Menu4Mu
  1. Run ‘load MENU D:/software/jmol/jmol.menu’ in the console, or add this command to the sartup script.