Home
Nanotubes Crystals
Matlab ChemDoodle
About Aviz

Conversion of 'xyz' files using Matlab

In order to convert 'xyz' files to a format suitable for the ChemDoodle library we will use a Matlab script which can be downloaded here.
We will also use a nanotube 'xyz' file as a working example which you can download here.
If you are using Chrome and the file opens instead of downloading, simply click Ctrl+s and save the file in the desired directory.

Nanotube Visualization - Part 1

In this section you will learn how to convert a nanotube 'xyz' file (obtained from the David Nazvovsky's tubeXYZ software which can be downloaded here) to a format which can later be visualized using the ChemDoodle library.
See part 2 for an explanation on how to visualize the matlab-generated code.

In this example we will use a (5,5) carbon nanotube with bond length of 1.42.

After downloading the matlab script, enter the following commands in the Matlab Command Window:

addpath('[path]');
xyz2chem;

where [path] specifies the full path of the folder where the xyz2chem.m file was saved.

If the path was entered correctly the script should be launched.
Follow the instructions on-screen and select the nanotube's xyz file.
Choose whether to extract the atom types from the xyz file. Do this only if the types specified in the file are legal atom type names. For example, 'C', 'Al' are legal names, 'B2' is not.
If you chose not to use the atom types specified in the 'xyz' file, click 'No' and then specify the desired atom. If your molecule has more than 1 atom type you will need to either change the 'xyz' file or manually change the generated code later on.
In the bonds' length specification window, enter 1.41 in the lower bound and 1.43 in the upper.
After the code finished running a window titled ChemDoodle Code should open. Copy the line of code inside the window, you will use it in part 2.

ChemDoodle Code Breakdown

Lets inspect the code that was generated from the carbon_nanotube.xyz file:

'1\n\n\n310450\n 0.0000 3.4273 34.0003 C\n 0.0000 3.4273 36.4461 C\n 0.0000 3.4273 14.4335 C\n 0.0000 3.4273 19.3252 C\n 0.0000 3.4273 4.6502 C\n 0.0000 3.4273 7.0960 C\n 0.0000 3.4273 9.5419 C\n 0.0000 3.4273 21.7711 C\n 0.0000 3.4273 24.2169 C\n 0.0000 3.4273 26.6627 C\n 0.0000 3.4273 29.1086 C\n 0.0000 3.4273 31.5544 C\n 0.0000 3.4273 11.9877 C\n 0.0000 3.4273 16.8794 C\n 0.0000 3.4273 38.8920 C\n 0.0760 4.1450 35.2232 C\n 0.0760 4.1450 37.6690 C\n 0.0760 4.1450 10.7648 C\n 0.0760 4.1450 15.6565 C\n 0.0760 4.1450 20.5481 C\n 0.0760 4.1450 5.8731 C\n 0.0760 4.1450 8.3189 C\n 0.0760 4.1450 13.2106 C\n 0.0760 4.1450 18.1023 C\n 0.0760 4.1450 22.9940 C\n 0.0760 4.1450 25.4398 C\n 0.0760 4.1450 27.8857 C\n 0.0760 4.1450 30.3315 C\n 0.0760 4.1450 32.7773 C\n 0.0760 4.1450 40.1149 C\n 0.2942 2.0381 4.6502 C\n 0.2942 2.0381 7.0960 C\n 0.2942 2.0381 9.5419 C\n 0.2942 2.0381 24.2169 C\n 0.2942 2.0381 26.6627 C\n 0.2942 2.0381 29.1086 C\n 0.2942 2.0381 31.5544 C\n 0.2942 2.0381 34.0003 C\n 0.2942 2.0381 21.7711 C\n 0.2942 2.0381 38.8920 C\n 0.2942 2.0381 41.3378 C\n 0.2942 2.0381 11.9877 C\n 0.2942 2.0381 14.4335 C\n 0.2942 2.0381 16.8794 C\n 0.2942 2.0381 19.3252 C\n 0.2942 2.0381 36.4461 C\n 0.6545 1.4128 37.6690 C\n 0.6545 1.4128 40.1149 C\n 0.6545 5.4417 25.4398 C\n 0.6545 1.4128 20.5481 C\n 0.6545 5.4417 32.7773 C\n 0.6545 5.4417 35.2232 C\n 0.6545 5.4417 40.1149 C\n 0.6545 1.4128 10.7648 C\n 0.6545 1.4128 13.2106 C\n 0.6545 1.4128 15.6565 C\n 0.6545 1.4128 18.1023 C\n 0.6545 1.4128 3.4273 C\n 0.6545 1.4128 5.8731 C\n 0.6545 1.4128 8.3189 C\n 0.6545 5.4417 8.3189 C\n 0.6545 5.4417 10.7648 C\n 0.6545 5.4417 13.2106 C\n 0.6545 5.4417 15.6565 C\n 0.6545 5.4417 18.1023 C\n 0.6545 5.4417 3.4273 C\n 0.6545 5.4417 5.8731 C\n 0.6545 5.4417 20.5481 C\n 0.6545 5.4417 22.9940 C\n 0.6545 5.4417 27.8857 C\n 0.6545 5.4417 30.3315 C\n 0.6545 1.4128 22.9940 C\n 0.6545 1.4128 25.4398 C\n 0.6545 1.4128 27.8857 C\n 0.6545 1.4128 30.3315 C\n 0.6545 1.4128 32.7773 C\n 0.6545 5.4417 37.6690 C\n 0.6545 1.4128 35.2232 C\n 1.1379 5.9777 26.6627 C\n 1.1379 5.9777 34.0003 C\n 1.1379 5.9777 36.4461 C\n 1.1379 5.9777 41.3378 C\n 1.1379 5.9777 4.6502 C\n 1.1379 5.9777 7.0960 C\n 1.1379 5.9777 9.5419 C\n 1.1379 5.9777 11.9877 C\n 1.1379 5.9777 14.4335 C\n 1.1379 5.9777 16.8794 C\n 1.1379 5.9777 19.3252 C\n 1.1379 5.9777 21.7711 C\n 1.1379 5.9777 24.2169 C\n 1.1379 5.9777 29.1086 C\n 1.1379 5.9777 31.5544 C\n 1.1379 5.9777 38.8920 C\n 1.7091 0.4618 13.2106 C\n 1.7091 0.4618 18.1023 C\n 1.7091 0.4618 22.9940 C\n 1.7091 0.4618 5.8731 C\n 1.7091 0.4618 8.3189 C\n 1.7091 0.4618 10.7648 C\n 1.7091 0.4618 40.1149 C\n 1.7091 0.4618 15.6565 C\n 1.7091 0.4618 20.5481 C\n 1.7091 0.4618 25.4398 C\n 1.7091 0.4618 27.8857 C\n 1.7091 0.4618 30.3315 C\n 1.7091 0.4618 32.7773 C\n 1.7091 0.4618 35.2232 C\n 1.7091 0.4618 37.6690 C\n 2.3682 6.6868 36.4461 C\n 2.3682 0.1677 38.8920 C\n 2.3682 6.6868 19.3252 C\n 2.3682 6.6868 24.2169 C\n 2.3682 6.6868 29.1086 C\n 2.3682 0.1677 11.9877 C\n 2.3682 0.1677 16.8794 C\n 2.3682 0.1677 21.7711 C\n 2.3682 6.6868 14.4335 C\n 2.3682 6.6868 4.6502 C\n 2.3682 6.6868 31.5544 C\n 2.3682 6.6868 34.0003 C\n 2.3682 6.6868 38.8920 C\n 2.3682 0.1677 4.6502 C\n 2.3682 0.1677 7.0960 C\n 2.3682 0.1677 9.5419 C\n 2.3682 6.6868 7.0960 C\n 2.3682 6.6868 9.5419 C\n 2.3682 6.6868 11.9877 C\n 2.3682 6.6868 16.8794 C\n 2.3682 0.1677 14.4335 C\n 2.3682 0.1677 19.3252 C\n 2.3682 0.1677 24.2169 C\n 2.3682 0.1677 26.6627 C\n 2.3682 0.1677 29.1086 C\n 2.3682 0.1677 31.5544 C\n 2.3682 0.1677 34.0003 C\n 2.3682 6.6868 21.7711 C\n 2.3682 6.6868 26.6627 C\n 2.3682 0.1677 36.4461 C\n 3.0742 6.8363 37.6690 C\n 3.0742 6.8363 8.3189 C\n 3.0742 6.8363 10.7648 C\n 3.0742 6.8363 15.6565 C\n 3.0742 6.8363 20.5481 C\n 3.0742 6.8363 25.4398 C\n 3.0742 6.8363 30.3315 C\n 3.0742 6.8363 5.8731 C\n 3.0742 6.8363 13.2106 C\n 3.0742 6.8363 18.1023 C\n 3.0742 6.8363 32.7773 C\n 3.0742 6.8363 35.2232 C\n 3.0742 6.8363 40.1149 C\n 3.0742 6.8363 22.9940 C\n 3.0742 6.8363 27.8857 C\n 3.7803 0.0182 31.5544 C\n 3.7803 0.0182 4.6502 C\n 3.7803 0.0182 7.0960 C\n 3.7803 0.0182 9.5419 C\n 3.7803 0.0182 11.9877 C\n 3.7803 0.0182 14.4335 C\n 3.7803 0.0182 16.8794 C\n 3.7803 0.0182 19.3252 C\n 3.7803 0.0182 21.7711 C\n 3.7803 0.0182 24.2169 C\n 3.7803 0.0182 38.8920 C\n 3.7803 0.0182 41.3378 C\n 3.7803 0.0182 26.6627 C\n 3.7803 0.0182 29.1086 C\n 3.7803 0.0182 34.0003 C\n 3.7803 0.0182 36.4461 C\n 4.4863 6.6868 35.2232 C\n 4.4863 6.6868 25.4398 C\n 4.4863 0.1677 20.5481 C\n 4.4863 0.1677 37.6690 C\n 4.4863 0.1677 40.1149 C\n 4.4863 0.1677 3.4273 C\n 4.4863 0.1677 5.8731 C\n 4.4863 0.1677 8.3189 C\n 4.4863 0.1677 10.7648 C\n 4.4863 0.1677 30.3315 C\n 4.4863 6.6868 5.8731 C\n 4.4863 6.6868 8.3189 C\n 4.4863 6.6868 10.7648 C\n 4.4863 6.6868 13.2106 C\n 4.4863 6.6868 15.6565 C\n 4.4863 6.6868 18.1023 C\n 4.4863 6.6868 22.9940 C\n 4.4863 6.6868 27.8857 C\n 4.4863 0.1677 13.2106 C\n 4.4863 0.1677 15.6565 C\n 4.4863 0.1677 18.1023 C\n 4.4863 0.1677 22.9940 C\n 4.4863 6.6868 20.5481 C\n 4.4863 6.6868 3.4273 C\n 4.4863 6.6868 30.3315 C\n 4.4863 6.6868 32.7773 C\n 4.4863 6.6868 37.6690 C\n 4.4863 6.6868 40.1149 C\n 4.4863 0.1677 25.4398 C\n 4.4863 0.1677 27.8857 C\n 4.4863 0.1677 32.7773 C\n 4.4863 0.1677 35.2232 C\n 5.1454 6.3927 26.6627 C\n 5.1454 6.3927 36.4461 C\n 5.1454 6.3927 7.0960 C\n 5.1454 6.3927 9.5419 C\n 5.1454 6.3927 11.9877 C\n 5.1454 6.3927 14.4335 C\n 5.1454 6.3927 16.8794 C\n 5.1454 6.3927 19.3252 C\n 5.1454 6.3927 21.7711 C\n 5.1454 6.3927 24.2169 C\n 5.1454 6.3927 29.1086 C\n 5.1454 6.3927 4.6502 C\n 5.1454 6.3927 31.5544 C\n 5.1454 6.3927 34.0003 C\n 5.1454 6.3927 38.8920 C\n 5.1454 6.3927 41.3378 C\n 5.7166 0.8768 13.2106 C\n 5.7166 0.8768 5.8731 C\n 5.7166 0.8768 8.3189 C\n 5.7166 0.8768 10.7648 C\n 5.7166 0.8768 27.8857 C\n 5.7166 0.8768 32.7773 C\n 5.7166 0.8768 15.6565 C\n 5.7166 0.8768 18.1023 C\n 5.7166 0.8768 20.5481 C\n 5.7166 0.8768 22.9940 C\n 5.7166 0.8768 25.4398 C\n 5.7166 0.8768 40.1149 C\n 5.7166 0.8768 30.3315 C\n 5.7166 0.8768 35.2232 C\n 5.7166 0.8768 37.6690 C\n 6.2000 5.4418 36.4461 C\n 6.2000 1.4128 11.9877 C\n 6.2000 5.4417 14.4335 C\n 6.2000 5.4417 19.3252 C\n 6.2000 5.4417 24.2169 C\n 6.2000 5.4417 29.1086 C\n 6.2000 5.4417 34.0003 C\n 6.2000 1.4128 16.8794 C\n 6.2000 1.4128 21.7711 C\n 6.2000 1.4128 38.8920 C\n 6.2000 1.4128 4.6502 C\n 6.2000 1.4128 7.0960 C\n 6.2000 1.4128 9.5419 C\n 6.2000 1.4128 26.6627 C\n 6.2000 1.4128 31.5544 C\n 6.2000 5.4417 4.6502 C\n 6.2000 5.4417 7.0960 C\n 6.2000 5.4417 9.5419 C\n 6.2000 5.4417 11.9877 C\n 6.2000 5.4417 16.8794 C\n 6.2000 5.4417 21.7711 C\n 6.2000 5.4417 26.6627 C\n 6.2000 1.4128 14.4335 C\n 6.2000 1.4128 19.3252 C\n 6.2000 1.4128 24.2169 C\n 6.2000 5.4417 31.5544 C\n 6.2000 5.4417 38.8920 C\n 6.2000 1.4128 29.1086 C\n 6.2000 1.4128 34.0003 C\n 6.2000 1.4128 36.4461 C\n 6.5603 4.8165 37.6690 C\n 6.5603 4.8165 15.6565 C\n 6.5603 4.8165 30.3315 C\n 6.5603 4.8165 35.2232 C\n 6.5603 4.8165 20.5481 C\n 6.5603 4.8165 25.4398 C\n 6.5603 4.8164 32.7773 C\n 6.5603 4.8164 40.1149 C\n 6.5603 4.8164 13.2106 C\n 6.5603 4.8164 18.1023 C\n 6.5603 4.8164 22.9940 C\n 6.5603 4.8164 27.8857 C\n 6.5603 4.8165 5.8731 C\n 6.5603 4.8165 8.3189 C\n 6.5603 4.8165 10.7648 C\n 6.7785 2.7096 31.5544 C\n 6.7785 2.7096 38.8920 C\n 6.7785 2.7096 21.7711 C\n 6.7785 2.7096 4.6502 C\n 6.7785 2.7096 7.0960 C\n 6.7785 2.7096 9.5419 C\n 6.7785 2.7096 11.9877 C\n 6.7785 2.7096 14.4335 C\n 6.7785 2.7096 29.1086 C\n 6.7785 2.7096 34.0003 C\n 6.7785 2.7096 16.8794 C\n 6.7785 2.7096 19.3252 C\n 6.7785 2.7096 24.2169 C\n 6.7785 2.7096 26.6627 C\n 6.7785 2.7096 41.3378 C\n 6.7785 2.7096 36.4461 C\n 6.8545 3.4273 30.3315 C\n 6.8545 3.4273 37.6690 C\n 6.8545 3.4273 20.5481 C\n 6.8545 3.4273 3.4273 C\n 6.8545 3.4273 5.8731 C\n 6.8545 3.4273 8.3189 C\n 6.8545 3.4273 10.7648 C\n 6.8545 3.4273 13.2106 C\n 6.8545 3.4273 40.1149 C\n 6.8545 3.4273 15.6565 C\n 6.8545 3.4273 18.1023 C\n 6.8545 3.4273 22.9940 C\n 6.8545 3.4273 27.8857 C\n 6.8545 3.4273 32.7773 C\n 6.8545 3.4273 25.4398 C\n 6.8545 3.4273 35.2232 C\n 1 16 1\n 1 29 1\n 1 38 1\n 2 16 1\n 2 17 1\n 2 46 1\n 3 19 1\n 3 23 1\n 3 43 1\n 4 20 1\n 4 24 1\n 4 45 1\n 5 21 1\n 5 31 1\n 6 21 1\n 6 22 1\n 6 32 1\n 7 18 1\n 7 22 1\n 7 33 1\n 8 20 1\n 8 25 1\n 8 39 1\n 9 25 1\n 9 26 1\n 9 34 1\n 10 26 1\n 10 27 1\n 10 35 1\n 11 27 1\n 11 28 1\n 11 36 1\n 12 28 1\n 12 29 1\n 12 37 1\n 13 18 1\n 13 23 1\n 13 42 1\n 14 19 1\n 14 24 1\n 14 44 1\n 15 17 1\n 15 30 1\n 15 40 1\n 16 52 1\n 17 77 1\n 18 62 1\n 19 64 1\n 20 68 1\n 21 67 1\n 22 61 1\n 23 63 1\n 24 65 1\n 25 69 1\n 26 49 1\n 27 70 1\n 28 71 1\n 29 51 1\n 30 53 1\n 31 58 1\n 31 59 1\n 32 59 1\n 32 60 1\n 33 54 1\n 33 60 1\n 34 72 1\n 34 73 1\n 35 73 1\n 35 74 1\n 36 74 1\n 36 75 1\n 37 75 1\n 37 76 1\n 38 76 1\n 38 78 1\n 39 50 1\n 39 72 1\n 40 47 1\n 40 48 1\n 41 48 1\n 42 54 1\n 42 55 1\n 43 55 1\n 43 56 1\n 44 56 1\n 44 57 1\n 45 50 1\n 45 57 1\n 46 47 1\n 46 78 1\n 47109 1\n 48101 1\n 49 79 1\n 49 91 1\n 50103 1\n 51 80 1\n 51 93 1\n 52 80 1\n 52 81 1\n 53 82 1\n 53 94 1\n 54100 1\n 55 95 1\n 56102 1\n 57 96 1\n 59 98 1\n 60 99 1\n 61 84 1\n 61 85 1\n 62 85 1\n 62 86 1\n 63 86 1\n 63 87 1\n 64 87 1\n 64 88 1\n 65 88 1\n 65 89 1\n 66 83 1\n 67 83 1\n 67 84 1\n 68 89 1\n 68 90 1\n 69 90 1\n 69 91 1\n 70 79 1\n 70 92 1\n 71 92 1\n 71 93 1\n 72 97 1\n 73104 1\n 74105 1\n 75106 1\n 76107 1\n 77 81 1\n 77 94 1\n 78108 1\n 79138 1\n 80121 1\n 81110 1\n 83119 1\n 84126 1\n 85127 1\n 86128 1\n 87118 1\n 88129 1\n 89112 1\n 90137 1\n 91113 1\n 92114 1\n 93120 1\n 94122 1\n 95115 1\n 95130 1\n 96116 1\n 96131 1\n 97117 1\n 97132 1\n 98123 1\n 98124 1\n 99124 1\n 99125 1\n100115 1\n100125 1\n101111 1\n102116 1\n102130 1\n103117 1\n103131 1\n104132 1\n104133 1\n105133 1\n105134 1\n106134 1\n106135 1\n107135 1\n107136 1\n108136 1\n108139 1\n109111 1\n109139 1\n110140 1\n110151 1\n111165 1\n112144 1\n112149 1\n113145 1\n113153 1\n114146 1\n114154 1\n115159 1\n116161 1\n117163 1\n118143 1\n118148 1\n119147 1\n120146 1\n120150 1\n121150 1\n121151 1\n122140 1\n122152 1\n123156 1\n124157 1\n125158 1\n126141 1\n126147 1\n127141 1\n127142 1\n128142 1\n128148 1\n129143 1\n129149 1\n130160 1\n131162 1\n132164 1\n133167 1\n134168 1\n135155 1\n136169 1\n137144 1\n137153 1\n138145 1\n138154 1\n139170 1\n140197 1\n141182 1\n142183 1\n143185 1\n144193 1\n145172 1\n146195 1\n147181 1\n148184 1\n149186 1\n150196 1\n151171 1\n152198 1\n153187 1\n154188 1\n155180 1\n155201 1\n156176 1\n156177 1\n157177 1\n157178 1\n158178 1\n158179 1\n159179 1\n159189 1\n160189 1\n160190 1\n161190 1\n161191 1\n162173 1\n162191 1\n163173 1\n163192 1\n164192 1\n164199 1\n165174 1\n165175 1\n166175 1\n167199 1\n167200 1\n168180 1\n168200 1\n169201 1\n169202 1\n170174 1\n170202 1\n171204 1\n171216 1\n172203 1\n172212 1\n173227 1\n174233 1\n175230 1\n177220 1\n178221 1\n179222 1\n180231 1\n181205 1\n181214 1\n182205 1\n182206 1\n183206 1\n183207 1\n184207 1\n184208 1\n185208 1\n185209 1\n186209 1\n186210 1\n187211 1\n187212 1\n188203 1\n188213 1\n189219 1\n190225 1\n191226 1\n192228 1\n193210 1\n193211 1\n194214 1\n195213 1\n195215 1\n196215 1\n196216 1\n197204 1\n197217 1\n198217 1\n198218 1\n199229 1\n200223 1\n201224 1\n202232 1\n203255 1\n204234 1\n205250 1\n206251 1\n207252 1\n208236 1\n209253 1\n210237 1\n211254 1\n212238 1\n213239 1\n214249 1\n215259 1\n216240 1\n217260 1\n219235 1\n219256 1\n220244 1\n220245 1\n221245 1\n221246 1\n222235 1\n222246 1\n223247 1\n223261 1\n224248 1\n224262 1\n225241 1\n225256 1\n226241 1\n226257 1\n227242 1\n227257 1\n228242 1\n228258 1\n229247 1\n229258 1\n230243 1\n231248 1\n231261 1\n232262 1\n232263 1\n233243 1\n233263 1\n234264 1\n234267 1\n235285 1\n236265 1\n236272 1\n237268 1\n237273 1\n238269 1\n238274 1\n239266 1\n239275 1\n240267 1\n240270 1\n241289 1\n242281 1\n243280 1\n244282 1\n245283 1\n246284 1\n247292 1\n248279 1\n249276 1\n250276 1\n250277 1\n251277 1\n251278 1\n252272 1\n252278 1\n253265 1\n253273 1\n254268 1\n254274 1\n255269 1\n255275 1\n256286 1\n257290 1\n258291 1\n259266 1\n259270 1\n260264 1\n260271 1\n261287 1\n262288 1\n263294 1\n264296 1\n265304 1\n266295 1\n267310 1\n268297 1\n269309 1\n270308 1\n271303 1\n272302 1\n273305 1\n274306 1\n275307 1\n276299 1\n277300 1\n278301 1\n279295 1\n279308 1\n280296 1\n280303 1\n281297 1\n281306 1\n282298 1\n282299 1\n283299 1\n283300 1\n284300 1\n284301 1\n285301 1\n285302 1\n286302 1\n286304 1\n287295 1\n287307 1\n288308 1\n288310 1\n289304 1\n289305 1\n290297 1\n290305 1\n291306 1\n291309 1\n292307 1\n292309 1\n293303 1\n294296 1\n294310 1\nM END\n';

The first number contains the number of atoms and the number of bonds in the molecule, that is 310 atoms and 450 bonds in our example.
Next the code specifies the coordinates and the type of each atom.
After the coordinates of all the atoms have been specified, the bonds between the atoms are shown. For example, the line ' 97132 1\n' specifies that there is 1 bond between atom 97 and atom 132.