How to set colors of atoms by index ? #892
Comments
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may be Or do you want customized colors? |
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I did this but it does not work idx_C1 = np.array([ 0, 1, 2, 5, 6, 7, 8, 9, 11, 13, 14, 23, 24,
28, 37, 38, 39, 40, 45, 46, 47, 50, 51, 52, 53, 54,
56, 58, 59, 68, 69, 73, 83, 84, 85, 86, 91, 92, 93,
96, 97, 98, 99, 100, 102, 104, 105, 114, 115, 119, 129, 130,
131, 132])
idx_C2 = np.array([ 3, 4, 12, 15, 22, 27, 33, 34, 48, 49, 57, 60, 67,
72, 79, 80, 94, 95, 103, 106, 113, 118, 125, 126])
idx_C3 = np.array([ 10, 29, 32, 55, 74, 77, 78, 101, 120, 123, 124, 137])
view = nv.show_file("D3-2.pdb")
view.add_representation('licorice', selection=idx_C1, color='red')
view.add_representation('licorice', selection=idx_C2, color='blue')
view.add_representation('licorice', selection=idx_C3, color='green')
viewwhere And yes, what I would like to do is to be able to give the color according to a give quantity (charge, spin ...) Thanks the pdb file is the following : |
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I am not sure about your system. It works fine like below:
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@gVallverdu I can reproduce your issue with your code + file. |
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I also reproduce your code and it works. |
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ah, you did not clear the default representation (for some reasons), this default color overlaps with your new ones.
Try this: |
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Ok, it works, but it is quite strange. Sometimes I have to execute the cell several times to get the widget to render the view.
Here is the code I used: import nglview as nv
import numpy as np
idx_C1 = np.array([ 0, 1, 2, 5, 6, 7, 8, 9, 11, 13, 14, 23, 24,
28, 37, 38, 39, 40, 45, 46, 47, 50, 51, 52, 53, 54,
56, 58, 59, 68, 69, 73, 83, 84, 85, 86, 91, 92, 93,
96, 97, 98, 99, 100, 102, 104, 105, 114, 115, 119, 129, 130,
131, 132])
idx_C2 = np.array([ 3, 4, 12, 15, 22, 27, 33, 34, 48, 49, 57, 60, 67,
72, 79, 80, 94, 95, 103, 106, 113, 118, 125, 126])
idx_C3 = np.array([ 10, 29, 32, 55, 74, 77, 78, 101, 120, 123, 124, 137])
view = nv.show_file("Angewandte/diastereomer_D3-2.pdb", default=False)
view.center()
view.add_representation("ball+stick")
view.add_representation('ball+stick', selection=idx_C1, color='red')
view.add_representation('ball+stick', selection=idx_C2, color='blue')
view.add_representation('ball+stick', selection=idx_C3, color='green')
viewGoing back to the beginning of the question, what I would like to do now is to give a color to each atom according to an atomic quantity (charge, spin ...). I can make a loop on this If not, I could try something and maybe try to contribute ... |
yeah, it might be related to the bug fixed in master branch: #882 |
Try to use |
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Where can I find the |
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it's http://nglviewer.org/ngl/api/manual/molecular-representations.html#ball-stick |
Hello
I have a molecule that I load from a PDB file and I would like to set the color of atoms from their index.
Thank you for your help
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