Hello,
Could you give an example function in which a color scale and not discrete colors are used? Thank you!
Best,
Sergio

@sperezconesa I personally don't know "how". @arose Do you have any suggestion? thanks.

Hi,

I can't get this example to work in Colab (works in local notebooks though).

Is there a way to do custom coloring by residue in colab?

Here is the code I tried.

Output from colab was a completely white structure
Output from local notebook was as shown above, with the blue section.

Cell 1

!pip install -q nglview pytraj
from google.colab import output
output.enable_custom_widget_manager()

Cell 2

import nglview as nv
from nglview.color import ColormakerRegistry

cm = ColormakerRegistry
cm.add_selection_scheme("awesome",
        [['blue', '1-10']])

v0 = nv.demo(default=False)
v0.center()
v0.add_cartoon(color='awesome')
v0

Hi,

I can't get this example to work in Colab (works in local notebooks though).

Is there a way to do custom coloring by residue in colab?

Here is the code I tried.

Output from colab was a completely white structure Output from local notebook was as shown above, with the blue section.

Cell 1

!pip install -q nglview pytraj
from google.colab import output
output.enable_custom_widget_manager()

Cell 2

import nglview as nv
from nglview.color import ColormakerRegistry

cm = ColormakerRegistry
cm.add_selection_scheme("awesome",
        [['blue', '1-10']])

v0 = nv.demo(default=False)
v0.center()
v0.add_cartoon(color='awesome')
v0

hi @seanrjohnson, there is nothing we can do about colab besides waiting for google to improve it.

This seems to be the only effective way at present.

Is this also supported for surfaces? I can't seem to get it to work. The surface gets created, but it is all white. It does work for the cartoon representation.

from nglview.color import ColormakerRegistry
cm = ColormakerRegistry
cm.add_selection_scheme('awesome', [['red', '1-10'], ['yellow', '222-300']])
view.add_representation('surface', component=2, color='awesome')

@mretier would you mind ask something like 'is is possible to custom color of the surface repr or not?', in NGL repo: https://github.com/nglviewer/ngl

cheers.

@hainm I asked them here. I'll keep you posted.

thanks @mretier

@hainm please check out the response in the above mentioned thread. It appears to be possible.

Is this also supported for surfaces? I can't seem to get it to work. The surface gets created, but it is all white. It does work for the cartoon representation.

from nglview.color import ColormakerRegistry
cm = ColormakerRegistry
cm.add_selection_scheme('awesome', [['red', '1-10'], ['yellow', '222-300']])
view.add_representation('surface', component=2, color='awesome')

@mretier You are using component=2 here, is that your intention?

@hainm yes, it was my intention in this specific case. When using the same code to apply to the cartoon representation it worked

@mretier I've made a comment here, is that similar to what you're trying? nglviewer/ngl#1005 (comment)

@hainm thanks for the comment. I was able to reproduce your results. Howevever, it does not seem to work with my own code that's a bit different. It's not clear to me why it wouldn't work in my case:

import nglview as nv
from nglview.color import ColormakerRegistry
from Bio.PDB import *

# new cell
parser = PDBParser()
# load Zymomonas mobilis alcohol dehydrogenase
Zmadh = parser.get_structure('3OWO', './3owo_Zmadh.pdb')
# remove second dimer structure (PDB file stores two dimer copies)
Zmadh[0].detach_child('C')
Zmadh[0].detach_child('D')

# new cell
cm = ColormakerRegistry
cm.add_selection_scheme('awesome', [['red', '1-10'], ['yellow', '222-300']])

# new cell
# display only a monomer of the dimer
view = nv.NGLWidget()
view.add_structure(nv.BiopythonStructure(Zmadh[0]['A']))
view.add_representation('surface', color='awesome')
view

@hainm could you elaborate what exactly you mean? How would if find out if my selection was incorrect?

@hainm thanks for your effort, the above code should be fully functional. For your convenience I attached the full code here as well as the .pdb file.
code and structure.zip

I could reproduce the issue with your code + file. Let me play more with it. Cheers.