Usage questions about nglview: Please ask here first [2]

[hainm]

For any questions relating to how/why/ ... Or anything you don't know where to ask.
For bug, suggestion or anything you want to ask separately, please open seperate issue

PS:

• QA-0: Usage questions: Please ask here first [0] #589
• QA-1: Usage questions about nglview: Please ask here first [1]  #785

[dprada]

Hi! Is there a way to work with the residue indices (0-th based), not the ids, in a selection?
I have a homodimer, and thereby two set of residues in the input pdb with the same ids, and a list of scalar values to color all residues with a new '_ColorScheme'. Is there a way to play with the position index of the scalar value being equal to the residue index, in order to avoid the chain and residue ids?

Thanks in advance!!

[hainm]

hi @dprada, I don't know yet on top of my head. Let me think a bit.

[mjw99]

Hello, thank you for all your work on this great tool.

I am trying to calculate and visualize a molecular electrostatic potential, on a specific electron density isosurface, kind of similar to this example with ngl (live example), but using PySCF and nglview, within a Jupyter notebook:

from pyscf import gto
from pyscf import dft
from pyscf.geomopt import berny_solver
from pyscf import __config__
from pyscf.tools import cubegen

import nglview as nv

# Default of 3.0 is too small for 6-31G*
setattr(__config__, 'cubegen_box_margin', 4.0)

h2o = gto.M(atom='      O 0.00000000,  0.000000,  0.119748;\
                        H 0.00000000,  0.761561, -0.478993;\
                        H 0.00000000, -0.761561, -0.478993',\
                        basis='6-31G*')
                        
h2o.build()
h2o.verbose = 0

method = dft.RKS(h2o)
method.grids.prune = dft.gen_grid.treutler_prune
method.grids.atom_grid = {"H": (50, 194), "O": (50, 194)}
method.xc = 'b3lypg'
method.scf()

opt_mol = berny_solver.optimize(method)

cubegen.density(opt_mol, 'water_den.cube', method.make_rdm1(), resolution=(1/6))
cubegen.mep(opt_mol, 'water_pot.cube', method.make_rdm1(), resolution=(1/6))

view = nv.NGLWidget()

view.add_component('water_den.cube', color="red")
view.component_0.add_surface(isolevelType="value", isolevel=0.002)

view.add_component('water_pot.cube')
view.component_1.add_surface(color='red')

view

I think I am close to getting this to work, but I am not sure how to use data from the two components together.

[dprada]

Dont' worry @hainm, it is something that can be done combining the chain and residues ids. I was wondering if there was a simpler way. But many thanks for your kind reply (as always).

[hainm]

I am trying to calculate and visualize a molecular electrostatic potential, on a specific electron density isosurface, kind of similar to this example with ngl (live example), but using PySCF and nglview, within a Jupyter notebook:

hi @mjw99
Is this what you're looking for? #804

[mjw99]

Dear Hai,
Thank you for the example; with a slightly modified form, and the example data files I can get your example to work:

import nglview as nv

v = nv.NGLWidget()

c0 = v.add_component('esp.mol')
c1 = v.add_component('esp.dx')

c1.clear()

c0.add_surface(
    color_scheme='volume',
      color_volume=c1,      
      colorScale='rwb',
      colorDomain=[ -0.05, 0.05 ],             
      opacity=0.5
)

v

However, with my initial example, a similar approach is still not working:

view = nv.NGLWidget()

c0 = view.add_component('water_den.cube')
c1 = view.add_component('water_pot.cube')
c0.clear()

c0.add_surface(color_scheme='volume', 
      color_volume=c1,
      colorScale='rwb',
      colorDomain=[ -0.05, 0.05 ],      
      opacity=0.5
)

view

As a side point, if I load these same CUBE files into VMD (using a protocol similar to the VMD section here ), they do display fine. Any ideas?

[jessevig]

Thank you for the great tool. Is it possible to set opacity to residues at specific indices or a range of indices? I'm using the cartoon representation. Thanks!

[hainm]

As a side point, if I load these same CUBE files into VMD (using a protocol similar to the VMD section here ), they do display fine. Any ideas?

@mjw99 Can you please try NGL live example first by using your files?

[hainm]

Thank you for the great tool. Is it possible to set opacity to residues at specific indices or a range of indices? I'm using the cartoon representation. Thanks!

hi @jessevig, may be use multiple cartoon representations. Saying you have 5 residues and want to set opacity for some of them.

view.add_cartoon("1,2,5")
view.add_cartoon("3,4", opacity=0.5)

[hainm]

@arose Does NGL support setting opacity for some residues in ONE representation? thanks.

[jessevig]

Is there a simple example for animating a protein structure to rotate? I found this but wasn't sure how to invoke it from the jupyter notebook: https://github.com/arose/ngl/blob/master/src/controls/animation-controls.ts
Thanks much!

[hainm]

@jessevig may be use view.control.spin
https://github.com/arose/nglview/blob/master/nglview/viewer_control.py#L86

[jessevig]

I thought I tried that one before, but it didn't show an animation associated with spinning, it just changed the viewing angle. Is it supposed to show the animation? Thanks.

[hainm]

@jessevig I see. Please use view._set_spin for now. I thought two methods are the same. :D