Visualization of an MDAnalysis Universe resets its translation

[Luis]

Setup:

1. I load a molecule with MDAnalysis from a PDB file.
2. Then I translate the molecule to a new position.
3. I visualize the molecule via nglview.show_mdanalysis

Problem:
During the visualization, the translation is reset, i.e. after the creation of the NGLView-Widget the coordinates of the molecule are the same again as in the PDB file.

Example:

import MDAnalysis as mda
from MDAnalysis.transformations.translate import translate
import numpy as np
import nglview as nv

pdb_path = 'temp.pdb'
structure1 = mda.Universe(pdb_path)
print('Before translation:')
for atom in structure1.atoms:
    print(atom.position)
translate(np.array([10,10,10]))(structure1.atoms)
print('After translation:')
for atom in structure1.atoms:
    print(atom.position)
nv_widget_1 = nv.show_mdanalysis(structure1)
print('After visualization:')
for atom in structure1.atoms:
    print(atom.position)
nv_widget_1

The output is:

Before translation:
[1. 0. 0.]
[ 0.  0. -1.]
[1. 0. 1.]
After translation:
[11. 10. 10.]
[10. 10.  9.]
[11. 10. 11.]
After visualization:
[1. 0. 0.]
[ 0.  0. -1.]
[1. 0. 1.]

I used this PDB file:

ATOM      1  N1  1MIMX   1       1.000   0.000   0.000  1.00  0.00      1M
ATOM      2  N2  1MIMX   1       0.000   0.000  -1.000  1.00  0.00      1M    
ATOM      3  R3  1MIMX   1       1.000   0.000   1.000  1.00  0.00      1M    
ENDMDL
CONECT    1    2    3
CONECT    2    1    3
CONECT    3    1    2
END

Version report
nglview version: 3.0.8
ipywidgets version: 8.1.1

[Hai Nguyen]

thanks @daandtu for your report. I don't know why on top of my head. The code is super simple:

nglview/nglview/adaptor.py

Lines 412 to 460 in d9e7740

 class MDAnalysisTrajectory(Trajectory, Structure): 
     '''MDAnalysis adaptor. 
  
     Can take either a Universe or AtomGroup. 
  
     Example 
     ------- 
     >>> import nglview as nv 
     >>> import MDAnalysis as mda 
     >>> u = mda.Universe(nv.datafiles.GRO, nv.datafiles.XTC) 
     >>> prot = u.select_atoms('protein') 
     >>> t = nv.MDAnalysisTrajectory(prot) 
     >>> w = nv.NGLWidget(t) 
     >>> w 
     ''' 
  
     def __init__(self, atomgroup): 
         self.atomgroup = atomgroup 
         self.ext = "pdb" 
         self.params = {} 
         self.id = str(uuid.uuid4()) 
  
     def get_coordinates(self, index): 
         self.atomgroup.universe.trajectory[index] 
         xyz = self.atomgroup.atoms.positions 
         return xyz 
  
     @property 
     def n_frames(self): 
         return self.atomgroup.universe.trajectory.n_frames 
  
     def get_structure_string(self): 
         try: 
             import MDAnalysis as mda 
         except ImportError: 
             raise ImportError( 
                 "'MDAnalysisTrajectory' requires the 'MDAnalysis' package") 
         u = self.atomgroup.universe 
         u.trajectory[0] 
         f = mda.lib.util.NamedStream(StringIO(), 'tmp.pdb') 
         atoms = self.atomgroup.atoms 
         # add PDB output to the named stream 
         with mda.Writer(f, atoms.n_atoms, multiframe=False) as w: 
             with warnings.catch_warnings(): 
                 warnings.simplefilter('ignore') 
                 w.write(atoms) 
         # extract from the stream 
         pdb_string = f.read() 
         return pdb_string