Visualization of an MDAnalysis Universe resets its translation

[daandtu]

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

[hainm]

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