NGLview won't display solvated system

Question

NGLview won't display solvated system

stefdoerr opened this issue 7 years ago · 14 comments

Version report

[sdoerr@loro Wed12:38 Downloads] python -c 'import nglview; print(nglview.__version__)'
0.6.5
[sdoerr@loro Wed12:40 Downloads] python -c 'import ipywidgets; print(ipywidgets.__version__)'
5.2.2

Hi, I'm trying to visualize a solvated system but it doesn't show anything. No protein, no ligand, no water. I tried deleting all configurations in .local/share/ and .jupyter and reinstalling conda from scratch and nglview as well and it still won't show anything.

I attach the two files. mol.pdb works fine. smol.pdb doesnt show anything

files.zip

import nglview
nglview.show_structure_file('mol.pdb')
nglview.show_structure_file('smol.pdb')

hainm commented 7 years ago

Answer 1 · 2017-07-12T14:06:23.000Z

@arose The current NGL version in nglview is 0.10.3. I tested smol.pdb in v0.10.4 here: http://nglviewer.org/ngl/ and work fine. Do you still keep 0.10.3 online?

Answer 2 · 2017-07-13T18:52:10.000Z

I will have a look.

I don't keep older version of the webapp running. However you can create a CodePen and load an older release of NGL.

Answer 3 · 2017-07-13T19:00:19.000Z

Works fine with the current dev version as well. I suspect this is an issue with the default representation in 0.10.3, I made some changes for 0.10.4 regarding that.

Answer 4 · 2017-07-13T19:03:47.000Z

it's not representation issue (try to clear and add lines/licorices but does not work). may be due to unsuccessful creation of Structure (or Component). Recal any of this?

Answer 5 · 2017-07-13T19:35:04.000Z

no, don't recall. Not sure if worth investigating as it works in the more recent releases. What do you think?

Answer 6 · 2017-07-13T19:42:10.000Z

I asked because I tried with latest version in npm (v0.10.4) but still can not resolve the issue.

Or may be because of caching in web browser when I built JS. What syntax to know NGL version?

NGL.__version__

?
:d

Answer 7 · 2017-07-13T20:13:25.000Z

NGL.Version

Answer 8 · 2017-07-14T03:33:58.000Z

@arose I dig deeper and here is the different

NOT work

nglview.show_structure_file('smol.pdb')

Work

view = nglview.NGLWidget()
view

view.add_component('./smol.pdb')

The 1st used blob while the 2nd load from filename.

Answer 9 · 2017-07-14T03:34:01.000Z

hainm commented 7 years ago

Answer 10 · 2017-07-14T03:34:57.000Z

https://github.com/arose/nglview/blob/master/js/src/widget_ngl.js#L772-L798

Answer 11 · 2017-07-23T03:33:38.000Z

@stefdoerr which notebook version you are using?

I think the v5 version restricts how much data will be sent from Python to frontend (JS).

[I 23:30:42.996 NotebookApp] Adapting to protocol v5.1 for kernel a100ee13-f7eb-4e2a-9bbe-e400bdcfd828
[W 23:31:10.938 NotebookApp] IOPub data rate exceeded.
    The notebook server will temporarily stop sending output
    to the client in order to avoid crashing it.
    To change this limit, set the config variable
    `--NotebookApp.iopub_data_rate_limit`.

I think your solvated system (4 MB) is pretty big for notebook v5. I am not sure what we can do. uhm.

Answer 12 · 2017-07-23T03:38:59.000Z

Here is dirty solution

jupyter notebook --NotebookApp.iopub_data_rate_limit=10000000

Answer 13 · 2017-07-23T04:02:55.000Z

Just tried with notebook v 5.1.0.dev. Works fine without doing above trick.

Close the issue now.