# Does Paraview know chemistry?
**URL:** https://discourse.paraview.org/t/does-paraview-know-chemistry/6942
**Category:** ParaView Support
**Created:** [April 13, 2021, 3:02pm UTC](https://discourse.paraview.org/t/does-paraview-know-chemistry/6942 "2021-04-13T15:02:59Z")
**Posts on this page:** 15
**Page:** 1
### Author:  [@Maria\_co](https://discourse.paraview.org/u/Maria_co)
#### Post date: [April 13, 2021, 3:02pm UTC](https://discourse.paraview.org/t/does-paraview-know-chemistry/6942/1 "2021-04-13T15:02:59Z")
Hi, I tried to upload a .cml file of a molecule in Paraview to find out if it communicated with Avogadro and in fact, to my great surprise, I found my molecule in the Paraview render view.
So I wonder: is it possible to create a molecule directly in Paraview rather than creating it in Avogadro and then opening it in Paraview?
I do not find any information on the guide about the topic
---
### Author:  [@nicolas.vuaille](https://discourse.paraview.org/u/nicolas.vuaille)
#### Post date: [April 14, 2021, 7:34am UTC](https://discourse.paraview.org/t/does-paraview-know-chemistry/6942/2 "2021-04-14T07:34:02Z")
ParaView is intended for display and analysis. Creating data is not what it is designed for.
That said, you can programatically create a molecule inside ParaView using `Programmable Source`, output set to `vtkMolecule`, and then write the appropriate vtk python code (mostly use `AppendAtom(atomicNumber, x, y ,z)` [method](https://vtk.org/doc/nightly/html/classvtkMolecule.html#a20a34f9761b098e181458c3a5c021ec7), and optionnally set `AtomData` or `BondData`)
---
### Author:  [@Maria\_co](https://discourse.paraview.org/u/Maria_co)
#### Post date: [May 3, 2021, 1:50pm UTC](https://discourse.paraview.org/t/does-paraview-know-chemistry/6942/3 "2021-05-03T13:50:47Z")
I found an external software that creates the molecule, and calculates the electron density, orbitals, etc …
This software creates a file in cube format. When I open the file with paraview, I can get the result with the gaussian cube reader but I can visualize the molecule but not the densities. Is there any filter that I may not know that allows me to achieve this?
---
### Author:  [@waveman](https://discourse.paraview.org/u/waveman)
#### Post date: [December 22, 2021, 2:26pm UTC](https://discourse.paraview.org/t/does-paraview-know-chemistry/6942/4 "2021-12-22T14:26:56Z")
This is also a topic that interests me. I have had the most success with paraview 5.9.1 and the .xyz format.
From there, I use the Chemistry: Compute Molecular Bonds filter to get a visualization of the bonds. This gives me usable results, but double bonds are missing. PDB format is hit or miss.
---
### Author:  [@waveman](https://discourse.paraview.org/u/waveman)
#### Post date: [December 22, 2021, 2:27pm UTC](https://discourse.paraview.org/t/does-paraview-know-chemistry/6942/5 "2021-12-22T14:27:47Z")
I am also trying to get this running:
[https://www.kitware.com/open-chemistry-avogadro-electronic-structure-in-jupyterlab/](https://www.kitware.com/open-chemistry-avogadro-electronic-structure-in-jupyterlab/)
---
### Author:  [@Chris\_Harris](https://discourse.paraview.org/u/Chris_Harris)
#### Post date: [December 22, 2021, 2:40pm UTC](https://discourse.paraview.org/t/does-paraview-know-chemistry/6942/6 "2021-12-22T14:40:31Z")
As @nicolas.vuaille said ParaView doesn’t have a molecule editor. However, this functionality is available in Avogadro. The result can be visualized in ParaView.
---
### Author:  [@Chris\_Harris](https://discourse.paraview.org/u/Chris_Harris)
#### Post date: [December 22, 2021, 2:42pm UTC](https://discourse.paraview.org/t/does-paraview-know-chemistry/6942/7 "2021-12-22T14:42:30Z")
@waveman Let us know how you get on with the JupyterLab integration.
---
### Author:  [@waveman](https://discourse.paraview.org/u/waveman)
#### Post date: [December 22, 2021, 3:18pm UTC](https://discourse.paraview.org/t/does-paraview-know-chemistry/6942/8 "2021-12-22T15:18:37Z")
Not well, so far. I’m not very good with node.js/npm, so that might be my problem.
Essentially, I am running into issues with the dependencies. If I understand it correctly, the syntax:
```auto
"@lumino/widgets": "^1.17.0"
```
means that it can be 1.17.0 or higher, as long as it’s \< 2.0. For example, lumino is now 2.6. Jupyterlab in the binder is at version 1.1.4. Jupyterlab is in the meantime at version 3.2.1.
```auto
jupyter labextension install @openchemistry/jupyterlab
```
gives me the following:
```auto
An error occurred.
ValueError: The extension "@openchemistry/jupyterlab" does not yet support the current version of JupyterLab.
Conflicting Dependencies:
JupyterLab Extension Package
>=1.19.0 <2.0.0 1.17.0 @lumino/widgets
See the log file for details: /tmp/jupyterlab-debug-2srd9aaa.log
```
Various attempts at convincing the conda nodejs (16.13.1) to create a yarn of a local version failed.
Any suggestions?
---
### Author:  [@Chris\_Harris](https://discourse.paraview.org/u/Chris_Harris)
#### Post date: [December 22, 2021, 3:24pm UTC](https://discourse.paraview.org/t/does-paraview-know-chemistry/6942/9 "2021-12-22T15:24:40Z")
@waveman I think this PR may resolve your issue: [Update reqs for @lumino deps. by mskblackbelt · Pull Request #70 · OpenChemistry/jupyterlab\_cjson · GitHub](https://github.com/OpenChemistry/jupyterlab_cjson/pull/70). I will cut an new release soon.
Chris
---
### Author:  [@waveman](https://discourse.paraview.org/u/waveman)
#### Post date: [December 23, 2021, 8:23am UTC](https://discourse.paraview.org/t/does-paraview-know-chemistry/6942/10 "2021-12-23T08:23:39Z")
When visualizing simulation results, it is inordinately useful to visualize the molecule with bonds together with electron densities, potentials etc.
---
### Author:  [@Chris\_Harris](https://discourse.paraview.org/u/Chris_Harris)
#### Post date: [December 23, 2021, 2:02pm UTC](https://discourse.paraview.org/t/does-paraview-know-chemistry/6942/11 "2021-12-23T14:02:48Z")
@waveman Please feel free to raise a issue with this feature request.
---
### Author:  [@waveman](https://discourse.paraview.org/u/waveman)
#### Post date: [December 24, 2021, 8:25am UTC](https://discourse.paraview.org/t/does-paraview-know-chemistry/6942/12 "2021-12-24T08:25:24Z")
Thanks. Done: paraview#21149.
---
### Author:  [@mwestphal](https://discourse.paraview.org/u/mwestphal)
#### Post date: [December 27, 2021, 1:10pm UTC](https://discourse.paraview.org/t/does-paraview-know-chemistry/6942/13 "2021-12-27T13:10:46Z")
[https://gitlab.kitware.com/paraview/paraview/-/issues/21149](https://gitlab.kitware.com/paraview/paraview/-/issues/21149)
---
### Author:  [@Himanshu\_Sharma](https://discourse.paraview.org/u/Himanshu_Sharma)
#### Post date: [December 24, 2024, 8:20am UTC](https://discourse.paraview.org/t/does-paraview-know-chemistry/6942/14 "2024-12-24T08:20:43Z")
I tried to open a Bohr-cml file in paraview. First time it showed the structure however agin when I opened it, it was showing only background
---
### Author:  [@nicolas.vuaille](https://discourse.paraview.org/u/nicolas.vuaille)
#### Post date: [December 24, 2024, 8:42am UTC](https://discourse.paraview.org/t/does-paraview-know-chemistry/6942/15 "2024-12-24T08:42:33Z")
Hi @Himanshu_Sharma ,
Do not hesitate to create your own topic, with details to reproduce your issue.