# Working with molecule data

**URL:** https://discourse.paraview.org/t/working-with-molecule-data/8075
**Category:** ParaView Support
**Created:** [September 24, 2021, 3:40am UTC](https://discourse.paraview.org/t/working-with-molecule-data/8075 "2021-09-24T03:40:00Z")
**Posts on this page:** 5
**Page:** 1

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### Author: ![woodscn](https://discourse.paraview.org/user_avatar/discourse.paraview.org/woodscn/32/3226_2.png) [@woodscn](https://discourse.paraview.org/u/woodscn)
#### Post date: [September 24, 2021, 3:40am UTC](https://discourse.paraview.org/t/working-with-molecule-data/8075/1 "2021-09-24T03:40:00Z")

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I’m working with atomistic data coming out of LAMMPS, written in XYZ format. When I open this dataset using the XYZ reader, it creates a vtkMolecule. There doesn’t seem to be a lot I can do with this type of dataset; even things like Reflect don’t work. Is there a way to convert a vtkMolecule to something more common, such as vtkUnstructured, or something like that?

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### Author: ![nicolas.vuaille](https://discourse.paraview.org/user_avatar/discourse.paraview.org/nicolas.vuaille/32/5873_2.png) [@nicolas.vuaille](https://discourse.paraview.org/u/nicolas.vuaille)
#### Post date: [September 24, 2021, 7:12am UTC](https://discourse.paraview.org/t/working-with-molecule-data/8075/2 "2021-09-24T07:12:49Z")

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You have the `Molecule to Lines` filter to get a polydata (one point per atom, one line per bond), with associated arrays.

Note the reverse exists also and is called `Convert Into Molecule`

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### Author: ![woodscn](https://discourse.paraview.org/user_avatar/discourse.paraview.org/woodscn/32/3226_2.png) [@woodscn](https://discourse.paraview.org/u/woodscn)
#### Post date: [September 29, 2021, 7:44pm UTC](https://discourse.paraview.org/t/working-with-molecule-data/8075/3 "2021-09-29T19:44:49Z")

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Thanks for your reply. Molecule to Lines does give me a polydata object. The thing that threw me off before is that it won’t render for anything other than 3D glyphs and Point Gaussian. Points, Surface, and all the rest leave me with a blank screen. I suspect this is because I don’t have any bonds in my dataset. Any thoughts?

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### Author: ![nicolas.vuaille](https://discourse.paraview.org/user_avatar/discourse.paraview.org/nicolas.vuaille/32/5873_2.png) [@nicolas.vuaille](https://discourse.paraview.org/u/nicolas.vuaille)
#### Post date: [September 30, 2021, 7:20am UTC](https://discourse.paraview.org/t/working-with-molecule-data/8075/4 "2021-09-30T07:20:04Z")

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ParaView rendering is based on cells.  
If you do not have cells but only points, most of rendering will be empty except for 3D Glyph and Point Gaussian that creates extra geometry at point locations.

And you guess correctly, `Molecule To Lines` create only cells for bounds.

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### Author: ![woodscn](https://discourse.paraview.org/user_avatar/discourse.paraview.org/woodscn/32/3226_2.png) [@woodscn](https://discourse.paraview.org/u/woodscn)
#### Post date: [September 30, 2021, 2:50pm UTC](https://discourse.paraview.org/t/working-with-molecule-data/8075/5 "2021-09-30T14:50:03Z")

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That makes sense. I am surprised that Points representation does not work, and I thought I remembered Surface rendering individual points in the absence of cell geometry for other datasets (vtkUnstructuredGrid?), but that was several versions ago now.