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I'm wondering how well Blender is suited for producing images from existing 2D (CDX, SMILES etc.) or 3D (PDB, XYZ, CIF etc.) chemical structures. Basically, the task is to convert a set of coordinates to a finite (e.g. a molecule) or a subset of infinite (e.g. a unit cell) graphical representation. Ideally it would be nice if a certain level of "chemistry awareness" would be present, such as typical interatomic distances, coordination numbers, atomic and ionic radii.

Is there an addon that can help chemists to use blender for their routine work?

There is a related question about crystal structure generation with Blender. I'm assuming that structure is already established.

andselisk
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  • I don't know of any addons specifically for those formats, but then again I never really searched. If there are any a simple google search should find them, iff there aren't, then any dedicated developer could probably write a simple Python addon for import easily, but I doubt anyone would be willing to just do it for free. Blender has been used for scientific visualizations quite frequently before so it seems very feasible – Duarte Farrajota Ramos Jul 12 '17 at 17:43
  • There is a lot that can be done with the animation nodes add-on ( https://github.com/JacquesLucke/animation_nodes ) or Sverchok ( https://github.com/nortikin/sverchok ). If you post sample data and an example of the kind of output desired, that might be enough to see if it can be done using those tools. – Ed Tate Jul 12 '17 at 18:08
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    This answer may be of interest. – sambler Jul 13 '17 at 06:23

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I'm very confident you can achieve what you want using Blender. Searching the web for "Blender for chemistry" gives you a number of hits including video tutorials and images what others did. Maybe this blog post is interesting for you:

https://patrickfuller.github.io/molecules-in-blender/

Furthermore I found an addon for PDB import/export:

https://wiki.blender.org/index.php/Extensions:2.6/Py/Scripts/Import-Export/PDB

PattimusPrime
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WolfiG
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  • This looks promising, yet it seems like Atomic Blender addon is abandoned and hasn't been in development since 2013, and it only allows importing PDB files (which is still something). Anyway, thank you for the starting point, as for me having very little experience with Blender and 3D this is helpful! – andselisk Jul 13 '17 at 01:12