notebook-molecular-visualization
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Autodesk
2D and 3D molecular visualization in Jupyter notebooks using 3DMol.js and D3.js
A question regarding this awesome tool: I'm trying to represent a chemical reaction in 3D with atom indices. I'd like the 2nd reactant, for example, to have consecutive atom indices...
Hi, Is there anyway to do what I'm suggesting in the title?
I've just done a clean install using the repo versions of `notebook-molecular-visualization` and `molviz` under conda py3 and I'm getting various issues. Most notably, the widget doesn't render - browser...
A function was added to view normal mode displacement vectors from QM packages.
Far from comprehensive, but catches a few Py3 problems I saw in trying to run Tutorial 3. Also specifies conda-forge `nodejs` package as a worthy way to get "npm", rather...
To reproduce: ``` mol = mdt.build_dna_helix('ACTGCGTA') viewer = mol.draw(display=True) viewer.ribbon() ``` ## got:  ## Result with moldesign 0.7.2 / nbmolviz 0.6.5: 
This is in the most recent `master` fb2eee08faca347444dc7bbf85de2d8792ccd6f2 and also MDT. You'll also need to check out the `visualization_json` branch of MDT, or this will throw an exception because of...
This actually looks cool, although it's probably not what we want :) **To reproduce:** In a notebook, execute this cell: ```python mol = mdt.from_pdb('3aid') drug = mol.chains['A'].get_ligand() viewer = mol.draw(display=True)...
This project should have a reasonable distinction between itself and [MDT](https://github.com/Autodesk/molecular-design-toolkit). Right now it seems to be arbitrary. Maybe the right way to divide them is that this would handle...
