tl;dr:
Click any launch binder badge on this page to use the demonstrations inside your browser.
cl_demo-binder: Jupyter notebook environment for demonstrating some structure work resources.
A launchable, working Jupyter-based environment that has a collection of demonstrations of useful resources on command line, or also accessible in Jupyter sessions, for manipulating structure files.
Meant to be self-contained and ready-to-go. No installations or copying of notebooks is necessary if launch binder is clicked. Everything will just work. Of course, static versions of the notebooks can also be used. I recommend rendering the static versions by placing the URLs into the nbviewer. The views provided by nbviewer look best and Github's rendering often times out (your mileage may vary).
I tried to include attributions for each resource when they were not mine; however, let me know if you catch an oversight or you'd like to suggest an improvement.
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pdbsum-binder - working with data from PDBsum integrated with Jupyter/Python
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jupyter-jsmol-binder - JMol Jsmol applets in Jupyter notebook
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Jupyter-desktop_with_pymo - PyMOL graphical user interface served via MyBinder.org
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pymol-binder - PyMOL running headless for command line/scripting and interaction with Python.
- In particular there are several notebooks dealing with fetching structures and color them.
- Demo of iterating over the residues of a protein chain and reporting the secondary structure designation assigned to each residue.
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Unipressed-binder - Current examples there include getting structure files for UniProt queries starting with various information.
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modelit-binder - Model.it software to produce a 3D model of DNA in bent confirmation combined with Jupyter ecosystem and PyMOL served via MyBinder.org
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AnimatePymolWithJmol - Easily animate PyMOL session scenes with Jmol to create an animated GIFs
See here for a listing of resources in a similar vein yet targeted to biological sequence data. In particular, see cl_demo-binder for the companion set to this one.
This repository is set up to make use of the binder service offered by MyBinder.org. See their site for more information about Binder.
Click launch binder below to start using the demonstrations.