On Colab, the snippets are stored in a Google Colab notebook. See this website for an excellent introduction to CCTBX (Computational Crystallography Toolbox). The colabcctbxsnips library is a collection of code fragments to aid in routine and non-routine computational tasks in protein crystallography. The URL for the snippets notebook is unused to access the snippets from a new notebook.
Click on the blue button below to open the notebook on Colab. Then, follow the instructions at the top of the notebook to copy the notebook to Google Drive and make it available to new Colab notebooks. This step has to be done only once. The snippets will be available on your next log-in; however, files and software installed on Colab will not be available on your next login.
This notebook can be viewed locally in the nteract.app -- an easy-to-install desktop application for viewing and editing Jupyter Notebook documents (*.ipynb)--, Jupyter Notebook, or Jupyter Lab, but utilization of the colabcctbxsnips library requires use of Colab.
You can use the snippet library in a Colab notebook connected to a local runtime (i.e., a local conda env). Please take a look at the connect pull-down for more instructions. You have to install a Jupyter extension in the conda env that you want to use, and then you start a Jupyter session with a command like the following:
jupyter notebook \
--NotebookApp.allow_origin='https://colab.research.google.com' \
--port=8889 \
--NotebookApp.port_retries=0Then, you copy the URL returned to the terminal by the Jupyter server and paste it into the Colab notebook's connect window. However, you still need an internet connection to connect to have Google Drive loaded so that you can access the snippet notebook.
Sample data files are located in the dataFiles folder. Copy this folder to Google Drive to ease accessing the sample data on Colab.
Similar snippets are available for local use in JupyterLab jupyterlabcctbxsnips. This library is for a menu-driven snippet extension.
I plan to make this library available for the Elyra snippet extension for Jupyter Lab shortly. It will be called taggedcctbxsnips. It will parallel the taggedpymolsnips library.
The CCTBX is under continuous development by a consortium of developers funded by the NIH. Some of the functions get renamed or deleted. Post an issue for functions that no longer work.
- Colab snippet talk ACA The Structural Science Society, 72nd Meeting, Portland, OR, 1 August 2022
- GhostText talk Oklahoma Data Science Workshop, Oklahoma City, OK, 21 July 2022 GhostText can be used to edit the code blocks in a computational notebook with a full-powered text editor. GhostText supports Sublime Text, VSC, Vim, Neovim, and Emacs.
- easypymol
- pymolshortcuts
- orgpymolpysnips
- rstudiopymolpysnips
- taggedpymolpysnips
- jupyterlabpymolpysnips
- colabOpenSourcePyMOLpySnips
- colabPyMOLpySnips
- PyMOLwallhangings
| Version | Changes | Date |
|---|---|---|
| Version 0.1 | Fixed typos in README.md | 2024 April 10 |
- NIH: R01 CA242845
- NIH: R01 AI088011
- NIH: P30 CA225520 (PI: R. Mannel)
- NIH P20GM103640 and P30GM145423 (PI: A. West)