Skip to content

CCTBX code fragment library in colab snippet notebook.

License

Notifications You must be signed in to change notification settings

MooersLab/colabcctbxsnips

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

40 Commits
 
 
 
 
 
 
 
 

Repository files navigation

colabcctbxsnips

Version License: MIT

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.

Open In Colab

Local viewing

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.

Using a local runtime

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=0

Then, 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

Sample data files are located in the dataFiles folder. Copy this folder to Google Drive to ease accessing the sample data on Colab.

Related project: jupyterlabcctbxsnips

Similar snippets are available for local use in JupyterLab jupyterlabcctbxsnips. This library is for a menu-driven snippet extension.

Future plans:

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.

Reporting errors

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.

Related slides

Related repositories

Update History

Version Changes Date
Version 0.1 Fixed typos in README.md 2024 April 10

Sources of funding

  • NIH: R01 CA242845
  • NIH: R01 AI088011
  • NIH: P30 CA225520 (PI: R. Mannel)
  • NIH P20GM103640 and P30GM145423 (PI: A. West)