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Version License: MIT

colabpymolpysnips:

Library of PyMOL Python snippets for running Incentive PyMOL in Google Colab notebooks

This notebook requires a PyMOL license file in your Google Drive.

version 0.3

For the notebook that uses the Open Source version of PyMOL, see.

Click on Colab badge to the right to open a notebook on Colab: Colab

See the first cell in the notebook for the installation instructions.

The installPyMOL snippet will install PyMOL in one click of a button. The installation process takes 3-10 minutes, so be patient. A progress bar monitors the installation.

Pre-requisites: you need a Google Drive with some unused disk space. Google Drive access comes with each Gmail account.

Step 1: Click on the above Colab link

This action will open the snippet notebook on Colab. The top of the screen should look like the following:

Step 2: Copy the snippet notebook to Google Drive

Use the `File/Save copy in Drive' pulldown menu item. If you run some code cells, you may get a message like the following:

Ignore this warning. Click on run anyway.

Step 3: Paste the URL of the snippet notebook into the settings

Paste the URL into the line Custom snippet notebook URL:

Step 4: Open a new Colab notebook

Step 5: Search for the installPyMOL snippet

Step 6: Insert the installPyMOL snippet into the new notebook and run

This takes 5-10 minutes. Ignore this warning:

Step 7: Insert the testPyMOL snippet and run

The result should be the following image:

Step 8: Save the finished Colab notebook to Google Drive or download it to your computer.

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Version Changes Date
Version 0.3 Added badges, funding, and update table 2024 May 8

Funding

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