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:

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:

<p align="center"><img src="images/topOFSnippetNotebook.png"></p>

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:

<p align="center"><img src="images/saveSnippetNotebookToGoogleDrive.png"></p>

Ignore this warning. Click on run anyway.

<p align="center"><img src="images/ignoreWarningAboutAuthorship.png"></p>

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

Paste the URL into the line Custom snippet notebook URL:

<p align="center"><img src="images/loadedNotebookSettings.png"></p>

Step 4: Open a new Colab notebook

<p align="center"><img src="images/openNewNotebook.png"></p>

Step 5: Search for the installPyMOL snippet

<p align="center"><img src="images/searchInstallPyMOL.png"></p>

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

<p align="center"><img src="images/installIncentivePyMOL.png"></p>

This takes 5-10 minutes. Ignore this warning:

<p align="center"><img src="images/ignoreThisError.png"></p>

Step 7: Insert the testPyMOL snippet and run

<p align="center"><img src="images/testPyMOL.png"></p>

The result should be the following image:

<p align="center"><img src="images/testResult.png"></p>

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

Related Repos

• easypymol
• pymolshortcuts
• pymolsnips
• orgpymolpysnips
• rstudiopymolpysnips
• taggedpymolpysnips
• jupyterlabpymolpysnips
• colabOpenSourcePyMOLpySnips
• PyMOLwallhangings

Update history

|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)