colabOpenSourcePyMOLpySnips

Library of PyMOL Python snippets for installing and running Open Source PyMOL on Google Colab via a Colab notebook

version 0.3

Click here for the notebook for the Incentive PyMOL.

Click on Colab badge to open the notebook on Colab:

Change 2023 May 14

Note that on 2023 May 14, Colab was using Python3.10. I changed the path in the script.

You will have to create a python env using python3.10 if you install open source pymol locally:

conda create -n pymol310 python=3.10 
conda -c conda install -c conda-forge pymol-open-source

Back to this notebook

See the first cell in the notebook for install instructions. I checked that this still works on 1 September 2022.

The installPyMOL snippet will install PyMOL with one click of a button. The installation process takes 5-10 minutes, so be patient. A progress bar monitors the progress of the installation.

This readme file is a work in progress.

Pre-requisite: a Google Drive 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 might 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 onto the line Custom snippet notebook URL:

Step 4: Open a new Colab notebook

Step 5: Seach for the installPyMOL snippet

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

This step takes 5-10 minutes. Ignore this warning:

Step 7: Insert the testPyMOL snippet and run

The result looks like the following image:

Step 8: Save the finished notebook to Google Drive or download the Colab notebook

Related Repos

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

Update history

Version	Changes	Date
Version 0.2	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)