https://github.com/mooerslab/colabpymolpysnips
Library of PyMOL Python snippets for Google Colab.
https://github.com/mooerslab/colabpymolpysnips
biomolecular-structure ca-trace code-fragments code-snippets colab colab-notebook drug-molecules grayscale ligand-binding-sites literate-programming molecular molecular-graphics molecular-surface notebook protein protein-structure pymol python ribbon-diagrams
Last synced: 17 days ago
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Library of PyMOL Python snippets for Google Colab.
- Host: GitHub
- URL: https://github.com/mooerslab/colabpymolpysnips
- Owner: MooersLab
- License: mit
- Created: 2021-12-08T14:04:33.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2024-05-08T10:08:36.000Z (about 1 year ago)
- Last Synced: 2025-05-08T01:46:34.038Z (17 days ago)
- Topics: biomolecular-structure, ca-trace, code-fragments, code-snippets, colab, colab-notebook, drug-molecules, grayscale, ligand-binding-sites, literate-programming, molecular, molecular-graphics, molecular-surface, notebook, protein, protein-structure, pymol, python, ribbon-diagrams
- Language: Jupyter Notebook
- Homepage:
- Size: 2.41 MB
- Stars: 5
- Watchers: 1
- Forks: 10
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: Citation.md
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README
[](https://opensource.org/licenses/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](https://github.com/MooersLab/colabOpenSourcePyMOLpySnips).
Click on Colab badge to the right to open a notebook on Colab:
[](https://colab.research.google.com/github/Mooerslab/colabpymolpysnips/blob/master/colabIncentivePyMOLpySnip03.ipynb)
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.
## Related Repos
- [easypymol](https://github.com/MooersLab/EasyPyMOL/edit/master/README.md)
- [pymolshortcuts](https://github.com/MooersLab/pymolshortcuts)
- [pymolsnips](https://github.com/MooersLab/pymolsnips)
- [orgpymolpysnips](https://github.com/MooersLab/orgpymolpysnips)
- [rstudiopymolpysnips](https://github.com/MooersLab/rstudiopymolpysnips)
- [taggedpymolpysnips](https://github.com/MooersLab/taggedpymolpysnips)
- [jupyterlabpymolpysnips](https://github.com/MooersLab/jupyterlabpymolpysnips)
- [colabOpenSourcePyMOLpySnips](https://github.com/MooersLab/colabOpenSourcePyMOLpySnips)
- [PyMOLwallhangings](https://github.com/MooersLab/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)