colabpymolpysnips

Library of PyMOL Python snippets for Google Colab.

https://github.com/mooerslab/colabpymolpysnips

Keywords

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: 6 months ago · JSON representation ·

Repository

Library of PyMOL Python snippets for Google Colab.

Basic Info

Host: GitHub
Owner: MooersLab
License: mit
Language: Jupyter Notebook
Default Branch: main
Homepage:
Size: 2.41 MB

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Stars: 6
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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

Created about 4 years ago · Last pushed almost 2 years ago

Metadata Files

Readme License Citation

README.md

Version

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:

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

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)

Owner

Name: Blaine Mooers
Login: MooersLab
Kind: user
Location: Oklahoma City, OK, USA
Company: University of Oklahoma Health Sciences Center

Website: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd-1
Twitter: MooersBlaine
Repositories: 22
Profile: https://github.com/MooersLab

Associate Professor of Biochemistry and Molecular Biology. RNA and protein crystallographer. Develops tools to ease the use of PyMOL. Drinks French Roast.

Citation (Citation.md)

Insert in the main body of the paper a paraphrased version of the following:

We used the colabpymolpysnips library to support using PyMOL in Google Colab notebooks (https://github.com/MooersLab/elyrapymolpysnips).

Cite this conference paper:

```bibtex
@inproceedings{Mooers2021ModernizingComputingByStructuralBiologists,
  year   = {2021},
  author = {Mooers, Blaine H. M.},
  title = {Modernizing computing by structural bioloigsts with Jupyter and Colab},
  booktitle = {Proc. of the 20th Python in Science Conference (SCIPY 2021)},
  pages = {14-22},
  organization = {SciPy.org},
  url = {http://conference.scipy.org/proceedings/scipy2021/pdfs/blaine_mooers.pdf}
}
```

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