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https://github.com/mooerslab/colabopensourcepymolpysnips

Code snippets for colab-notebooks running open-source PyMOL
https://github.com/mooerslab/colabopensourcepymolpysnips

google-colab literate-programming molecular-graphics open-source-pymol pymol

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Code snippets for colab-notebooks running open-source PyMOL

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README

        

![Version](https://img.shields.io/static/v1?label=colabOpenSourcePyMOLpySnips&message=0.1&color=brightcolor)
[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)

# 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](https://github.com/MooersLab/colabpymolpysnips/edit/main/README.md) for the notebook for the Incentive PyMOL.

Click on Colab badge to open the notebook on Colab:
[![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Mooerslab/colabOpenSourcePyMOLpySnips/blob/main/colabOpenSourcePyMOLpySnips02.ipynb)

### 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:

```bash
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](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)
- [colabPyMOLpySnips](https://github.com/MooersLab/colabPyMOLpySnips)
- [PyMOLwallhangings](https://github.com/MooersLab/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)