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Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"![Version](https://img.shields.io/static/v1?label=colabpymolpysnips\u0026message=0.3\u0026color=brightcolor)\n[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)\n\n\n# colabpymolpysnips: \n\n## Library of PyMOL Python snippets for running Incentive PyMOL in Google Colab notebooks\n#### This notebook requires a PyMOL license file in your Google Drive.\n##### version 0.3\n\n#### For the notebook that uses the Open Source version of PyMOL, [see](https://github.com/MooersLab/colabOpenSourcePyMOLpySnips).\n\nClick on Colab badge to the right to open a notebook on Colab:\n[![Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Mooerslab/colabpymolpysnips/blob/master/colabIncentivePyMOLpySnip03.ipynb)\n\n\nSee the first cell in the notebook for the installation instructions.\n\nThe `installPyMOL` snippet will install PyMOL in one click of a button.\nThe installation process takes 3-10 minutes, so be patient.\nA progress bar monitors the installation. \n\nPre-requisites: you need a Google Drive with some unused disk space. \nGoogle Drive access comes with each Gmail account.\n\n\n### Step 1: Click on the above Colab link\nThis action will open the snippet notebook on Colab.\nThe top of the screen should look like the following:\n\n\u003cp align=\"center\"\u003e\u003cimg src=\"images/topOFSnippetNotebook.png\"\u003e\u003c/p\u003e\n\n\n### Step 2: Copy the snippet notebook to Google Drive\n\nUse the `File/Save copy in Drive' pulldown menu item. \nIf you run some code cells, you may get a message like the following:\n\n\u003cp align=\"center\"\u003e\u003cimg src=\"images/saveSnippetNotebookToGoogleDrive.png\"\u003e\u003c/p\u003e\n\nIgnore this warning. Click on `run anyway`.\n\u003cp align=\"center\"\u003e\u003cimg src=\"images/ignoreWarningAboutAuthorship.png\"\u003e\u003c/p\u003e\n\n\n### Step 3: Paste the URL of the snippet notebook into the settings\n\nPaste the URL into the line `Custom snippet notebook URL`:\n\n\u003cp align=\"center\"\u003e\u003cimg src=\"images/loadedNotebookSettings.png\"\u003e\u003c/p\u003e\n\n\n### Step 4: Open a new Colab notebook\n\n\u003cp align=\"center\"\u003e\u003cimg src=\"images/openNewNotebook.png\"\u003e\u003c/p\u003e\n\n\n### Step 5: Search for the installPyMOL snippet\n\n\u003cp align=\"center\"\u003e\u003cimg src=\"images/searchInstallPyMOL.png\"\u003e\u003c/p\u003e\n\n\n### Step 6: Insert the installPyMOL snippet into the new notebook and run\n\n\u003cp align=\"center\"\u003e\u003cimg src=\"images/installIncentivePyMOL.png\"\u003e\u003c/p\u003e\n\nThis takes 5-10 minutes. \nIgnore this warning:\n\n\u003cp align=\"center\"\u003e\u003cimg src=\"images/ignoreThisError.png\"\u003e\u003c/p\u003e\n\n\n### Step 7: Insert the testPyMOL snippet and run\n\n\u003cp align=\"center\"\u003e\u003cimg src=\"images/testPyMOL.png\"\u003e\u003c/p\u003e\n\nThe result should be the following image:\n\n\u003cp align=\"center\"\u003e\u003cimg src=\"images/testResult.png\"\u003e\u003c/p\u003e\n\n\n### Step 8: Save the finished Colab notebook to Google Drive or download it to your computer.\n\n\n## Related Repos\n\n- [easypymol](https://github.com/MooersLab/EasyPyMOL/edit/master/README.md)\n- [pymolshortcuts](https://github.com/MooersLab/pymolshortcuts)\n- [pymolsnips](https://github.com/MooersLab/pymolsnips)\n- [orgpymolpysnips](https://github.com/MooersLab/orgpymolpysnips)\n- [rstudiopymolpysnips](https://github.com/MooersLab/rstudiopymolpysnips)\n- [taggedpymolpysnips](https://github.com/MooersLab/taggedpymolpysnips)\n- [jupyterlabpymolpysnips](https://github.com/MooersLab/jupyterlabpymolpysnips)\n- [colabOpenSourcePyMOLpySnips](https://github.com/MooersLab/colabOpenSourcePyMOLpySnips)\n- [PyMOLwallhangings](https://github.com/MooersLab/PyMOLwallhangings)\n\n\n## Update history\n\n|Version      | Changes                                                                                                                                    | Date                 |\n|:-----------:|:------------------------------------------------------------------------------------------------------------------------------------------:|:--------------------:|\n| Version 0.3 |  Added badges, funding, and update table                                                                                                   | 2024 May 8           |\n\n## Funding\n- NIH: R01 CA242845, R01 AI088011\n- NIH: P30 CA225520 (PI: R. Mannel); P20GM103640 and P30GM145423 (PI: A. West)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmooerslab%2Fcolabpymolpysnips","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmooerslab%2Fcolabpymolpysnips","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmooerslab%2Fcolabpymolpysnips/lists"}