{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# PyMol useable via Binder (no graphical user interface)\n", "\n", "My collection demonstrating using Pymol here.\n", "\n", "A very basic demo of running PyMol via this interface is included **on this page** [here](#Basic-example) just below the list of 'Available Notebooks'. \n", "For more practical uses of PyMol, select a notebook from this index of availabe demostration notebooks below. \n", "\n", "----\n", "\n", "## Available Notebooks\n", "\n", "- Index (this Jupyter notebook) has a basic script execution example below this list of notebooks. Scroll down to START THERE.\n", "- [Demo of Getting a Structure and Producing an Image](notebooks/demo_fetch.ipynb)\n", "- [Demo of Setting an Orientation](notebooks/demo_orient.ipynb)\n", "- [Demo of Dealing with PyMol colors](notebooks/demo_colors.ipynb)\n", "- [Demo of Sampling Various Combinations of Applying A Color Palette to a Complex](notebooks/demo_palette.ipynb)\n", "- [Demo of Applying a Color Combination Choice to a Complex](notebooks/demo_apply_combo.ipynb)\n", "- [Demo of Iterating over residue secondary structure](notebooks/demo_residue_secondary_structure.ipynb)\n", "- [Demo of Superimposing Two Structures via PyMOL Super Command](notebooks/demo_superimpose.ipynb)\n", "- [Demo of Unfolding Region of Protein Chain via PyMOL](notebooks/demo_unfold_segment.ipynb)\n", "- [Demo of Unfolding Region of Protein Chain via PyMOL - involving Pandas](notebooks/demo_unfold_segment_inv_Pandas.ipynb)\n", "- [TBD](TBD.ipynb)\n", "- [TBD](TBD.ipynb)\n", "- [TBD](TBD.ipynb)\n", "\n", "
If you haven't used one of these notebooks before, they're basically web pages in which you can write, edit, and run live code. They're meant to encourage experimentation, so don't feel nervous. Just try running a few cells and see what happens!.
\n", "\n", "\n", " Some tips:\n", "