{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Demonstrates sampling various combinations of applying colors from a specific palette to the chains of a large macromolecular complex\n", "\n", "This notebook will demonstrate automated coloring of a complex with a lot of chains by various combinations from a set palette using binderized PyMol. Random shuffles of your color palette will be cycled to color all the chains and metals.The idea being you can find a per chains/metals color list that matches your needs or at least is close. The color lists for the corresponding are generated in a text file as the images are produced. The 'one' closest to what you want you can than use as a basis for further modification. \n", "\n", "This builds on all the previous demos plus rather advanced usage of Python and Jupyter notebook magics, and so you should be familiar with the previous demos at least and then play around.\n", "\n", "The code is set up to be general. You can run it with the defaults now and it should work. With a little change to the specified places, you can make it address your favorite structure and colors.\n", "\n", "As it relies on colors a lot, you should see [Demo of Dealing with PyMol colors](notebooks/demo_colors.ipynb).\n", "\n", "Return to [the first page](index.ipynb) for a list of the demonstrations available.\n", "\n", "----\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", "