{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Superimpose Structures via PyMOL by python script\n", "\n", "This notebook was prompted by a response to [this biostars question](https://www.biostars.org/p/9528492/#9528492). \n", "It assumes you worked through the code on the 'Index' notebook and then the first available notebook in this series already.\n", "\n", "Note, that the Biostar's question specifically asked to use PyMOL's `super` command. I generally use `pair_fit` in PyMOL when I need precise per residue matching, and as discussed [here](https://nbviewer.org/github/fomightez/cl_demo-binder/blob/master/notebooks/Determine%20residues%20that%20match%20to%20a%20reference%20from%20MSA%20and%20use%20to%20construct%20fit%20commands.ipynb) prefer these days to let [TM-align](https://zhanggroup.org/TM-align/) do 'overall' structure-to-structure structural alignments.\n", "\n", "\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", "