{ "cells": [ { "cell_type": "markdown", "metadata": { "slideshow": { "slide_type": "slide" } }, "source": [ "# PyMOL part 3 (of 3)\n", ">Biochemistry laboratories - 201\n", ">\n", ">Jean-Yves Sgro -jsgro@wisc.edu\n", "\n", "\n", "
\n", "
\n", "\n", "Find this document at [**`http://go.wisc.edu/p52b90`**](http://go.wisc.edu/p52b90)\n", "
\n",
"*Note*: To see as slides click on at the top right. To revert back to page view click on when on the first slide.\n",
"\n"
]
},
{
"cell_type": "markdown",
"metadata": {
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"source": [
"## Set-up\n",
"\n",
"- check your name on the attendees list\n",
"- choose an iMac\n",
"- login with your ***NetID***"
]
},
{
"cell_type": "markdown",
"metadata": {
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},
"source": [
"## Finding PyMOL\n",
"\n",
"- Click on the \"Finder\" at the bottom right of the **\"Dock\"** on the bottom of the screen. |\n",
"\n",
"- This will open a new window.\n",
"- On the left click on **\"Applications\"**\n",
"- In the alphabetical list choose **\"MacPyMOL\"** or **\"MacPyMOL.app\"** and double click. This will open PyMOL on your screen.\n"
]
},
{
"cell_type": "markdown",
"metadata": {
"slideshow": {
"slide_type": "slide"
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"source": [
"## PyMOL book: \n",
"- start on page 111\n",
"- end on page 162\n",
"\n",
"> This book is a loaner with a number marked on it. \n",
"**Please do not take with you!**\n",
"\n",
"## To get your own book in PDF format:\n",
"- After class fill-in the one page \"evaluation\" form for this class \n",
"- BONUS 1: Complete in-color **PDF of PyMOL workbook** used in class\n",
"- BONUS 2: Official \"**Introduction to PyMOL**\" by DeLano Scientific\n",
"\n",
"The evaluation is anonymous. [Evaluation link on Qualtrics](https://uwmadison.co1.qualtrics.com/jfe/form/SV_23nbufaj8kHQ4Hb) \n",
"
short URL: **[http://go.wisc.edu/ajt167](http://go.wisc.edu/ajt167)**\n",
"\n",
"Evaluation survey will be unlocked at specific times."
]
},
{
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"source": [
"# Today's menu\n",
"\n",
"* Movie making for the impatient - Scenes export (p 111)\n",
"* Simple animations (p 116)\n",
"* Advanced movie commands (p 121)\n",
"* NMR models & animation (p 127)\n",
"* Multimeric structure: rhinovirus A16 (p 135)\n",
"* Scripts (p 140)\n",
"* Subsets (p 148)\n",
"* Choosing a style: PyMOLWiki gallery (p 154)\n",
"* Morphing (p 155)\n",
"* Optional: Electron density maps (p163)"
]
},
{
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"source": [
"## PyMOL movie commands\n",
"\n",
"| _Movie programs_ | _Definitions and complete parameters_ |\n",
"|---|---|\n",
"| `movie.rock` | movie.rock(first,last,angle=30,phase=0,loop=1,axis='y')\n",
"| `movie.roll` | movie.roll(first,last,loop=1,axis='y')\n",
"| `movie.zoom` | movie.zoom(first,last,step=1,loop=1,axis='z')\n",
"| `movie.screw`| movie.screw(first,last,step=1,angle=30,phase=0,loop=1, axis='y')\n",
"| `movie.sweep`| movie.sweep(pause=0,cycles=1)\n",
"| `movie.pause`| movie.pause(pause=15,cycles=1)\n",
"| `movie.nutate`| movie.nutate(first,last,angle=30,phase=0,loop=1,shift=math.pi/2.0,factor=0.01)\n",
"| `movie.tdroll` |movie.tdroll(first,rangex,rangey,rangez,skip=1)\n",
"| `movie.timed_roll` | timed_roll(period=12.0,cycles=1,axis='y')\n",
"| `movie.load`| movie.load(\\*args,\\*\\*kw)\n"
]
},
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"metadata": {
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"slide_type": "slide"
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"source": [
"## Saving the Movie as Frames\n",
"\n",
"Movie can be saved as individual frames to be assembled in 3rd party software. However, since PyMOL can make movies directly this info is now less relevant - here for general information.\n",
"\n",
"| _Software_ | _Link_ |\n",
"|---|---|\n",
"| **QuickTime™Pro** (Mac / PC / 29.99$) | http://www.apple.com/quicktime/extending |\n",
"| **VideoMach** (PC – (standard of Pro) | http://www.gromada.com |\n",
"| **ImageMagick** (Open Source, free) | http://www.imagemagick.org |\n",
"| **Avidemux** (Open Source, free) <- recommended by PyMolWiki | http://avidemux.sourceforge.net |\n"
]
}
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