PyMOL part 3 (of 3)

Biochemistry laboratories - 201

Jean-Yves Sgro [email protected]

Find this document at http://go.wisc.edu/p52b90

Note: To see as slides click on at the top right. To revert back to page view click on when on the first slide.

Set-up

  • check your name on the attendees list
  • choose an iMac
  • login with your NetID

Finding PyMOL

  • Click on the "Finder" at the bottom right of the "Dock" on the bottom of the screen. |

  • This will open a new window.

  • On the left click on "Applications"
  • In the alphabetical list choose "MacPyMOL" or "MacPyMOL.app" and double click. This will open PyMOL on your screen.

PyMOL book:

  • start on page 111
  • end on page 162

This book is a loaner with a number marked on it.
Please do not take with you!

To get your own book in PDF format:

  • After class fill-in the one page "evaluation" form for this class
  • BONUS 1: Complete in-color PDF of PyMOL workbook used in class
  • BONUS 2: Official "Introduction to PyMOL" by DeLano Scientific

The evaluation is anonymous. Evaluation link on Qualtrics
short URL: http://go.wisc.edu/ajt167

Evaluation survey will be unlocked at specific times.

Today's menu

  • Movie making for the impatient - Scenes export (p 111)
  • Simple animations (p 116)
  • Advanced movie commands (p 121)
  • NMR models & animation (p 127)
  • Multimeric structure: rhinovirus A16 (p 135)
  • Scripts (p 140)
  • Subsets (p 148)
  • Choosing a style: PyMOLWiki gallery (p 154)
  • Morphing (p 155)
  • Optional: Electron density maps (p163)

PyMOL movie commands

Movie programs Definitions and complete parameters
movie.rock movie.rock(first,last,angle=30,phase=0,loop=1,axis='y')
movie.roll movie.roll(first,last,loop=1,axis='y')
movie.zoom movie.zoom(first,last,step=1,loop=1,axis='z')
movie.screw movie.screw(first,last,step=1,angle=30,phase=0,loop=1, axis='y')
movie.sweep movie.sweep(pause=0,cycles=1)
movie.pause movie.pause(pause=15,cycles=1)
movie.nutate movie.nutate(first,last,angle=30,phase=0,loop=1,shift=math.pi/2.0,factor=0.01)
movie.tdroll movie.tdroll(first,rangex,rangey,rangez,skip=1)
movie.timed_roll timed_roll(period=12.0,cycles=1,axis='y')
movie.load movie.load(*args,**kw)

Saving the Movie as Frames

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.

Software Link
QuickTime™Pro (Mac / PC / 29.99$) http://www.apple.com/quicktime/extending
VideoMach (PC – (standard of Pro) http://www.gromada.com
ImageMagick (Open Source, free) http://www.imagemagick.org
Avidemux (Open Source, free) <- recommended by PyMolWiki http://avidemux.sourceforge.net