====== Cheat Sheet ======
  * http://medschool.lsuhsc.edu/biochemistry/docs/PyMOL-QuickRef-0905.pdf
====== Cook Book ======
===== Startup file of pymol on windows =====
On Windows, use 'pymolrc', 'pymolrc.py' or 'pymolrc.pym'. For global
defaults (all users), you can place a .pymolrc file in C:\Program
Files\DeLano Scientific\PyMOL (or C:\Program Files\PyMOL\PyMOL). You can
launch PyMOL from the applications menu or from the icon on your desktop (if
you placed one there).

===== Change coordinates by mouse =====
  * Click "Mouse Mode" until you see "3-Button Editing", and then use mouse following the instruction [[https://stackoverflow.com/questions/19958043/change-dihedral-angles-using-the-mouse-in-pymol | Ref]]
    * Shift + left click to rotate
    * Shift + middle click to translate
  * Ctrl + right click on a bond to show dihedral angle
  * Ctrl + left click and drag to change dihedral angle

===== Electrostatic surface =====
  * [[http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-pymol#TOC-Performing-the-electrostatics-calcu | Using APBS]]
  * [[http://kpwu.wordpress.com/2011/04/12/pymol-electrostaic-surface-view/ | Using Delphi]]

===== Change number of threads =====
  * http://biology.stackexchange.com/questions/2088/turn-off-multithreading-in-pymol

===== RNA/DNA representation =====
  * http://kpwu.wordpress.com/2012/05/24/pymol-different-colors-of-nucleic-acid-rings/
  * http://kpwu.wordpress.com/2011/07/26/pymol-example-of-dna/
  * http://kpwu.wordpress.com/2011/07/28/pymol-dna-example-ii/
  * http://www.pymolwiki.org/index.php/Examples_of_nucleic_acid_cartoons
  * Example:
<code>
set orthoscopic, on
bg_color white
set cartoon_ring_mode, 1
set cartoon_ring_transparency, 0.3
set cartoon_ring_color, green
color green
viewport 480, 480
ray
</code>

===== Make a movie =====
  * http://pelican.rsvs.ulaval.ca/mediawiki/index.php/PyMOL_tips_and_tricks
  * Make a animation for rotating a molecule
<code>
cmd.movie.add_roll(2.0, axis='y', start=1)
set ray_trace_frames, 1
mpng snapshot/mov

# after that you can convert the snapshots into animation under Linux by
# convert -delay 20 snapshot/*.png out.gif
</code>
====== Installation ======
===== From compiled package =====
  * Unpack it and run ./setup.sh
  * copy the created "pymol" to /home/usr/bin

===== From source =====
  * http://blog.163.com/cmh_lj/blog/static/10081230420117431119912/
====== Tutorial ======
  * http://pymol.sourceforge.net/newman/user/S0220commands.html
  * https://pymolwiki.org/index.php/Selection_Algebra
  * [[http://www.pymolwiki.org | pymol wiki]]
  * [[http://pymol.sourceforge.net/newman/user/toc.html | obsolete]]
  * http://www.ucl.ac.uk/~rmhasek/pymol.html
  * http://www.chem.umass.edu/~jhardy/BMS2006Files/pymol%20morphing/
  * http://www.csb.yale.edu/userguides/graphics/pymol/electro.html
  * http://www-cryst.bioc.cam.ac.uk/members/zbyszek/figures_pymol#move
  * http://www.pymolwiki.org/index.php/Displaying_Biochemical_Properties#Polar_surface_area
  * http://pymol.sourceforge.net/newman/user/S0220commands.html