Practical Pymol for Beginners - Revision history

Cchem: 1 revision

2017-04-03T02:46:07Z

1 revision

Speleo3: print syntax for python 2+3

2017-03-06T17:05:31Z

print syntax for python 2+3

Bell: 1 revision

2015-12-14T04:40:40Z

1 revision

Tlinnet: /* Learning More... */

2015-11-19T23:39:55Z

Learning More...

Bell: 30 revisions

2014-03-28T03:08:49Z

30 revisions

Jaredsampson: /* The Python MiniShell */ corrected typo, added `tags to commands instead of bold font weight`


2013-11-21T14:19:09Z
The Python MiniShell:  corrected typo, added <code> tags to commands instead of bold font weight

				
				
				
				
				
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				Revision as of 14:19, 21 November 2013
				
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  ====The Python MiniShell ====   ====The Python MiniShell ====
− Taking this one level higher, you can write little code snippets, like 10-20+ lines of code that perform some specific task and wrap these in the '''python''' and '''python end''' commands.  (If your script ever makes a mistake, you can abort the endeavor with '''end''' instead of '''python end'''.  The power here is that none of your command are executed until you type '''python end'''.  Confused?  Here's the above example in using the wrapper: + Taking this one level higher, you can write little code snippets, like 10-20+ lines of code that perform some specific task and wrap these in the <code>python</code> and <code>python end</code> commands.  (If your script ever makes a mistake, you can abort the endeavor with <code>end</code> instead of <code>python end</code>.  The power here is that none of your command are executed until you type <code>python end</code>.  Confused?  Here's the above example in using the wrapper:
  <source lang="python">   <source lang="python">
  python   python
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  python end   python end
  </source>   </source>
− The [[python]] command gives you complete access to the Python shell & '''python end''' just brings you back into PyMOL's shell.  Also, note that PyMOL saves information across instantiations of the '''python''' command.  For example, + The <code>[[python]]</code> command gives you complete access to the Python shell and <code>python end</code> brings you back into PyMOL's shell.  Also, note that PyMOL saves information across instantiations of the <code>python</code> command.  For example,
  <source lang="python">   <source lang="python">
  # enter mini python shell   # enter mini python shell
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  python end   python end
    
− # no we're back in PyMOL; where PyMOL knows about the value + # now we're back in the normal PyMOL shell, where PyMOL knows about the value
  print ff   print ff



Jaredsampson: changed capitalization of PyMOL
2013-11-21T14:03:58Z
changed capitalization of PyMOL

				
				
				
				
				
				← Older revision
				Revision as of 14:03, 21 November 2013
				
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− Although PyMol has a powerful and flexible interface, it is complex, and can appear daunting to new users. This guide is intended to introduce the PyMol interface and basic tasks without leaving the mouse behind.   + Although PyMOL has a powerful and flexible interface, it is complex, and can appear daunting to new users. This guide is intended to introduce the PyMOL interface and basic tasks without leaving the mouse behind.  
    
− ==The PyMol Interface== + ==The PyMOL Interface==
− When PyMol is opened, two windows appear. The smaller window (called the "External GUI" in PyMol documentation) contains the menu bar ('''File''', '''Edit''', '''Help''', '''Display''', etc), shortcut buttons for common commands, and the command line. + When PyMOL is opened, two windows appear. The smaller window (called the "External GUI" in PyMOL documentation) contains the menu bar ('''File''', '''Edit''', '''Help''', '''Display''', etc), shortcut buttons for common commands, and the command line.
    
  [[Image:Viewer_guide.png|right|thumb|The PyMol Viewer Window]]   [[Image:Viewer_guide.png|right|thumb|The PyMol Viewer Window]]
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  ===About the command line===   ===About the command line===
− The PyMol command line is a great tool that lets the experienced user change all sorts of options that simply don't appear in the point-and-click graphical interface. It can also be a lot faster. Combined with scripting, it is a powerful option for automating tasks and making intricate sets of changes. But, it's complex, and page upon page of PyMol documentation cover these commands, so we're going to ignore them as much as possible. + The PyMOL command line is a great tool that lets the experienced user change all sorts of options that simply don't appear in the point-and-click graphical interface. It can also be a lot faster. Combined with scripting, it is a powerful option for automating tasks and making intricate sets of changes. But, it's complex, and page upon page of PyMOL documentation cover these commands, so we're going to ignore them as much as possible.
    
  Although this guide may include some text commands and links to more advanced documentation, they're purely optional and meant to be informative.     Although this guide may include some text commands and links to more advanced documentation, they're purely optional and meant to be informative.  
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  ==Getting started: explore a protein==   ==Getting started: explore a protein==
− PyMol is great for casual visualization of biological molecules. In this example, a PDB file describing a protein is loaded and its style and color are tweaked. + PyMOL is great for casual visualization of biological molecules. In this example, a PDB file describing a protein is loaded and its style and color are tweaked.
    
  [[Image:Kchannel-rainbow.png|thumb|right|The end result will look something like this]]   [[Image:Kchannel-rainbow.png|thumb|right|The end result will look something like this]]
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  ====Sessions====   ====Sessions====
− A PymOL sessions retains the state of your PyMOL instance.  You can save the session to disk and reload it later.  You can setup a complicated scene, with transitions and more, and simply save it as a PyMOL Session (.pse) file.  Use, '''File'''=>'''Save Session''' or '''Save Session As...'''. + A PyMOL sessions retains the state of your PyMOL instance.  You can save the session to disk and reload it later.  You can setup a complicated scene, with transitions and more, and simply save it as a PyMOL Session (.pse) file.  Use, '''File'''=>'''Save Session''' or '''Save Session As...'''.
    
  Loading sessions is just as easy: '''File'''=>'''Load''' and choose your session file.   Loading sessions is just as easy: '''File'''=>'''Load''' and choose your session file.



Tlinnet: /* Introduction and Very Simple Scripting */
2012-06-05T09:16:39Z
Introduction and Very Simple Scripting

				
				
				
				
				
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				Revision as of 09:16, 5 June 2012
				
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  Because of the way PyMOL is built on top of the Python interpreter, any command that PyMOL doesn't recognize it passes on to Python to execute.  This is a '''very''' handy feature--you essentially have a live Python interpreter you can interact with, which makes your life much easier.  Take the following for example:   Because of the way PyMOL is built on top of the Python interpreter, any command that PyMOL doesn't recognize it passes on to Python to execute.  This is a '''very''' handy feature--you essentially have a live Python interpreter you can interact with, which makes your life much easier.  Take the following for example:
− <source lang="python" line="1"> + <source lang="python">
  f = 10.   f = 10.
  for x in range(0,100,10):   for x in range(0,100,10):



Tlinnet: /* The Python MiniShell */
2012-06-05T09:16:27Z
The Python MiniShell

				
				
				
				
				
				← Older revision
				Revision as of 09:16, 5 June 2012
				
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  ====The Python MiniShell ====   ====The Python MiniShell ====
  Taking this one level higher, you can write little code snippets, like 10-20+ lines of code that perform some specific task and wrap these in the '''python''' and '''python end''' commands.  (If your script ever makes a mistake, you can abort the endeavor with '''end''' instead of '''python end'''.  The power here is that none of your command are executed until you type '''python end'''.  Confused?  Here's the above example in using the wrapper:   Taking this one level higher, you can write little code snippets, like 10-20+ lines of code that perform some specific task and wrap these in the '''python''' and '''python end''' commands.  (If your script ever makes a mistake, you can abort the endeavor with '''end''' instead of '''python end'''.  The power here is that none of your command are executed until you type '''python end'''.  Confused?  Here's the above example in using the wrapper:
− <source lang="python" line="1"> + <source lang="python">
  python   python
  f = 10.   f = 10.
Line 130:
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  </source>   </source>
  The [[python]] command gives you complete access to the Python shell & '''python end''' just brings you back into PyMOL's shell.  Also, note that PyMOL saves information across instantiations of the '''python''' command.  For example,   The [[python]] command gives you complete access to the Python shell & '''python end''' just brings you back into PyMOL's shell.  Also, note that PyMOL saves information across instantiations of the '''python''' command.  For example,
− <source lang="python" line="1"> + <source lang="python">
  # enter mini python shell   # enter mini python shell
  python   python



Folf: /* Introduction and Very Simple Scripting */
2009-07-10T10:27:51Z
Introduction and Very Simple Scripting

				
				
				
				
				
				← Older revision
				Revision as of 10:27, 10 July 2009
				
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  Scripting in PyMOL ranges from very simple to very intricate.  You can make a simple loop (say rotating a molecule one-degree at a time) or execute full featured scripts.  Once you've got the basics of PyMOL down, learning scripting will greatly enhance your productivity and capabilities.   Scripting in PyMOL ranges from very simple to very intricate.  You can make a simple loop (say rotating a molecule one-degree at a time) or execute full featured scripts.  Once you've got the basics of PyMOL down, learning scripting will greatly enhance your productivity and capabilities.
    
− Because of the way PyMOL is built on top of the Python interpreter, any command that PyMOL doesn't recognize it passes on to python to execute.  This is a '''very''' handy feature--you essentially have a live Python interpreter you can interact with, which makes your life much easier.  Take the following for example: + Because of the way PyMOL is built on top of the Python interpreter, any command that PyMOL doesn't recognize it passes on to Python to execute.  This is a '''very''' handy feature--you essentially have a live Python interpreter you can interact with, which makes your life much easier.  Take the following for example:
  <source lang="python" line="1">   <source lang="python" line="1">
  f = 10.   f = 10.

@@ Line 147: / Line 147: @@
 ==== Learning More... ====
 To learn more about scripting check out:
 *[[Simple_Scripting]] introduction
 *[[Advanced_Scripting]] pages

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Practical Pymol for Beginners - Revision history

Cchem: 1 revision

Speleo3: print syntax for python 2+3

Bell: 1 revision

Tlinnet: /* Learning More... */

Bell: 30 revisions

Jaredsampson: /* The Python MiniShell */ corrected typo, added tags to commands instead of bold font weight

Jaredsampson: changed capitalization of PyMOL

Tlinnet: /* Introduction and Very Simple Scripting */

Tlinnet: /* The Python MiniShell */

Folf: /* Introduction and Very Simple Scripting */

Jaredsampson: /* The Python MiniShell */ corrected typo, added `tags to commands instead of bold font weight`