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When Pymol [[Launching PyMOL|launches]], it will read custom settings and functions from a pymolrc file, if it exists. This is simply a script in PyMOL command syntax or in python syntax, depending on the suffix.
 
When Pymol [[Launching PyMOL|launches]], it will read custom settings and functions from a pymolrc file, if it exists. This is simply a script in PyMOL command syntax or in python syntax, depending on the suffix.
  
The typical location on Windows would be:
+
== Open a pymolrc File for Editing ==
  
C:\Users\YOU\pymolrc.pml
+
On Windows: '''Start > Run''' and then paste
  
and on a Unix/Linux-type system (including Mac OS X):
+
notepad "%HOMEDRIVE%%HOMEPATH%\pymolrc.pml"
  
  /home/YOU/.pymolrc
+
On Unix/Linux-type system (including Mac OS X): Open a terminal and type
 +
 
 +
  nano ~/.pymolrc
  
 
== Technical Details ==
 
== Technical Details ==
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* Several directories are searched, in order:
 
* Several directories are searched, in order:
 
** $HOME
 
** $HOME
** $HOMEPATH + $HOMEDRIVE (on Windows)
+
** $HOMEDRIVE + $HOMEPATH (on Windows)
 
** $PYMOL_PATH
 
** $PYMOL_PATH
 
* PyMOL will even load multiple pymolrc files, however only either with dot or without dot, and only from the same directory. But you could for example have two scripts ''.pymolrc-settings.py'' and ''.pymolrc-misc.py'' in your home directory.
 
* PyMOL will even load multiple pymolrc files, however only either with dot or without dot, and only from the same directory. But you could for example have two scripts ''.pymolrc-settings.py'' and ''.pymolrc-misc.py'' in your home directory.
 +
* You can query which pymolrc files have been loaded:
 +
 +
PyMOL> print invocation.options.deferred
  
 
== Example ==
 
== Example ==
  
 
<source lang="python">
 
<source lang="python">
 +
# simple test: change background color of PyMOL window
 +
bg blue
 +
 
# this will run the script in the specified location
 
# this will run the script in the specified location
 
run /path/to/home/pymol/load_sep.py
 
run /path/to/home/pymol/load_sep.py
  
 +
# your favorite settings
 
set movie_loop, 0
 
set movie_loop, 0
 
set two_sided_lighting, 1
 
set two_sided_lighting, 1
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set stick_radius, 0.3
 
set stick_radius, 0.3
  
# set fetch_path
+
# save fetched PDB files here
 
set fetch_path, /your/fetch/path
 
set fetch_path, /your/fetch/path
  
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cmd.extend("co",color_obj.color_obj)
 
cmd.extend("co",color_obj.color_obj)
 
</source>
 
</source>
 +
 +
== Reload a pymolrc File ==
  
 
To reload a pymolrc file (e.g. after editing .pymolrc, or after running [[reinitialize]]), [[Running Scripts|run it]] like any other script:
 
To reload a pymolrc file (e.g. after editing .pymolrc, or after running [[reinitialize]]), [[Running Scripts|run it]] like any other script:
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[[Category:Launching]]
 
[[Category:Launching]]
 +
[[Category:Scripting]]

Revision as of 12:39, 14 August 2013

When Pymol launches, it will read custom settings and functions from a pymolrc file, if it exists. This is simply a script in PyMOL command syntax or in python syntax, depending on the suffix.

Open a pymolrc File for Editing

On Windows: Start > Run and then paste

notepad "%HOMEDRIVE%%HOMEPATH%\pymolrc.pml"

On Unix/Linux-type system (including Mac OS X): Open a terminal and type

nano ~/.pymolrc

Technical Details

  • The leading dot is optional, so everything that starts with .pymolrc or pymolrc will be found by PyMOL. Files with dot take precedence over files without dot.
  • Files ending on .py (or .pym) will be parsed as python scripts, files ending on .pml or without suffix will be parsed as PyMOL command syntax.
  • Several directories are searched, in order:
    • $HOME
    • $HOMEDRIVE + $HOMEPATH (on Windows)
    • $PYMOL_PATH
  • PyMOL will even load multiple pymolrc files, however only either with dot or without dot, and only from the same directory. But you could for example have two scripts .pymolrc-settings.py and .pymolrc-misc.py in your home directory.
  • You can query which pymolrc files have been loaded:
PyMOL> print invocation.options.deferred

Example

# simple test: change background color of PyMOL window
bg blue

# this will run the script in the specified location
run /path/to/home/pymol/load_sep.py

# your favorite settings
set movie_loop, 0
set two_sided_lighting, 1

set label_size, 60
set label_outline_color, 1
set label_color, 0
set label_position, [0, 0, 10]

# for images:
#   antialias =1 smooths jagged edges, 0 turns it off
set antialias, 1

#   stick_radius -adjust thickness of atomic bonds
set stick_radius, 0.3

# save fetched PDB files here
set fetch_path, /your/fetch/path

# Personal short-cut to color_obj function
import color_obj
cmd.extend("co",color_obj.color_obj)

Reload a pymolrc File

To reload a pymolrc file (e.g. after editing .pymolrc, or after running reinitialize), run it like any other script:

@~/.pymolrc

or

run ~/.pymolrc.py

See Also