Pymolrc

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:
  • current working directory
  • $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

• save_settings
• Launching PyMOL