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.
Creating pymolrc files is a convenient way of loading individualized settings.
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
Multiple pymolrc files
PyMOL will even load multiple pymolrc files, however only either with dot or without dot, and only from the same directory.
You can have multiple scripts: e.g. pymolrc-settings.pml and pymolrc-misc.pml in your home directory.
- pymolrc-settings.pml can e.g. be used to define 'permanent' custom Settings that you rarely change
- pymolrc-misc.pml can e.g. be used to define more transient custom Settings, such as Working Directory or Fetch Path
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