Launching PyMOL

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PyMOL can be started from the command line or from a Python script. Also, PyMOL has lots of command line options that one can pass in to affect PyMOL's behavior. For example, one can load a few proteins and even execute a script all from the commandline. Also, there's a .pymolrc file that initializes PyMOL each time PyMOL is executed.

Invoking PyMOL and reading startup commands from a file


Assuming the executable is in your $PATH, simply issue


together with any Command_Line_Options and arguments (pdb files, pse files, map files and so forth) you require.

Whenever PyMol starts, a user-created '~/.pymolrc' file containing commands is run. All you need to do is create ".pymolrc" and place it in your home directory. Alternatively, you can instead create "" which contains actual Python code instead of just PyMOL commands. See an example .pymolrc).


On Windows, use 'pymolrc', '' 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).

Alternatively, if you want to change the default directory for data, you can just put the path to the new default directory in the "Start In" field of the "shortcut link" that is used to launch Pymol. To do this, right click on the "shortcut link" that is used to launch Pymol, click on "Properties" and then, in the "Start In" field, type in the path to the new default data directory. Then click "OK" and the changes are complete.



  • Double-click the application's icon
  • Issue the unix command
    open -a MacPyMOL
  • Directly invoking the unix executable
  • If MacPyMOL is set as the default application to open pdb, pse and other such files, double-clicking any of those files (or issuing the unix open command) will start also pymol and load the file you clicked on.

The third one assumes the application has been placed in /Applications, so adjust the absolute path if you have it elsewhere. If you directly invoke the unix executable to launch pymol, it has the advantage that you can pass Command_Line_Options and arguments to it in the usual way. You might wish to make an alias:

alias pymol=/Applications/Xtal/

(leave out the equal sign for tcsh) or symbolic link

sudo ln -s /Applications/Xtal/ /usr/local/bin/pymol

or use this shell script I wrote: pymol shell script (and zsh function) to invoke pymol on the command line. It uses OS X 10.4's mdfind to locate the executable.


MacPyMOL can also be run from within IDLE. Make sure you use Fink's IDLE, not Mac IDLE:

which idle2.5     # should return the following
/sw/bin/idle2.5   # Fink's IDLE.

Reading the pymolrc file

In each case, PyMol will read the contents of the user's ~/.pymolrc file and/or ~/ file (as with Linux). Here is one example of a MacOSX-specific .pymolrc file with a script enabling interaction via the PowerMate Dial. A couple of simple lines to put in your .pymolrc might be to respectively change to your favorite directory and increase the window size:

cd ~/Documents/structures/
viewport 750,750

Launching PyMOL from an external application

If PYMOL_PATH, LD_LIBRARY_PATH, and TCL_LIBRARY are correctly defined, then you can launch PyMOL from an external Python program as shown in examples/devel/ nb.: This approach is not recommended, since the PyMOL launching process is subject to change without warning. The recommended approach is to just use PyMOL as your python interpreter:

pymol -r <>
pymol -qcr <>

Running PyMOL in batch mode

To perform PyMOL commands from stdin (file, pipe) without opening an OpenGL window use the following Command_Line_Options:

pymol -cq

Suppressing PyMOL output

To suppress most of PyMOL's normal chatter, just type on the PyMOL command line:

feedback disable,all,actions
feedback disable,all,results

or, from Python (API):"disable","all","actions")"disable","all","results")

Launching Python scripts

Running a Python script from PyMOL, usually the command:


Is enough. Of course, the file needs to be in the working directory. For more detailed examples, see the commands to launch Python scripts when starting PyMOL. Asynchronous means, that a new Python thread is started:

pymol     # synchronous, in PyMOL module
pymol -r  # synchronous in __main__ module
pymol -l  # asychronous in a new module

You can also launch python programs from within PyMOL with the commands:

run        # synchronous in pymol module
run,main   # synchronous in __main__ module

spawn        # asychronous in a new module
spawn,global # asychronous in the PyMOL module
spawn,main   # asychronous in the __main__ module

Overwriting Default Settings

If you don't like the cartoon default color and want to change default settings for it, from green to slate, you add the command line to do this in $HOME/.pymolrc. Here, 'set cartoon_color, slate'

Windows users can do this with a pymolrc file.