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Simple Scripting

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This page discusses writing your own simple scripts for PyMOL. If you're looking to download scripts try the Script Library.

One of the more powerful features of PyMOL is that it supports Python scripting. That gives you the power of using all the Python libraries, especially the the Python API to write programs in other languages and then send the results back into PyMOL. Some useful extensions to PyMOL can be found in our Script Library.

General Scripts

General PyMOL scripting is done in Python. It's really quite simple, just write your function (following a couple simple rules) and then let PyMOL know about it by using the cmd.extend command. Here's the simple recipe for writing your own simple scripts for PyMOL:

To write them:

  1. Write the function, let's call it doSimpleThing, in a Python file, let's call the file
  2. Add the following command to the end of the file

To use them:

  1. simply import the script into PyMOL:
    run /home/userName/path/toscript/
  2. Then, just type the name of the command: doSimpleThing and pass any needed arguments.

That's it. Your script can, through Python, import any modules you need and also edit modify objects in PyMOL.

Getting PyMOL Data into your Script

To get PyMOL data into your script you will need to somehow get access to the PyMOL objects and pull out the data. For example, if you want the atomic coordinates of a selection of alpha carbon atoms your Python function may do something like this (all PyMOL functions are referenced in the See Also section, below):

# Import PyMOL's stored module.  This will allow us with a 
# way to pull out the PyMOL data and modify it in our script.
# See below.
from pymol import stored

def functionName( userSelection ):
    # this array will be used to hold the coordinates.  It
    # has access to PyMOL objects and, we have access to it.
    stored.alphaCarbons = []

    # let's just get the alpha carbons, so make the
    # selection just for them
    userSelection = userSelection + " and n. CA"

    # iterate over state 1, or the userSelection -- this just means
    # for each item in the selection do what the next parameter says.
    # And, that is to append the (x,y,z) coordinates to the stored.alphaCarbon
    # array.
    cmd.iterate_state(1, selector.process(userSelection), "stored.alphaCarbons.append([x,y,z])")

    # stored.alphaCarbons now has the data you want.

    ... do something to your coordinates ...

Getting Data From your Script into PyMOL

Usually this step is easier. To get your data into PyMOL, it's usually through modifying some object, rotating a molecule, for example. To do that, you can use the alter or alter_state commands. Let's say for example, that we have translated the molecular coordinates from the last example by some vector (we moved the alpha carbons). Now, we want to make the change and see it in PyMOL. To write the coordinates back we do:

# we need to know which PyMOL object to modify.  There could be many molecules and objects
# in the session, and we don't want to ruin them.  The following line, gets the object
# name from PyMOL
objName = cmd.identify(sel2,1)[0][0]

# Now, we alter each (x,y,z) array for the object, by popping out the values
# in stored.alphaCarbons.  PyMOL should now reflect the changed coordinates.


Here's a script I wrote for cealign. It takes two selections of equal length and computes the optimal overlap, and aligns them. See Kabsch for the original code. Because this tutorial is for scripting and not optimal superposition, the original comments have been removed.

def optAlign( sel1, sel2 ):
        @param sel1: First PyMol selection with N-atoms
        @param sel2: Second PyMol selection with N-atoms

        # make the lists for holding coordinates
        # partial lists
        stored.sel1 = []
        stored.sel2 = []
        # full lists
        stored.mol1 = []
        stored.mol2 = []

        # -- CUT HERE
        sel1 = sel1 + " and N. CA"
        sel2 = sel2 + " and N. CA"
        # -- CUT HERE

        # This gets the coordinates from the PyMOL objects
        cmd.iterate_state(1, selector.process(sel1), "stored.sel1.append([x,y,z])")
        cmd.iterate_state(1, selector.process(sel2), "stored.sel2.append([x,y,z])")

        # ...begin math that does stuff to the coordinates...
        mol1 = cmd.identify(sel1,1)[0][0]
        mol2 = cmd.identify(sel2,1)[0][0]
        cmd.iterate_state(1, mol1, "stored.mol1.append([x,y,z])")
        cmd.iterate_state(1, mol2, "stored.mol2.append([x,y,z])")
        assert( len(stored.sel1) == len(stored.sel2))
        L = len(stored.sel1)
        assert( L > 0 )
        COM1 = numpy.sum(stored.sel1,axis=0) / float(L)
        COM2 = numpy.sum(stored.sel2,axis=0) / float(L)
        stored.sel1 = stored.sel1 - COM1
        stored.sel2 = stored.sel2 - COM2
        E0 = numpy.sum( numpy.sum(stored.sel1 * stored.sel1,axis=0),axis=0) + numpy.sum( numpy.sum(stored.sel2 * stored.sel2,axis=0)
        reflect = float(str(float(numpy.linalg.det(V) * numpy.linalg.det(Wt))))
        if reflect == -1.0:
                S[-1] = -S[-1]
                V[:,-1] = -V[:,-1]
        RMSD = E0 - (2.0 * sum(S))
        RMSD = numpy.sqrt(abs(RMSD / L))
        U =, Wt)
        # ...end math that does stuff to the coordinates...

        # update the _array_ of coordinates; not PyMOL the coords in the PyMOL object
        stored.sel2 = - COM2), U) + COM1
        stored.sel2 = stored.sel2.tolist()

        # This updates PyMOL.  It is removing the elements in 
        # stored.sel2 and putting them into the (x,y,z) coordinates
        # of mol2.

        print "RMSD=%f" % RMSD

        cmd.orient(sel1 + " and " + sel2)

# The extend command makes this runnable as a command, from PyMOL.
cmd.extend("optAlign", optAlign)

Basic Script Body

Want an easy block of working code to start your function from? Just copy/paste the following into your Python editor and get going!

# --
from pymol import cmd, stored

def yourFunction( arg1, arg2 ):
    # Your code goes here
    print "Hello, PyMOLers"
    print "You passed in %s and %s" % (arg1, arg2)
    print "I will return them to you in a list.  Here you go."
    return (arg1, arg2)

cmd.extend( "yourFunction", yourFunction );