Script Tutorial

Introduction

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. You can even use the Python API to write programs in other languages and then send the results back into PyMOL (this is what cealign does). The PyMOLWiki has a rather extensive script_library full of useful scripts (feel free to add your own).

General Scripts

Scripting follows a simple recipe, in PyMOL.

To write them:

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

   cmd.extend(doSimpleThing,doSimpleThing)
   

To use them:

1. simply import the script into PyMOL:

   run /home/userName/path/toscript/pyProgram.py
   

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.alphaCabons = []

    # 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.
cmd.alter_state(1,objName,"(x,y,z)=stored.alphaCarbons.pop(0)")

Advanced Scripts

Example

See the source code for cealign.

See Also

stored, iterate_state, identify.