I am making a script that loads in two molecules as arguments in the command line. I want to then align these molecules and make a pretty picture of the molecules that were input as arguments in the comand line but I am not sure how to name them as objects. I don't know how to select the new objects because they will have different names depending on the inputed arguments. My attempt is below.


from sys import argv
my_argv = argv[1:]
print my_argv[0], my_argv[1]

from pymol import cmd, stored 

def align_heme(arg1, arg2 ):
        cmd.create(obj1, arg1)  #I know this line won't work. I need to use the                                            #object name. but it depends on the input.