Oh, I see what your saying. This is a python question.

from sys import argv

c_arg1 = argv[1]
c_arg2 = argv[2]

from pymol import cmd, stored 

def align_heme(arg1, arg2 ):
cmd.load(arg1)
cmd.load(arg2)
        cmd align(arg1,arg2)
#cmd.create(obj1, arg1) #There is no need to create an object here.

align_heme(c_arg1,c_arg2)





On Feb 4, 2014, at 6:57 PM, Yarrow Madrona <amadrona@uci.edu> wrote:

Hello,

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.

-Yarrow
----------------------------------------------------------------------------------------------------------

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.load(arg1)
cmd.load(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.

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