Hi, I tried what you have asked for and could not find the way to do it if you run the script from pymol. What I found is you can first ask for user's input and hen download the pdb file and then launch pymol in python with subprocess and load the pdb file. Here are two solutions for this: one with urllib, another one with Biopython. Hope this can help.

1. with urllib

import os

import subprocess

from six.moves import urllib

import pymol

# get pdb code from user

pdb_code = str(input('Please input your pdb code: '))

# download pdb file from PDB and save to local

#with urllib.request.urlopen('http://files.rcsb.org/download/{}.pdb'.format(pdb_code)) as fullurl:

#content = fullurl.read().decode("utf-8")

result = urllib.request.urlopen('http://files.rcsb.org/download/{}.pdb'.format(pdb_code)).read().decode("utf-8")

output = open('/home/jianyu/Desktop/{}.pdb'.format(pdb_code), 'w')

output.write(result)

output.close()

# launch pymol and load the downloaded file

pdb_file_path='/home/jianyu/Desktop/{}.pdb'.format(pdb_code)

bashCommand = 'pymol {}'.format(pdb_file_path)

stderr, stdout = subprocess.Popen(bashCommand, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()

2. with biopython

import os

import subprocess

import pymol

import Bio

from Bio.PDB import PDBList

# getting input from user

pdb_code = input('Please input your pdb code: ')

# download pdb file

pdbl = PDBList()

PDBlist2=[pdb_code]

for i in PDBlist2:

pdbl.retrieve_pdb_file(i,pdir='/home/jianyu/Desktop/PDB')

# launch pymol and load pdb file

pdb_file_path='/home/jianyu/Desktop/PDB/{}.cif'.format(pdb_code)

bashCommand = 'pymol {}'.format(pdb_file_path)

stderr, stdout = subprocess.Popen(bashCommand, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()