Hi all, I'd like to execute pymol like: pymol -c script.py arg1 arg2 arg3 arg4.
(1) Reading into PyMolWiki http://www.pymolwiki.org/index.php/Scripting, I've learned that I have to type: pymol -c script.py -- arg1 arg2 arg3 arg4 and then add to my script: from sys import argv my_argv =3D argv[argv.index("--"):] print my_argv[1], my_argv[2] But it doesn work! "Traceback (most recent call last): File "/home/campa/SOFTWARE/pymol/modules/pymol/parser.py", line 285, in parse parsing.run_file(exp_path(args[nest][0]),pymol_names,pymol_names) File "/home/campa/SOFTWARE/pymol/modules/pymol/parsing.py", line 407, in run_file execfile(file,global_ns,local_ns) File "rotamermod3.py", line 45 my_argv =3D argv[argv.index("--"):] ^ SyntaxError: invalid syntax" (2) Then I found an alternatively procedure http://sourceforge.net/mailarchive/message.php?msg_id=e4c539ed0708011206nf6dc1a1r257f7311f42aa59e%40mail.gmail.com Identical command: pymol -c script.py -- arg1 arg2 arg3 arg4 But I have to add into my script.py the following: argv = sys.argv[sys.argv.index('--') + 1:] options,args = parser.parse_args(args=argv) But it doesn't work neither: AttributeError: 'module' object has no attribute 'argv' Can someone give a light in how to call arguments in pymol -c script.py? Thanks a lot, Josep Maria Campanera,
