Dear sir: Your suggestions do work well! The problems have been resolved well by your help. Thank you very much! Best Wishes Tao Cui From:Eric Pettersen Date:2011-03-16 05:12 Subject:Re: [chimera-dev] [Chimera-users] error: from DockPrep import prep To:wascm Cc:Greg Couch,chimera-dev BB,UCSF Chimera Mailing List On Mar 15, 2011, at 5:37 AM, wascm wrote: Dear sir: Thanks for the detailed reply! When the following code was added to the start of sciprt: import chimeraInit chimeraInit.init(nogui=True, silent=True) The interpreter print the following confused error: --------------------------------------------- Traceback (most recent call last): File "./xx.py", line 5, in <module> chimeraInit.init(nogui=True, silent=True) TypeError: init() takes at least 1 argument (2 given) There was an oversight in the code Greg provided: chimeraInit.init takes a mandatory "argv" argument, which is exactly like sys.argv. ----------------------------------------------- it's really easy and convenient to running python script with chimera. The reason for i want to run python script independently is that i want add some custom command option. However, if i run python script with chimera, it's hard for me to add some custom command option and handle it in the script though getopt module. For example, when i run some command like this: chimera –nogui test.py -t test test.py ################### #!/usr/bin/python t=None try: opts, args = getopt.getopt(sys.argv[1:], "t:") except getopt.GetoptError, err: pass finally: for arg_k, arg_v in opts: if (arg_k =="-t"): t=arg_v #################################### This will raise running exception! is there a way for me to add the coustom option to python script and run the script with chimera? Yes. Use a --script argument, like this: chimera --nogui --script "test.py -t test" --Eric