Ok Eric, I think you can ignore my last email. I realised I can use “chimera –nogui –debug” to make the chimera command line appear and then I can open my .cmd file from there.

Yes, on Windows there really is no concept of "standard input" and "standard output" so in addition to --nogui you also have to supply --console (or --debug, which implies a console window) in order to see standard output and to supply standard input.  We will try to make it so that --nogui with no script argument will also bring up a console window.

However, the point of my previous mail was that you don't need to type commands.  If you just do this:

chimera --nogui myscript.py

Then Chimera will run "myscript.py" in nogui mode.  You don't need to get a command prompt and type "open myscript.py".

But I realised also I cant save the reply log, which contain the rmsd information I need (my result!! T.T)

 

I found this codet on the chimera mailing list:

def save_reply_log(path):

   from chimera import dialogs

   r = dialogs.find('reply')

   text = r.text.get('1.0', 'end')

   f = open(path, 'w')

   f.write(text)

   f.close()

 

save_reply_log("/tmp/tmplog.txt")

 

but how do I incorporate this into my .cmd..? or must I now script in python..?

There is no reply log in nogui mode.  All the output will come to the console window.  In order to copy from the console window you will need to right-click in the title bar of the console window.

--Eric

                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        http://www.cgl.ucsf.edu