[Chimera-users] Scripting to write / save multiple models into single pdb file
pett at cgl.ucsf.edu
Mon Mar 15 14:41:14 PDT 2010
On Mar 12, 2010, at 8:22 PM, Sumitro Harjanto wrote:
> 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
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')
> 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.
UCSF Computer Graphics Lab
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