[Chimera-users] Scripting to write / save multiple models into single pdb file

Eric Pettersen 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')
>    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 Pettersen
                         UCSF Computer Graphics Lab

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