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

Eric Pettersen pett at cgl.ucsf.edu
Tue Mar 9 11:16:56 PST 2010

Hmm, it seems that you have the Model Panel set to autostart in your  
preferences.  Now, Chimera probably should ignore autostarting tools  
when it is in nogui mode, but currently it doesn't.  So what you will  
have to do for now (until we fix this) is to start Chimera normally,  
turn off the autostart of the Model Panel (and any other graphical  
tools probably), save the new preferences, and then run your script.

If you look in the "Preferences" preference category, it will show the  
location of the preferences file.  You could squirrel away your  
original preferences file somewhere, make the version with no  
autostarting, copy that somewhere, and then put your original version  
back.  You would then be able to use the no-autostarting preferences  
by specifying it's location with the --preferences startup option.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Mar 8, 2010, at 7:32 PM, Sumitro Harjanto wrote:

> Hi Eric,
> Thanks for the suggestion. I don’t really script, I usually use a c+ 
> + code / excel to generate the command (.cmd) files. Should be okay  
> for the automation for now, if I run into any problem then I will  
> post it up here again. =]
> Mean while I try running the command “chimera.exe –nogui” in PATH/ 
> chimera/bin but got the following error message. I followed the  
> instruction and copy over the debug message (below). any advise? I’m  
> on a win7 X86 platform btw.
> Thanks,
> Sumitro
> -----------------------------------------------------------------------------------------------------
> Chimera failed abnormally; the exit code was: 1
> Use –debug command line option for the full error message.
> --------------------------------------------------------------------------------------------------
> Cannot execute 'gzip': no automatic decompression of .Z files
> Traceback (most recent call last):
>   File "E:\Chimera\share\__main__.py", line 65, in <module>
>     value = chimeraInit.init(sys.argv)
>   File "E:\Chimera\share\chimeraInit.py", line 401, in init
>     extension.startup(startExtensions)
>   File "E:\Chimera\share\chimera\extension\base.py", line 1056, in  
> startup
>     manager.autostartTools(extNames)
>   File "E:\Chimera\share\chimera\extension\base.py", line 959, in  
> autostartTools
>     emo.activate()
>   File "E:\Chimera\share\ModelPanel\ChimeraExtension.py", line 23,  
> in activate
>     display(self.module('base').ModelPanel.name)
>   File "E:\Chimera\share\chimera\dialogs.py", line 77, in display
>     dialog = find(name, create=1)
>   File "E:\Chimera\share\chimera\dialogs.py", line 62, in find
>     return d()
>   File "E:\Chimera\share\chimera\baseDialog.py", line 523, in __init__
>     BaseDialog.__init__(self, master, *args, **kw)
>   File "E:\Chimera\share\chimera\baseDialog.py", line 244, in __init__
>     self.fillInUI(self.__top)
>   File "E:\Chimera\share\ModelPanel\base.py", line 217, in fillInUI
>     self._addColumns()
>   File "E:\Chimera\share\ModelPanel\base.py", line 436, in _addColumns
>     self._buildTable()
>   File "E:\Chimera\share\ModelPanel\base.py", line 454, in _buildTable
>     % len(filter(lambda s: s == 1, self.shownColumns)))
>   File "E:\Chimera\bin\Lib\lib-tk\Tix.py", line 1306, in __init__
>     cnf, kw)
>   File "E:\Chimera\bin\Lib\lib-tk\Tix.py", line 307, in __init__
>     self.tk.call(widgetName, self._w, *extra)
> _tkinter.TclError: invalid command name "tixScrolledHList"
> Return code: 1
> Press return or enter to to exit

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