[Chimera-users] drawing a symmetry axis

[Tom Goddard]

Hi Philip,

  Indentation of lines is important in Python.  All the lines except the 
ones with "#" in front (which are not executed) have to be indented by 
the same amount.

    Tom


Philip wrote:
> Hi Tom,
> thanks for your answer. I modified the file, but unfortunately it does not work. I get this error, when i execute "ac ai":
>
>
> <type 'exceptions.IndentationError'> Exception in Tk callback
>   Function: <bound method MidasUI.processCommand of <Midas.midas_ui.MidasUI instance at 0x0A805670>> (type: <type 'instancemethod'>)
>   Args: (<Tkinter.Event instance at 0x042A2EE0>,)
>   Event type: KeyPress (type num: 2)
> Traceback (innermost last):
>   File "D:\programme\Chimera\bin\lib\site-packages\Pmw\Pmw_1_3\lib\PmwBase.py", line 1747, in __call__
>     return apply(self.func, args)
>   File "D:\programme\Chimera\share\Midas\midas_ui.py", line 247, in processCommand
>     midas_text.makeCommand(text)
>   File "D:\programme\Chimera\share\Midas\midas_text.py", line 62, in makeCommand
>     f(c, args)
>   File "D:\programme\Chimera\share\Accelerators\ChimeraExtension.py", line 25, in accel_cmd
>     accelerator_command(cmdname, args)
>   File "D:\programme\Chimera\share\Accelerators\__init__.py", line 160, in accelerator_command
>     d.accelerator_command(cmdname, args)
>   File "D:\programme\Chimera\share\Accelerators\gui.py", line 169, in accelerator_command
>     a.invoke()
>   File "D:\programme\Chimera\share\Accelerators\__init__.py", line 19, in invoke
>     self.function()
>   File "D:\programme\Chimera\share\Accelerators\standard_accelerators.py", line 213, in illustrate_alignment
>     import MatchDomains
> <type 'exceptions.IndentationError'>: unexpected indent (__init__.py, line 183)
>
> ================================================
>   Event contents:
>     char: 
>
>     delta: 13
>     height: ??
>     keycode: 13
>     keysym: Return
>     keysym_num: 65293
>     num: ??
>     serial: 3506
>     state: 8
>     time: 144097452
>     type: 2
>     widget: .92813112.176183536.176196984.177090688.177090928
>     width: ??
>     x: -28
>     x_root: 652
>     y: 18
>     y_root: 681
>
> Maybe this helps to find the problem.
>
> Philip
>
>
>
>
>
> -------- Original-Nachricht --------
>   
>> Datum: Thu, 11 Dec 2008 16:49:56 -0800
>> Von: Thomas Goddard <goddard at cgl.ucsf.edu>
>> An: Philip Wurm <jpw1 at gmx.de>
>> CC: chimera-users at cgl.ucsf.edu
>> Betreff: Re: [Chimera-users] drawing a symmetry axis
>>     
>
>   
>> Hi Philip,
>>
>>    I don't know an easy way to show the symmetry axis of your dimer as a 
>> line or rod using the normal Chimera commands.  But you could do this by 
>> modifying the keyboard shortcut ai Python code.
>>
>>    You would edit the file
>>
>> 	chimera/share/MatchDomains/__init__.py
>>
>> or on the Mac it would be
>>
>> 	Chimera.app/Contents/Resources/share/MatchDomains/__init__.py
>>
>> (and on the Mac you'd need to click the Chimera icon and choose "Show 
>> package contents" to see in the Chimera.app folder).
>>
>>    You would change the transform_schematic() routine (line 171) code from
>>
>> #    tarray = ((0,1,2),(0,2,3))
>>      tarray = ((0,1,2),(0,2,3),(0,1,5),(0,5,4),(1,2,6),(1,6,5),
>>                (2,3,7),(2,7,6),(3,0,4),(3,4,7),(4,5,6),(4,6,7))
>>      g1 = sm.addPiece(varray, tarray, from_rgba)
>> #    g1.displayStyle = g1.Mesh
>>
>>      from Matrix import xform_matrix, apply_matrix
>>      tf = xform_matrix(xform)
>>      corners2 = [apply_matrix(tf, p) for p in corners]
>>      varray2 = corners2
>>      g2 = sm.addPiece(varray2, tarray, to_rgba)
>> #    g2.displayStyle = g2.Mesh
>>
>>
>> to
>>
>> #    tarray = ((0,1,2),(0,2,3))
>>      tarray = ((0,1,1),)
>> #    tarray = ((0,1,2),(0,2,3),(0,1,5),(0,5,4),(1,2,6),(1,6,5),
>> #              (2,3,7),(2,7,6),(3,0,4),(3,4,7),(4,5,6),(4,6,7))
>>      g1 = sm.addPiece(varray, tarray, from_rgba)
>>      g1.displayStyle = g1.Mesh
>>      g1.lineThickness = 3
>>
>>      from Matrix import xform_matrix, apply_matrix
>>      tf = xform_matrix(xform)
>>      corners2 = [apply_matrix(tf, p) for p in corners]
>>      varray2 = corners2
>> #    g2 = sm.addPiece(varray2, tarray, to_rgba)
>> #    g2.displayStyle = g2.Mesh
>>
>> Then restart Chimera and use the script you referred to.  It will draw a 
>> line for the axis with width 3 pixels.  In the future we will try to add 
>> some simpler capability to find and show symmetry axes.
>>
>> 	Tom
>>
>>
>> Philip Wurm wrote:
>>     
>>> Hi,
>>> i have a protein dimer and i would like to show the symmetry axis. I 
>>> found a script in this mailing list:
>>>
>>> http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-October/003140.html
>>>
>>> which works quite nice. But i would like to have a nicer representation 
>>> of my symmetry axis, not this two slabs. Just a line or thin rod would 
>>> be nice.
>>>
>>> Does anyone know how to do this?
>>>
>>> Thanks,
>>> Philip
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>>       
>
>