[Chimera-users] drawing a symmetry axis

[Philip]

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

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