drawing a symmetry axis
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
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@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@cgl.ucsf.edu> An: Philip Wurm <jpw1@gmx.de> CC: chimera-users@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@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Psssst! Schon vom neuen GMX MultiMessenger gehört? Der kann`s mit allen: http://www.gmx.net/de/go/multimessenger
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@cgl.ucsf.edu> An: Philip Wurm <jpw1@gmx.de> CC: chimera-users@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@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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