[Chimera-users] Movie trajectory/restart header greater than 80

Francesco Pietra chiendarret at gmail.com
Sat Aug 23 01:35:34 PDT 2014


Hallo:
I am trying to replay some old movie of molecular dynamics trajectories
(Amber prmtop/dcd). At that time (a couple of years ago I had Chimera of
those times) I get the following error message

IOError: Trajectory/Restart header line is greater than 80 characters --
invalid!

File
"/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py", line
354, in SetupFrame

raise IOError, "Trajectory/Restart header line is greater than 80
characters -- invalid!

See reply log for Python traceback.

The latter reads:
<type 'exceptions.IOError'> Exception in Tk callback
  Function: <function command at 0x315ccf8> (type: <type 'function'>)
  Args: ()
Traceback (innermost last):
  File
"/opt/UCSF/Chimera64-1.7/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py",
line 1747, in __call__
    return apply(self.func, args)
  File "/opt/UCSF/Chimera64-1.7/share/chimera/baseDialog.py", line 449, in
command
    getattr(s, buttonFuncName(txt))()
  File "/opt/UCSF/Chimera64-1.7/share/chimera/baseDialog.py", line 704, in
OK
    self.Apply()
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/EnsembleLoader.py", line
92, in Apply
    self.callback)
  File
"/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/__init__.py", line
60, in loadEnsemble
    callback)
  File
"/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/__init__.py", line
73, in loadEnsemble
    ensemble = Prmtop_Traj(prmtop, trajectory, startFrame, endFrame)
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py",
line 191, in __init__
    self.trajectory.addFile(trajectory)
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/__init__.py", line 183, in
addFile
    self.trajs.append(self.addFunc(trajFile))
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py",
line 190, in <lambda>
    lambda f: Trajectory(self.prmtop, f))
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py",
line 264, in __init__
    self.SetupFrame()
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py",
line 354, in SetupFrame
    raise IOError, "Trajectory/Restart header line is greater than 80
characters -- invalid!!"
<type 'exceptions.IOError'>: Trajectory/Restart header line is greater than
80 characters -- invalid!!

IOError: Trajectory/Restart header line is greater than 80 characters --
invalid!!

  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py",
line 354, in SetupFrame
    raise IOError, "Trajectory/Restart header line is greater than 80
characters -- invalid!!"

See reply log for Python traceback.


<type 'exceptions.IOError'> Exception in Tk callback
  Function: <function command at 0x4732230> (type: <type 'function'>)
  Args: ()
Traceback (innermost last):
  File
"/opt/UCSF/Chimera64-1.7/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py",
line 1747, in __call__
    return apply(self.func, args)
  File "/opt/UCSF/Chimera64-1.7/share/chimera/baseDialog.py", line 449, in
command
    getattr(s, buttonFuncName(txt))()
  File "/opt/UCSF/Chimera64-1.7/share/chimera/baseDialog.py", line 704, in
OK
    self.Apply()
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/EnsembleLoader.py", line
92, in Apply
    self.callback)
  File
"/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/__init__.py", line
60, in loadEnsemble
    callback)
  File
"/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/__init__.py", line
73, in loadEnsemble
    ensemble = Prmtop_Traj(prmtop, trajectory, startFrame, endFrame)
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py",
line 191, in __init__
    self.trajectory.addFile(trajectory)
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/__init__.py", line 183, in
addFile
    self.trajs.append(self.addFunc(trajFile))
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py",
line 190, in <lambda>
    lambda f: Trajectory(self.prmtop, f))
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py",
line 264, in __init__
    self.SetupFrame()
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py",
line 354, in SetupFrame
    raise IOError, "Trajectory/Restart header line is greater than 80
characters -- invalid!!"
<type 'exceptions.IOError'>: Trajectory/Restart header line is greater than
80 characters -- invalid!!

IOError: Trajectory/Restart header line is greater than 80 characters --
invalid!!

  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py",
line 354, in SetupFrame
    raise IOError, "Trajectory/Restart header line is greater than 80
characters -- invalid!!"

See reply log for Python traceback.


<type 'exceptions.IOError'> Exception in Tk callback
  Function: <function command at 0x4632758> (type: <type 'function'>)
  Args: ()
Traceback (innermost last):
  File
"/opt/UCSF/Chimera64-1.7/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py",
line 1747, in __call__
    return apply(self.func, args)
  File "/opt/UCSF/Chimera64-1.7/share/chimera/baseDialog.py", line 449, in
command
    getattr(s, buttonFuncName(txt))()
  File "/opt/UCSF/Chimera64-1.7/share/chimera/baseDialog.py", line 704, in
OK
    self.Apply()
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/EnsembleLoader.py", line
92, in Apply
    self.callback)
  File
"/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/__init__.py", line
60, in loadEnsemble
    callback)
  File
"/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/__init__.py", line
73, in loadEnsemble
    ensemble = Prmtop_Traj(prmtop, trajectory, startFrame, endFrame)
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py",
line 191, in __init__
    self.trajectory.addFile(trajectory)
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/__init__.py", line 183, in
addFile
    self.trajs.append(self.addFunc(trajFile))
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py",
line 190, in <lambda>
    lambda f: Trajectory(self.prmtop, f))
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py",
line 264, in __init__
    self.SetupFrame()
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py",
line 354, in SetupFrame
    raise IOError, "Trajectory/Restart header line is greater than 80
characters -- invalid!!"
<type 'exceptions.IOError'>: Trajectory/Restart header line is greater than
80 characters -- invalid!!

IOError: Trajectory/Restart header line is greater than 80 characters --
invalid!!

  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py",
line 354, in SetupFrame
    raise IOError, "Trajectory/Restart header line is greater than 80
characters -- invalid!!"

See reply log for Python traceback.


<type 'exceptions.IOError'> Exception in Tk callback
  Function: <function command at 0x3bd6500> (type: <type 'function'>)
  Args: ()
Traceback (innermost last):
  File
"/opt/UCSF/Chimera64-1.7/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py",
line 1747, in __call__
    return apply(self.func, args)
  File "/opt/UCSF/Chimera64-1.7/share/chimera/baseDialog.py", line 449, in
command
    getattr(s, buttonFuncName(txt))()
  File "/opt/UCSF/Chimera64-1.7/share/chimera/baseDialog.py", line 704, in
OK
    self.Apply()
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/EnsembleLoader.py", line
92, in Apply
    self.callback)
  File
"/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/__init__.py", line
60, in loadEnsemble
    callback)
  File
"/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/__init__.py", line
73, in loadEnsemble
    ensemble = Prmtop_Traj(prmtop, trajectory, startFrame, endFrame)
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py",
line 191, in __init__
    self.trajectory.addFile(trajectory)
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/__init__.py", line 183, in
addFile
    self.trajs.append(self.addFunc(trajFile))
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py",
line 190, in <lambda>
    lambda f: Trajectory(self.prmtop, f))
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py",
line 264, in __init__
    self.SetupFrame()
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py",
line 354, in SetupFrame
    raise IOError, "Trajectory/Restart header line is greater than 80
characters -- invalid!!"
<type 'exceptions.IOError'>: Trajectory/Restart header line is greater than
80 characters -- invalid!!

IOError: Trajectory/Restart header line is greater than 80 characters --
invalid!!

  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py",
line 354, in SetupFrame
    raise IOError, "Trajectory/Restart header line is greater than 80
characters -- invalid!!"

See reply log for Python traceback.


<type 'exceptions.IOError'> Exception in Tk callback
  Function: <function command at 0x46cb488> (type: <type 'function'>)
  Args: ()
Traceback (innermost last):
  File
"/opt/UCSF/Chimera64-1.7/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py",
line 1747, in __call__
    return apply(self.func, args)
  File "/opt/UCSF/Chimera64-1.7/share/chimera/baseDialog.py", line 449, in
command
    getattr(s, buttonFuncName(txt))()
  File "/opt/UCSF/Chimera64-1.7/share/chimera/baseDialog.py", line 704, in
OK
    self.Apply()
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/EnsembleLoader.py", line
92, in Apply
    self.callback)
  File
"/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/__init__.py", line
60, in loadEnsemble
    callback)
  File
"/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/__init__.py", line
73, in loadEnsemble
    ensemble = Prmtop_Traj(prmtop, trajectory, startFrame, endFrame)
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py",
line 191, in __init__
    self.trajectory.addFile(trajectory)
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/__init__.py", line 183, in
addFile
    self.trajs.append(self.addFunc(trajFile))
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py",
line 190, in <lambda>
    lambda f: Trajectory(self.prmtop, f))
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py",
line 264, in __init__
    self.SetupFrame()
  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py",
line 354, in SetupFrame
    raise IOError, "Trajectory/Restart header line is greater than 80
characters -- invalid!!"
<type 'exceptions.IOError'>: Trajectory/Restart header line is greater than
80 characters -- invalid!!

IOError: Trajectory/Restart header line is greater than 80 characters --
invalid!!

  File "/opt/UCSF/Chimera64-1.7/share/Trajectory/formats/Amber/Amber.py",
line 354, in SetupFrame
    raise IOError, "Trajectory/Restart header line is greater than 80
characters -- invalid!!"

See reply log for Python traceback.




Thanks for advice as to reply those movies

francesco pietra
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