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

Eric Pettersen pett at cgl.ucsf.edu
Mon Aug 25 11:35:21 PDT 2014


Hi Francseco,
	Firstly, you should use the bug reporter to send these kinds of things rather than sending them to chimera-users, since I doubt anyone else on this list is interested.  Regardless, looking at where this error occurred I can tell you are choosing the wrong format in the MD Movie tool.  You are choosing Amber.  That format expects the coordinates to be native Amber formats, not DCD.  You need to choose the "NAMD (prmtop/DCD)" format in order to show your trajectory.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Aug 23, 2014, at 1:35 AM, Francesco Pietra <chiendarret at gmail.com> wrote:

> 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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