[Chimera-users] Problem loading trajectories ....

[Eric Pettersen]

Hi Sharada,
	I fixed this problem on November 22nd, which means it made it into  
the 1.2318 snapshot release.  Now, that release is only available for  
Linux and Mac but I'm guessing you're using Linux so you should be  
okay if you download it.  If you're using some other platform let me  
know and I'll send you a file with the fix in it that you can drop  
into your Chimera.

--Eric

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

On Jan 22, 2007, at 9:58 PM, sharada wrote:

> Dear Chimera-users,
>
>     Hello, I am a brand new entry into this forum. I  have started  
> using chimera recently. I use Gromacs for my molecular modeling  
> work.  Till I become friendly with chimera I need your valuable  
> suggestions and cooperations. I  request you to kindly  bear with  
> my very silly doubts and questions. Let me explain my problem.
>     I have a protein of 35 residues and have simulated in a box of  
> water for 10ns. My protein has charge so in order to neutralize it  
> I have added counterions randomly placed them in the solvent 
> (water). The  counter ions that I am adding are Cl- ions. I have  
> created a *.trr file of the tracjectory for this 10ns. I would like  
> to visulaize this trajectory using chimera. I am using Tools /MD/ 
> Ensemble Analysis /MD Movie to load the trr file. when I do so I am  
> getting the following error:
>
> Unknown molecule type: CL-
> TypeError: __len__() should return an int
> (see reply log for Python traceback info)
> Traceback (most recent call last):
>   File "/usr/local/chimera/share/__main__.py", line 59, in ?
>     value = chimeraInit.init(sys.argv)
>   File "CHIMERA/share/chimeraInit.py", line 318, in init
>     tkgui.eventLoop()
>   File "CHIMERA/share/chimera/tkgui.py", line 2675, in eventLoop
>   File "CHIMERA/lib/python2.4/lib-tk/Tkinter.py", line 965, in  
> mainloop
>     self.tk.mainloop(n)
>   File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/ 
> PmwBase.py", line 1751, in __call__
>   File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/ 
> PmwBase.py", line 1814, in _reporterror
>   File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/ 
> PmwBase.py", line 1377, in displayerror
>   File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/ 
> PmwBase.py", line 1747, in __call__
>   File "CHIMERA/share/chimera/baseDialog.py", line 231, in <lambda>
>   File "CHIMERA/share/chimera/baseDialog.py", line 473, in OK
>   File "CHIMERA/share/Trajectory/EnsembleLoader.py", line 87, in Apply
>   File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line  
> 56, in loadEnsemble
>   File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line  
> 67, in loadEnsemble
>   File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line  
> 30, in __init__
>   File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line  
> 218, in __init__
>   File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line  
> 229, in _readHeader
>   File "CHIMERA/lib/python2.4/xdrlib.py", line 194, in unpack_fstring
>     if j > len(self.__buf):
> TypeError: __len__() should return an int
>
> What exactly is the problem ? How to solve it ?
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