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@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 ? _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users