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

Hi Eric, This has been reported and logged as problem report 3279 in our bug database: "stereo zaps atomspec balloons." However, the initial report was for Windows, so we are glad you are providing this additional helpful information and another nudge to solve the problem. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jan 23, 2007, at 12:09 PM, Eric Dawson wrote:

Hi,

We are using Chimera production release version 1.2304 on Red Hat Linux and SGI. When going from quad-buffered stereo mode to mono, the balloon help as well as atom/bond balloon info is toggled 'off'. This can be re-enabled within the session by toggling the balloon options manually under Preferences, however I don't think this behavior existed in previous versions of Chimera. Alternatively, the balloons can be restored by saving the session and restarting the chimera software.

We use the balloon feature frequently to teach command line selection syntax in our molecular graphics workshops. I wonder if anyone else has encountered this behavior linked to hardware stereo. Thank you for looking into this issue.

Eric

______________________________________________________________________

Eric S. Dawson, Ph.D. CSB Computation, Education & Outreach Research Instructor, Biochemistry Center for Structural Biology (CSB) 5137 MRBIII Vanderbilt University Nashville, TN 37232-8755 Tel: (615)-936-5579 (MRB III) Tel: (615)-322-3303 (5119 SC) Fax: (615)-936-2211

"All that is gold does not glitter, not all those who wander are lost." J.R.R. Tolkien - Fellowship of the Ring _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users