<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi Sharada,<DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>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.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>--Eric</DIV><DIV><BR><DIV> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>Eric Pettersen</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>UCSF Computer Graphics Lab</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN><A href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</A></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN><A href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</A></FONT></P> </DIV><BR><DIV><DIV>On Jan 22, 2007, at 9:58 PM, sharada wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite">Dear Chimera-users,<BR> <BR> 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.<BR> 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:<BR><BR><FONT size="4"><SPAN style="font-style: italic;">Unknown molecule type: CL-</SPAN><BR style="font-style: italic;"><SPAN style="font-style: italic;">TypeError: __len__() should return an int</SPAN><BR style="font-style: italic;"><SPAN style="font-style: italic;">(see reply log for Python traceback info)</SPAN><BR style="font-style: italic;"><SPAN style="font-style: italic;">Traceback (most recent call last):</SPAN><BR style="font-style: italic;"><SPAN style="font-style: italic;"> File "/usr/local/chimera/share/__main__.py", line 59, in ?</SPAN><BR style="font-style: italic;"><SPAN style="font-style: italic;"> value = chimeraInit.init(sys.argv)</SPAN><BR style="font-style: italic;"><SPAN style="font-style: italic;"> File "CHIMERA/share/chimeraInit.py", line 318, in init</SPAN><BR style="font-style: italic;"><SPAN style="font-style: italic;"> tkgui.eventLoop()</SPAN><BR style="font-style: italic;"><SPAN style="font-style: italic;"> File "CHIMERA/share/chimera/tkgui.py", line 2675, in eventLoop</SPAN><BR style="font-style: italic;"><SPAN style="font-style: italic;"> File "CHIMERA/lib/python2.4/lib-tk/Tkinter.py", line 965, in mainloop</SPAN><BR style="font-style: italic;"><SPAN style="font-style: italic;"> self.tk.mainloop(n)</SPAN><BR style="font-style: italic;"><SPAN style="font-style: italic;"> File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1751, in __call__</SPAN><BR style="font-style: italic;"><SPAN style="font-style: italic;"> File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1814, in _reporterror</SPAN><BR style="font-style: italic;"><SPAN style="font-style: italic;"> File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1377, in displayerror</SPAN><BR style="font-style: italic;"><SPAN style="font-style: italic;"> File "CHIMERA/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1747, in __call__</SPAN><BR style="font-style: italic;"><SPAN style="font-style: italic;"> File "CHIMERA/share/chimera/baseDialog.py", line 231, in <lambda></SPAN><BR style="font-style: italic;"><SPAN style="font-style: italic;"> File "CHIMERA/share/chimera/baseDialog.py", line 473, in OK</SPAN><BR style="font-style: italic;"><SPAN style="font-style: italic;"> File "CHIMERA/share/Trajectory/EnsembleLoader.py", line 87, in Apply</SPAN><BR style="font-style: italic;"><SPAN style="font-style: italic;"> File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line 56, in loadEnsemble</SPAN><BR style="font-style: italic;"><SPAN style="font-style: italic;"> File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line 67, in loadEnsemble</SPAN><BR style="font-style: italic;"><SPAN style="font-style: italic;"> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 30, in __init__</SPAN><BR style="font-style: italic;"><SPAN style="font-style: italic;"> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 218, in __init__</SPAN><BR style="font-style: italic;"><SPAN style="font-style: italic;"> File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 229, in _readHeader</SPAN><BR style="font-style: italic;"><SPAN style="font-style: italic;"> File "CHIMERA/lib/python2.4/xdrlib.py", line 194, in unpack_fstring</SPAN><BR style="font-style: italic;"><SPAN style="font-style: italic;"> if j > len(self.__buf):</SPAN><BR style="font-style: italic;"><SPAN style="font-style: italic;">TypeError: __len__() should return an int</SPAN></FONT><BR><BR>What exactly is the problem ? How to solve it ?<BR><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Chimera-users mailing list</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users</A></DIV> </BLOCKQUOTE></DIV><BR></DIV></BODY></HTML>