Moo!, The .tpr file format is basically undocumented, so it's possible that I've done something wrong somewhere in my code that reads it. Nonetheless, every trajectory I have access to works correctly (bonds show up). Could you send me your .tpr file? It would also be nice if you could send a corresponding .trr file with a frame or two of your trajectory so I can verify that everything looks okay when I'm done, but it's not strictly necessary if it's hard for you to make one. It has been suggested that I support allowing the use of .gro files instead of .tpr files. WIth a .gro file I would have to guesstimate connectivity and chemical elements, but in some cases (possibly this one for instance) it may be preferable. --Eric Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu On Apr 16, 2007, at 1:29 AM, Moo Cow wrote:
I believe one has to have a very recent chimera in order to be able to read gromacs trajectories. I have "beta version 1 build 2376 2007/04/11
It is terrific that chimera can read the trajectories (without problem), but it then does not seem to join the atoms with bonds (it certainly does so for normal pdb files). My trajectory is displayed as a set of lonely unbonded atoms.
I believe I checked for obvious mistakes on my part. I went to the tutorial, found the lines repr stick and so on. They gave no error message, but did not help. Many thanks for any advice.
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