[Chimera-users] gromacs trajectory - only atoms, no bonds

[Eric Pettersen]

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 at 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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