[Chimera-users] netCDF trajectories?

Eric Pettersen pett at cgl.ucsf.edu
Wed Nov 24 15:48:50 PST 2004

Hi Frank,
	I've added MMTK/NetCDF support to Chimera now.  That will teach me not  
to say that something "looks simple" :-).  MMTK is fairly well  
structured, but its extensive use of subclasses and "mix-in" classes  
makes it really hard to tell from the documentation what  
attributes/methods each class supports.  "dir()" was really my friend  
	Anyway, the support will be in our snapshot which should be out at the  
end of next week.  There will also be a new tool for seeing RMSD  
differences in a trajectory.

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

On Nov 22, 2004, at 5:22 PM, John R. Frank wrote:

>>> Based on this posting, I deduce that Chimera's Movie capability  
>>> cannot
>>> yet display netCDF trajectories:
>>> http://www.cgl.ucsf.edu/pipermail/chimera-users/2004-June/000171.html
>>> MMTK generates netCDF trajectories.  Can you recommend any
>>> already-built tools for converting them to multi-model PDBs?  Or,
>>> perhaps you can direct me to the parts of Chimera where I could help
>>> add netCDF trajectory support?
>> 	Your deduction is correct.  DCD support is in there but not
>> netCDF.  Given MMTK's fairly clean layout of its trajectory info, I
>> think it would be faster for me to add the support than guiding you in
>> adding it.  Just FYI, it's not reasonably straightforward to add a new
>> format and outside people have done it, but in this particular case I
>> should just do it (unless you anticipate wanting yet more formats, in
>> which case I _should_ show you how).
>> 	What I would definitely need is an example trajectory or two.
>> Can you provide such?
> Tom,  attached is a simple .nc trajectory generated from this example  
> code
> provided on the MMTK Web site:
> http://starship.python.net/crew/hinsen/MMTK/Manual/Examples/ 
> Trajectories/snapshot.py.html
> You can regenerate this yourself by installing MMTK and running the  
> python
> on that page.  Here's where to get MMTK:
> http://starship.python.net/crew/hinsen/MMTK/download.html
> Other examples are listed here:
> http://starship.python.net/crew/hinsen/MMTK/examples.html
> Thanks!  Let me know what else I can do to help.
> Yours, John
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