Tom and other users,
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?
John
-- ___________________________ John R. Frank jrf@mit.edu Physics Graduate Student mobile: 857-928-0614
On Nov 21, 2004, at 1:09 PM, John R. Frank wrote:
Tom and other users,
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?
Hi John, 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?
Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu
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/sna...
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
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 here. 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@cgl.ucsf.edu http://www.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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