[chimerax-users] MD trajectories in ChimeraX

[Eric Pettersen]

Hi David,
	I mean a PDB of the simulated system (or any structure format ChimeraX supports) and then a coordinate file like nc.  So you might have to generate a PDB -- I think that's something else cpptraj does.

--Eric

> On Aug 24, 2020, at 3:04 PM, David Slochower <slochower at gmail.com> wrote:
> 
> Hi Eric, thanks. I'm sure the code for parsing the `prmtop` is beastly.
> 
> When you say "open a structure first [...]", do you mean load an `inpcrd` and `nc` for the trajectory? My understanding is that without the topology, connectivity would need to be inferred. Or are you thinking `pdb` and `nc` together? 
> 
> And yup, `cpptraj` is a good option, but I don't want to create DCD copies of all my trajectories just yet. Especially since I don't believe Amber supports writing DCD trajectories from `pmemd.cuda`.
> 
> On Mon, Aug 24, 2020 at 1:53 PM Eric Pettersen <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>> wrote:
> Hi David,
> 	I don't think we are planning on implementing MD metafiles -- I think the plan is the same as for the current DCD and XTC/TRR support:  open a structure first and then load additional coordinate sets into it from the coordinates file.  So you wouldn't use 'prmtop' at all and would use the 'nc' file to load additional coordinates into a structure corresponding to your simulation.  Avoiding the need to write code to parse a prmtop file is a big advantage because such code is a big effort to write, and typically needs updating much more frequently than code just to read coordinate files, which rarely change in format.
> 	I will open a feature-request ticket in our bug-tracking database for this, so you'll be notified when something gets implemented.  In the interim, CPPTRAJ <https://amber-md.github.io/cpptraj/CPPTRAJ.xhtml#toc-Subsubsection-10.5.7> can convert nc files to Gromacs xtc/trr (or DCD), so you could use that to convert your trajectories into a format that ChimeraX can read.
> 
> --Eric
> 
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
> 
> 
>> On Aug 24, 2020, at 11:04 AM, David Slochower <slochower at gmail.com <mailto:slochower at gmail.com>> wrote:
>> 
>> Hi, are there any plans to implement a "metafile" interface (e.g., http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#metafile <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#metafile>) for loading trajectories with ChimeraX?  In particular, it would be great to be able to load `prmtop` and `nc` trajectories, even if it were available only through the command line and without a GUI. (This can be considered a follow up to this message: http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-December/000773.html <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-December/000773.html>)
>> 
>> I'm aware of the Molecular Dynamics Viewer in the Toolshed, but that appears to be geared for multi-PDB trajectories.
>> 
>> Thanks.
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