[chimerax-users] MD trajectories in ChimeraX

[David Slochower]

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> 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> 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)
> 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
> )
>
> I'm aware of the Molecular Dynamics Viewer in the Toolshed, but that
> appears to be geared for multi-PDB trajectories.
>
> Thanks.
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20200824/e45c1ba9/attachment-0001.html>