[chimera-dev] developing my own trajectory parser

[Dennis N Bromley]

Hi Eric,

Thank you very much for your help.  My data is happily loading away. :)

I have two more questions regarding loading:
1. My trajectory can contain multiple models (i.e. multiple proteins, not
just protein + ligand).  How do I specify that?
2. My data is actually coming from a streaming source where the other end
of the stream could add molecules or change the structure.  I know how to
catch that message, but how would I tell Chimera that the structure had
changed and I need to re-do all the models and residue counts and names and
such (all the stuff from the GetDict() call)?

thank you!
-denny-





On Mon, May 20, 2013 at 10:18 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Denny,
>         Hardly a newbie question!  Anyway, there actually is documentation
> for adding a format at the end of the MD Movie help page:
>
>
> http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/movie/movie.html#newformats
>
> You should read that and see how far it gets you.  Feel free to send any
> questions here or directly to me -- that will help me determine where the
> documentation needs more detail.
>         BTW, you were certainly on the right track in that you need to add
> a folder to Trajectories/formats that supports your format.  Though unless
> your format is based on DCD files, Gromacs is probably a better example to
> look at than Charmm.
>         Anyway, like I said, don't be shy with the questions!
>
> --Eric
>
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu
>
> On May 17, 2013, at 9:37 PM, Dennis N Bromley <dbromley at uw.edu> wrote:
>
> > Hi,
> >
> > I apologize if this is a newbie question - I've searched for material
> but didn't seem to find any answers.
> >
> > I would like to write a plugin that allows chimera to parse up my own
> trajectory format.  I would like it to be seekable rather than loading the
> whole shebang into memory at once.  Is there an example trajectory parser
> out there or maybe someone could point me in the right direction?  I saw
> charmm.py, which might be a good place to start, but I am not sure of which
> bits I need to replicate.  Any pointers on a good place to begin looking
> would be very appreciated.
> >
> > thank you!
> > -denny-
> >
> >
> >
> > _______________________________________________
> > Chimera-dev mailing list
> > Chimera-dev at cgl.ucsf.edu
> > http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev
>
>
>
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