[chimera-dev] developing my own trajectory parser

[Dennis N Bromley]

Thank you Eric!. :)

So, rather than model, I guess I should say "multiple proteins", or, as I
am looking at ligands as well, "multiple molecules".  Basically I want to
show a few proteins (wild type + a few mutants) and some small molecules
that I have docked using Vina.

I don't know how to tell Chimera about more than one molecule.  Right now I
just specify lots of residues and atoms and bonds in the GetDict()
function, but, so far as I can tell, I haven't specified that those
structures belong to any particular molecule or protein.  How do I indicate
that *this* residue and atom belong to molecule #1 and *that* residue and
atom belong to molecule #2?

Also, I built a simple stand-alone trajectory plugin to nail down the basic
plugin mechanics.  The plugin simply creates a single water molecule and
pushes it around on demand, so there are no file dependencies.  I have
attached the files in case somebody else finds them useful.  All you need
to do is stick them in the "<Chimera>\share\trajectory\formats\Waterdemo"
directory.  I'll update it with the results of this discussion to show how
to load multiple molecules and such.

thanks again!
-denny-







On Wed, May 29, 2013 at 11:34 AM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> On May 29, 2013, at 10:46 AM, Dennis N Bromley <dbromley at uw.edu> wrote:
>
> Hi Eric,
>
> Thank you very much for your help.  My data is happily loading away. :)
>
>
> Hi Denny, happy to hear it!
>
> 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?
>
>
> I'm not sure I understand the issue.  In Chimera, a "model" can have
> multiple proteins.  A model is just biological data that came from a single
> data source (*e.g.* a PDB file, an MRC file) and is always moved/rotated
> as a whole.  Help me out here. :-)
>
> 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)?
>
>
> Like VMD, Chimera employs the paradigm that trajectories don't change
> composition over time.  Despite that, you can change the composition of
> your trajectory "by hand" by calling the correct atom/bond/residue
> creation/deletion calls yourself (*i.e.* the Molecule methods newAtom,
> newBond, newResidue, deleteAtom, deleteBond, deleteResidue).  You would
> need to set the coordinates of any new atoms via their setCoord method.  If
> you do nothing about it, the coordinates of these new atoms in previous
> frames will be at the origin.
>
> Let me know what additional help you need.
>
> --Eric
>
>                          Eric Pettersen
>
>                         UCSF Computer Graphics Lab
>
>                         http://www.cgl.ucsf.edu
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-dev/attachments/20130531/7b52360d/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: __init__.py
Type: application/octet-stream
Size: 1396 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-dev/attachments/20130531/7b52360d/attachment.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Waterdemo.py
Type: application/octet-stream
Size: 5510 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-dev/attachments/20130531/7b52360d/attachment-0001.obj>