[chimera-dev] developing my own trajectory parser

[Eric Pettersen]

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


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