[chimera-dev] developing my own trajectory parser

[Dennis N Bromley]

Hey, thanks Eric!  I will take a look and see if I can make it work.
-denny-





On Mon, Jun 3, 2013 at 12:02 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Denny,
> I'm guessing the issue is that since the entire molecular system of your
> trajectory is treated as a single model, it is awkward to work on one
> particular protein in it.  For instance, if you had two copies of the same
> protein you would want them numbered the same but would also like to be
> able to work on specific residues of a single copy, whereas a command such
> as "color red :121" always colors residue 121 in all the copies.
>  All I can offer here is the ability to give each protein a distinct
> chain ID.  To that end, I have added another optional key to the GetDict
> handling:  "chains".  It should return a list the same length as the number
> of residues, containing the desired chain IDs (solvent could be given
> "water", or same as nearby protein, or blank [a space]).
>  It's not a great solution, but I hope it's good enough.  The change will
> be in the next successful daily build (dated June 3 or later).
>
> --Eric
>
> On May 31, 2013, at 12:44 PM, Dennis N Bromley <dbromley at uw.edu> wrote:
>
> 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
>>
>>
>>
> <__init__.py><Waterdemo.py>_______________________________________________
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