[chimera-dev] Creating graphics objects from Python code

[Konrad Hinsen]

On 7 Jan 2011, at 19:12, Tom Goddard wrote:

>  You can use the Chimera BILD format without creating a temporary  
> file by creating a string containing the commands, then use StringIO  
> to make a file object from that string and open it.  For example,
>
>    from StringIO import StringIO
>    bild = StringIO(".cylinder %g %g %g %g %g %g %g\n"
>                % (end1[0], end1[1], end1[2], end2[0], end2[1],  
> end2[2], radius))
>    from chimera import openModels
>    model = openModels.open(bild, type="Bild", identifyAs='My  
> annotations', sameAs = mol)

That's already a lot better than my temporary file solution.

> The identifyAs argument assigns the name to the new model that will  
> be shown in the Model Panel dialog.  The sameAs argument says that  
> the new model should be aligned with the specified model (same  
> positioning transform).

And those options make it even better.

>  To avoid that limitation I have sometimes resorted to using (some  
> say abusing) the Chimera Molecule object for showing annotations.   
> The Chimera Volume Tracer tool lets you place spherical markers and  
> connect them by cylindrical links,

That's what I have been doing until now, but I don't see how I can get  
arrows through Molecule objects.

> None of the annotation display techniques combine flexibility with  
> ease of use.  I suggest using BILD if possible.

Sounds reasonable. Thanks for your explanations!

Konrad.
--
---------------------------------------------------------------------
Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research at  khinsen dot fastmail dot net
---------------------------------------------------------------------