[Chimera-users] will chimeraX support the BILD file format?

Elaine Meng meng at cgl.ucsf.edu
Mon Nov 20 10:56:10 PST 2017


Just to add to the discussion, a related feature is the “shape” command in Chimera, which makes surfaces of various shapes (sphere, cylinder, etc.)
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html>

ChimeraX does not have a similar command at this point, but we had discussed possibly adding it and making it easier to specify the locations and orientations of the shapes, more like they are specified in the Bild format.

Advantages of a “shape”-like command are being able to use a command script rather than having to make an external file, and the ability to recolor the shapes after creation (at least in Chimera, you can’t recolor Bild objects after reading in the file).  However, for people who already have Bild generation processes in place, it may still be desirable to have Bild input too.

Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 16, 2017, at 5:17 PM, Francois BERENGER <berenger at bioreg.kyushu-u.ac.jp> wrote:
> 
> On 11/17/2017 09:53 AM, Greg Couch wrote:
>> We've been debating that.  The bild format has many commands. Which ones
>> do you use?  I ask because I have code that implements the transforms,
>> color, and shape commands, but not any of the line drawing, polygon or
>> marker commands.  Does that work for you?
> 
> I use most of the drawing commands, to create graphical annotations
> (arrows, boxes, spheres).
> And I love the fact that they can be colored and made transparent.
> 
> The whole format is potentially useful to me.
> 
> This is a big advantage of Chimera over pymol for example.
> Don't loose that.
> Pymol is a mess for that and it forces you to go down to Python.
> Going through a simple specialized text format like BILD is a huge win.
> 
> The BILD file format is trivial to generate by hands (for quick test)
> and via any programming language (when in production).
> 
> Regards,
> F.
> 
>>     -- Greg
>> 
>> On 11/16/2017 04:35 PM, Francois BERENGER wrote:
>>> Hello,
>>> 
>>> https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html
>>> 
>>> I am a huge fan of this chimera feature, so I hope it will
>>> not disappear (trivial to create graphical annotations by hand
>>> or via a program).
>>> 
>>> Regards,
>>> F.




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