[Chimera-users] Fwd: [ccp4bb] adding some user-defined graphical objects in a PDB file (and displaying them)

[Francois Berenger]

On 10/26/2012 11:56 PM, Elaine Meng wrote:
> Hello,
> PDB format is for atoms/bonds, not graphical objects.  Although you could have "fake" atoms and bonds, the display choices would still be just those available for atoms (dots and lines, sticks, ball & stick, spheres).
>
> For graphical objects, Chimera understands a few different formats.  You could use "Help... Search Documentation" in the Chimera menu, search for "graphical objects," then click link "Input File Types," and in that page see the bottom section: other 3D objects. Probably "Bild" or "VRML" would be the most relevant to you.  "Bild" is the simpler format, easy to understand and write.

I'm amazed to see that Chimera is able to display VRML.

Recently, I was looking for a free VRML viewer on Linux and did not find 
one.
Maybe Amaya from w3c could display them, but I don't remember well and 
it was not very stable.

I'll look into the Bild format too.

Thanks a lot for these insights,
Francois.

> Another possibility is to use the Chimera "shape" command (see instructions using command: help shape).  It makes surfaces in different shapes.  However, to save those you would probably need to save a Chimera session file.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Oct 25, 2012, at 9:46 PM, Francois Berenger wrote:
>
>>
>> -------- Original Message --------
>> Subject: [ccp4bb] adding some user-defined graphical objects in a PDB file (and displaying them)
>> Date: Fri, 26 Oct 2012 10:25:10 +0900
>> From: Francois Berenger <berenger at RIKEN.JP>
>> Reply-To: Francois Berenger <berenger at RIKEN.JP>
>> To: CCP4BB at JISCMAIL.AC.UK
>>
>> Hello,
>>
>> For some new project, I'd like to be able to generate things
>> and store them in PDB format.
>>
>> For example, a triangle, a line segment, a square,
>> a cube, a sphere, an arrow, etc.
>> Being able to change the color and "line width" would be nice.
>>
>> Is there some official recommended way of doing this?
>>
>> Is there some software able to read and display such
>> graphical annotations of PDB files?
>> I'll also need the format description in that case.
>>
>> I want to be able to process a PDB file and store the result
>> of my processing in the same PDB file as some kind of annotation.
>>
>> My current way of doing this is to discretize my objects as H atoms
>> in some other output PDB file, but that's just a temporary workaround.
>>
>> My current search got me this:
>> http://www.cgl.ucsf.edu/eccc1/
>> So, maybe there is some support for what I am looking for into
>> Chimera.
>>
>> Thanks a lot for your suggestions,
>> Francois.
>