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

Greg Couch gregc at cgl.ucsf.edu
Fri Oct 26 16:58:59 PDT 2012


Wow, this dredges up ancient memories.  The annotated PDB format is known 
as the PDBRUN format.  A draft version of the paper describing the format, 
that was in the Journal of Molecular Graphics, can be found at: 
<http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.61.4701>.

As you have noticed, embedding graphics objects into PDB files is not 
common.  There is only one program, that I am aware of, that is currently 
available and implements a subset of the PDBRUN format: the conic program 
that is distributed as part of UCSF Chimera.  However, conic only supports 
the viewing annotations and not any of the graphical object annotations,
so that's not going to help you.

So, I'd recommend abandoning the idea of keeping everything in a PDB file. 
Instead, you could use a Chimera session file and Elaine's suggestion of 
use Chimera's shape command and/or VRML or bild files.  Or you could 
export all of the graphical data to 3D editor/viewer like Blender or Maya,
and manipulate the graphics objects there.

     HTH,

     Greg

On Fri, 26 Oct 2012, 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.
>
>
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