[Chimera-users] Fwd: [ccp4bb] adding some user-defined graphical objects in a PDB file (and displaying them)
berenger at riken.jp
Sun Oct 28 19:15:13 PDT 2012
On 10/27/2012 08:58 AM, Greg Couch wrote:
> 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:
> 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.
I think I'll go for the .bild files.
The example in
is interesting enough to me.
It looks human-readable and easy to generate by programs.
Thanks a lot,
> you could export all of the graphical data to 3D editor/viewer like
> Blender or Maya,
> and manipulate the graphics objects there.
> 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
>> 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:
>> So, maybe there is some support for what I am looking for into
>> Thanks a lot for your suggestions,
>> Chimera-users mailing list
>> Chimera-users at cgl.ucsf.edu
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