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

Francois Berenger 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:
> <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.

I think I'll go for the .bild files.

The example in
chimera-1.6.2/share/chimera/helpdir/UsersGuide/bild.html
is interesting enough to me.

It looks human-readable and easy to generate by programs.

Thanks a lot,
F.

>  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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