On 10/26/2012 12:16 PM, James Stroud wrote:
> This sounds like something that a PDB file is not intended to do. I think everyone has universally agreed to the PDB specification at the RCSB, which makes no provisions for arbitrary objects, as cool as they would be.
I see that there was a proposal for extension in order to support
kind of what I need:
"Annotating PDB files with scene information"
Gregory S. Couch, Eric F. Pettersen, Conrad C. Huang, Thomas E. Ferrin
http://www.sciencedirect.com/science/article/pii/026378559500003O#
doi = "10.1016/0263-7855(95)00003-O",
An interesting citation from the paper:
"We propose that the extensions to the PDB presented here
be adopted by the molecular modeling community for in-
corporation into visualization programs."
> But you could put your information into REMARK records, which are free-form. Maybe you could then find some people to honor your specification or build an implementation yourself...
>
> ================
> 21st century solution
> ================
>
> The simplest way, would be to write a "converter" that embeds a pymol script into REMARK records and a preprocessor for pymol that extracts them and feeds them into the pymol stream.
>
> If you write the implementation then you have a de facto standard. It would take a handful of lines of code. Write it in python and claim the mantle of coolness and the disdain of python detractors everywhere!
>
> You could set up a home page using wikispaces or even the pymol wiki, pointing to your implementation that you keep on github.
>
>
> James
>
>
> On Oct 25, 2012, at 7:25 PM, Francois Berenger wrote:
>
>> 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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