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.
