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.
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.
