On 10/26/2012 12:29 PM, Francois Berenger wrote:
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.
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...
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21st century solution
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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.
That's an idea.
I may have a look at Pymol's support for user-defined object indeed
(specification and rendering).
I found this up to now:
Compiled Graphics Objects
http://pymol.sourceforge.net/newman/user/S0500cgo.html
http://www.pymolwiki.org/index.php/CGO_Text
and this for arrows at least:
http://www.pymolwiki.org/index.php/Modevectors
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!
I was looking for something already existing, as I guess
I'm not the first person to need this (for productivity reasons also).
You could set up a home page using wikispaces or even the pymol wiki,
pointing to your implementation that you keep on github.
I do have a github page, and do open source what's worth it. ;)
Thanks,
F.
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.
