On Thu, Nov 29, 2012 at 4:50 PM, Craig James <cja...@emolecules.com> wrote:
> Hi,
>
> And now for something completely different ... I'm looking for an image of
> a DNA strand that's quite long and that I can manipulate.
>
> Is there an editor program and a template that I could use to create such
> a thing? What I'm looking for is a DNA strand that on the macroscopic
> level is also spiral, so that it can be made to look like it's wrapping
> around a tree a bit like a snake. This is for art, not chemistry.
>
I assume you want something like chromatin. The classic work on this was
?25 years ago by Nelson Max.
http://www.cs.ucdavis.edu/people/faculty/max.html He animated all the way
from atoms to organisms. and represented the coiling of DNA in chromosomes.
It depends how much time you have and whether you want to reuse the
technology in the future. I would generate a coiled coil geometrically and
then - if you feel chemical unhappy with the local geometry minimise as
Geoff suggests. The geometry is fairly simple (and can be done in
JUMBO/CML) You generate a fragment (say a rung of DNA) and then apply a
transformation matrix representing a helical transformation - this could be
by 30 degrees or any other angle - doesn't have to be rational. Of the form:
cost sint 0
-sint cost 0
0 0 dz
This will give you a helix.
If you transform this transformation about another axis you will get a
coiled coil. I'd then suggest minimising the fragment and applying the
transformation repeatedly to the result.
Since DNA is very common in crystal structures you will probably find that
refinement programs will do this for you - e.g. COOT. They have to be able
to fit distorted DNA into electron density. You could also simply ask on
the CCP4 mailing list.
P.
> Seriously!
>
> Thanks!
> Craig
>
> (P.S. I have an alter ego. This has nothing to do with eMolecules.)
>
>
> ------------------------------------------------------------------------------
> Keep yourself connected to Go Parallel:
> VERIFY Test and improve your parallel project with help from experts
> and peers. http://goparallel.sourceforge.net
> _______________________________________________
> Blueobelisk-discuss mailing list
> blueobelisk-disc...@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
>
>
--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
------------------------------------------------------------------------------
Keep yourself connected to Go Parallel:
TUNE You got it built. Now make it sing. Tune shows you how.
http://goparallel.sourceforge.net
_______________________________________________
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
