Re: [Jmol-users] DNA B-form to Z-form transition

[Eric M. <em...@mi...>]

At 12/2/05, you wrote:
>Eric, where is that dnabz.pdb?

Dear Angel and Miguel,

At the Atlas (http://www.umass.edu/microbio/chime/pe_alpha/atlas/atlas.htm)
at "DNA B form to Z form transition",
click "View the model in Jmol",
then download the model from Jmol's menu.

Or right click on "View the model in Jmol" and Copy Link Location, which=20
copies this:

http://firstglance.jmol.org/fg.htm?mol=3Dhttp%3A//www.umass.edu/microbio/chi=
me/pe_alpha/atlas/molslides/dnabz/dnabz.pdb

 From which you can see the URL of the PDB file after "mol=3D", namely,
http://www.umass.edu/microbio/chime/pe_alpha/atlas/molslides/dnabz/dnabz.pdb

The original empirical model is the published 2ACJ.

In 2ACJ, the backbone has no breaks.
In the dnabz.pdb version, there are breaks. The PDB files differ in a=20
number of ways, but it is not obvious to me why the breaks appear in=
 dnabz.pdb.


> > QUESTION: I have not been able to discern why Jmol shows breaks in the=
 DNA
> > backbone near the transition (but not at it!) in the theoretical model
> > (dnabz.pdb), while Jmol shows no such breaks in the original 2ACJ.
> > Enlightenment will be appreciated.
>=B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7=
 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7 =B7
>  Dr. Angel Herraez
>  Dep. Bioquimica y Biologia Molecular, Universidad de Alcala
>  E-28871 Alcala de Henares  (Madrid), Spain
>  fax: +34-91 885 45 85

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