[Chimera-users] extending DNA for a figure

[Elaine Meng]

On Aug 13, 2009, at 12:00 AM, Janet G Yang wrote:

> Hi Elaine,
>
> I'm a grad student in Geeta Narlikar's lab, and I've been to a few  
> of your Chimera tutorials at UCSF and found them very helpful.  I  
> have a less analytical and more aesthetic structural task, and I'm  
> wondering if you might have any insight.  I would like to make a  
> figure showing the structure of the nucleosome with some extra DNA  
> docked in at the edges.  The crystal structure of the nucleosome  
> contains 147 bp wrapped around the histone octamer, and I would like  
> to extend out the DNA on one side.  I think I could just take the  
> structure of the nucleosome, and that of some B form DNA, and  
> somehow align them together.  Is there a good way to do this?
>
> Thanks a bunch
> janet

Hi Janet,
My guess is that lots of people run across similar aesthetic issues --  
making a figure is partly art, after all!

Everything you say sounds reasonable.  First you would need to get the  
extra B-form DNA, then position it relative to the nucleosome structure.

(1) Getting the extra DNA. This could be from another PDB structure,  
or built using standard B-form parameters.  The NDB atlas <http://ndbserver.rutgers.edu/atlas/xray/index.html 
 > lists nucleic acid structures in categories such as B-DNA; you can  
use "File...Fetch by ID" in Chimera to fetch using NDB identifiers.   
Those structures might be shorter or less regular than what you need.   
Here is a server that will build canonical structures to order:  <http://structure.usc.edu/make-na/server.html 
 >  (I admit I haven't actually tried using it, but it looks promising)

(2) Positioning the extra DNA relative to the nucleosome structure.   
You could position it by hand and/or by matching overlapping sets of  
atoms.  Positioning by hand requires activating/deactivating models  
for motion so that they can be moved relative to one another -- you  
would do that with the checkboxes below the Command Line, or with the  
"A(ctive)" checkboxes in the Model Panel.  Matching would be done with  
the "match" command.  It may be tedious to figure out the atom naming  
in the two structures and then figure out which sets of atoms to match  
to get the best result, but I don't really see any way around that  
trial and error process, unless you are really skilled at just  
positioning the structures by hand.  I would probably do some matching  
and then maybe make slight manual adjustments depending on how it  
looked.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>

My answer was based on the understanding that you just want the DNA to  
trail away in a somewhat straight path, rather than continuing on  
curling as in the nucleosome.  If you wanted that continued curling,  
there might be some fancy ways to do it with several copies of a  
curved segment and symmetry operators, but that is beyond my skill set!

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                     http://www.cgl.ucsf.edu/home/meng/index.html