[Chimera-users] stick representation after selection / DNA helical axis

[Elaine Meng]

Hi Damien,
The connections are drawn between one atom per residue because "auto-chaining" is turned on.  If you were showing different atoms, for example P only, those atoms would be connected instead.

You can turn off auto-chaining in the model attributes panel (in Model Panel, choose model on left, click "attributes..." button on right to show that panel) or Selection Inspector, or with a command, for example:

setattr m autochain 0

You can add connections between any pairs of atoms you like using PseudoBond Reader (in menu under Tools... Depiction).
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.html>
The pseudobond display style (stick or wire) etc. could be controlled in the pseudobond attributes panel or Selection Inspector.

You can define axes, planes, or centroids based on any sets of atoms you like using Axes/Planes/Centroids (in menu under Tools... Structure Analysis) or command "define"... for example:

open 1bna
define axis color blue radius 1.0 name ax1 @n1 
define axis color red radius 1.0 name ax2 @p

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>

Depending on how you think the helical axis should be defined, however, you may want to look into programs outside of Chimera that were written specifically for analyzing nucleic acid structures, e.g. Curves+ ... there is a web server:
http://gbio-pbil.ibcp.fr/cgi/Curves_plus
... see also:
<http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761274/>
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-December/005851.html>

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

On Dec 3, 2012, at 8:54 AM, Damien Larivière wrote:

> Dear all,
> I used the command sel @N1 @N3 to select the N1 and N3 atoms of a nucleic acid structure (like 1bna).
> 
> when I do "show only" in Actions / Atoms&Bonds, a specific representation is displayed as in the image below: sticks connect N1 atoms of one strand and N3 atoms of the other strand. 
> 
> May you tell me the meaning of this representation and how can I modify it (I mean, how to change the type of atoms to be connected)?
> 
> In fact, I would like to visually apprehend the helical axis. Is there a way to calculate and display this axis in Chimera?
> 
> Many thanks for your help
> Damien