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

Damien Larivière damien.fgfondat at gmail.com
Mon Dec 3 10:28:09 PST 2012

Dear Elaine,

Many many thanks for your help.

About the helical axis, I'm going to look at Curves+ carefully.


2012/12/3 Elaine Meng <meng at cgl.ucsf.edu>

> 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
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