# [Chimera-users] length of a curved alpha helix

Elaine Meng meng at cgl.ucsf.edu
Fri Dec 12 12:04:09 PST 2008

```Hi Andy,
The question becomes philosophical: what really is the length of a
curved helix?  I suspect you are thinking a curved tube could
represent its axis, and the length would be the distance from end to
end of the straightened tube.  I can't think of any way in Chimera to
measure that.

Some possibilities that are not quite the same thing:

(A) measure a series of backbone atom-atom distances and add them up.
This would be a zigzag distance that would be an upper bound on the
actual helix length.  Of course, you could measure a single distance
from an atom on one end to an atom on the other end, but I assume that
is not really what you want.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances
>

(B) decide to model the curved helix as several straight segments.
For example, residues 1-9 as one segment, 10-19 as another, etc.  For
each segment, select the residues and use Axes to create an axis.  The
length of the axis is reported.  Add them together.  Again this will
be a series of straight lines and probably an upper bound to what you
had in mind. Or, you could draw one Axis for the whole helix, but
again it would be straight.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes
>

(C) you could do something really crazy like put a tape measure up to
the screen and curve it along the helix.  You could calibrate by
comparing to a linear distance measurement also on the screen.  You'd
probably want to use "orthographic" projection to avoid artifacts from
the "perspective" projection (see Tools... Viewing Controls...
Camera).  This would be really crude and approximate, however.  Tom G
gets credit for this idea.  8-)

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
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

On Dec 10, 2008, at 11:26 AM, Anindito Sen wrote:

> Dear All
> I was wondering as how can I measure the length of "curved" alpha
> helix.
> Thanks
> Andy
>
> Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry
> and Molecular Genetics University of Virginia Box 800733
> Charlottesville, VA 22908

```