[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.

(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.

(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 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

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

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