[Chimera-users] length of a curved alpha helix

Tom Goddard goddard at cgl.ucsf.edu
Fri Dec 12 12:19:13 PST 2008

Hi Andy,

  I was credited with the idea of using a tape measure.  But now I have 
some sensible ideas.  The length of the curved alpha helix is probably 
going to differ by a miniscule amount from the length measured directly 
between its two end points.  For example, a 20 degree circular arc is 
only half a percent longer (1.005 times as long) as the straight segment 
between its end points.  So I'd suggest a more meaningful quantification 
of a curved half helix is "how many degrees does it curve".  You can 
think about how to define that -- we don't have any predefined notion in 
Chimera of how many degrees a helix curves.  Probably a sensible meaning 
of that since the curve is not a circular segment is to instead think 
about how far the middle of the bent helix deviates off the straight 
line connecting its end points.


Elaine Meng wrote:
> 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
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