[Chimera-users] length of a curved alpha helix
goddard at cgl.ucsf.edu
Fri Dec 12 12:19:13 PST 2008
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.
> (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
>> 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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