I'm sorry if this question is somewhat basic...
I'm comparing three homologous proteins, and I'd like to determine a
number of facts to be able to rigorously compare them... I'd like to
know the angle formed by two crossed helices, the angle of kinking in
a kinked helix, and the distance between two separated helices that
are nearly parallel to one another along the y axis, but not parallel
along any other axis.
Could anyone recommend any software to rigorously determine distances
and angles in differently oriented helices? My guess is that I'd need
some kind of a program that can draw vectors through the helices, and
find minimum distances between the vectors, or to use them to define
angles...
What do people normally use to determine these details?
any suggestions would be great, thanks,
~Natasha Keith
UC Berkeley
Wemmer lab
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