I don't know of any standard programs that do this, but I have a couple of programs that do this sort of thing, using a "standard" helix as a reference and the clipper libraries. I could send you the code if you like, though you'd probably have to hack them to do exactly what you want (I found that easier than trying to write a completely general program for doing every sort of comparison.
Phil On 15 Aug 2010, at 08:29, 商元 wrote: > Dear all, > I want to compare the conformational change of two similar structures, > using one alpha helix as the reference. Then, how can I get a vector that can > represent both the position and direction of the helix? Is there any > well-known software can do this？ > Or, should I build a cylinder model, with parameters [radius,bottom > center(x1,y1,z1),top center(x1,y2,z2)], using the coordinates of C,C(alpha) > and N to fit these parameters? > Thanks for any suggestions > > Regards, > Yuan SHANG
