I've put a couple of example programs that do this sort of thing (using the clipper libraries) in
ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/helixanglethings.tar.gz Phil 1) helixangle.cpp Calculate angle beween two helices Superimpose standard helix on two specified chains & ranges, then calculate angle between them 2) kinky.cpp Analyse change of helix axis directions between 2 structures On 17 Aug 2010, at 09:49, Tom Oldfield wrote: > Yuan SHANG > > 1) DIY > The way that has been used is to calculate the inertia tensor matrix for > helix (or > any other secondary structure element). You can chose backbone atoms or just > the CA atoms. Then calculate the eigen vectors and values from this and the > largest > eigen vector will be the best fit vector to the helix - and its lambda will > define its > "length". For a strand or sheet you can use this method too. > This was the standard way from molecular simulation work to look at > simplified dynamics of proteins. > > 2) The program Squid > http://www.ebi.ac.uk/~oldfield/squid/ (1992, 1998) > has lots of different analysis methods for proteins including calculating > vectors for helices, the angles between helices (torsion/distance/opening) > and other things. > You only problem is that it is very old (1988) and written in Fortran and > requires > a little effort to install - sorry - I no longer support it. There is a pre > compiled linux-32 bit > version and I still do all my structure analysis with it. > http://www.ebi.ac.uk/~oldfield/xsquid - though this requires installation > data too. > > > Tom > >> Fitting a helix is not trivial. >> >> If you have access to windows and mathematica, then you might try helfit. >> (Otherwise, you could implement the algorithm yourself and then share your >> code with the rest of us ;-) >> >> >> http://dx.doi.org/10.1016/j.compbiolchem.2008.03.012 >> >> >> James >> >> >> On Aug 15, 2010, at 12:29 AM, 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
