The problem with the inertial matrix approach is that it is very sensitive to end effects on the helix, ie a helix is not a perfect cylinder. So superimposing an "ideal" helix is more reliable Phil
On 17 Aug 2010, at 10:17, Francois Berenger wrote: > Hello, > > Is there some C or C++ code out there doing what you described in 1). > > If not, is there a very detailed explanation of this procedure somewhere, > detailed enough in order to implement it (just getting > the best fit vector and its "length", no other parameters)? > > Thanks a lot, > Francois. > > 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
