When I started doing various analyses of conformational changes in AP2 (bending of helical solenoids, see supp data fig S2 for Jackson et al, Cell 141, 1220-1229 (2010)) I was first going to do lots of scripting around this sort of thing, but Kevin Cowtan persuaded me that it was easier to program exactly what you want to do, and that his clipper libraries made it very easy (in C++). The couple of example programs I posted show a framework that I've used in a series of little programs to do such analyses, and I've found it easier just to hack the programs within such a framework rather than to try to write some entirely general and flexible system. Clipper lets you select coordinate range, superimpose them, extract vectors (or indeed inertial tensors if you want: I found that didn't work well) in a reasonably straightforward way.
I'm sure there are other ways to do it, but this suits me Phil On 17 Aug 2010, at 10:53, Eleanor Dodson wrote: > As someone said - this is quite hard unless you have a very long helix - any > ragged end bits can dominate the fit of one feature to another. > > > In your case I think I would use SSM to superpose the two similar structures > , then LSQKAB to fit any feature to its related one using the original > molecule, plus the second one after the SSM overlap. > > LSQKAB will give you the relative rotation of any feature to its partner - > look the the polar angles to get a estimate of rotation, and the translation > to find how far apart the 2 features are. > > This is different to getting the direction of the helix. Centre of mas is > easy LSQKAB gives you that, but the vector is easisest found with a bit of > arithmetic. > Find COM of residues 1-3 say and COM of residues n to n-3, > vector connects these two COMs - direction cosines are > xv/(sqrt(xv*xv +yv*yv +zv*zv) yv/(sqrt(xv*xv +yv*yv +zv*zv .. > > length is a function of number of residues > > The $CLIBD/fraglib/theor-helix-70.pdb suggests ~ 14.8A per 10 residues.. > Eleanor > > > Phil Evans wrote: >> 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
