Sorry to come in on this so/ too late. One way of getting an arbitrarily long helix perfectly aligned along the Z axis is to use the polar coordinates of Arnott & Dover (1967) J. Mol.Biol 40:209-212 which are derived from fibre diffraction. As Eleanor says these can then be aligned with your helix with LSQKAB
I have an old badly-written Fortran program (I wrote it for a Vax, but it still compiles and runs in g95 - isn't Fortran wonderful?) that takes Arnott & Dover's polar coordinates and converts them to a helix of any required length* in PDB (or Diamond!) format. It also places atoms on the helix axis making it easy to calculate the vectors of the newly rotated helix. If Yuan Shang would like it I can send the program and/or a very long helix to him. best wishes Pete *limited by the PDB's f8.3 coordinate format to about 600 or 6000 residues depending on whether you do or don't need a space between the y and z coodinates 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 Prof Peter Artymiuk Krebs Institute Department of Molecular Biology & Biotechnology University of Sheffield Sheffield S10 2TN ENGLAND
