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
