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
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