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
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