I've put a couple of example programs that do this sort of thing (using the clipper libraries) in
ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/helixanglethings.tar.gz
Phil
1) helixangle.cpp
Calculate angle beween two helices
Superimpose standard helix on two specified chains & ranges,
then calculate angle between them
2) kinky.cpp
Analyse change of helix axis directions between 2 structures
On 17 Aug 2010, at 09:49, 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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