[Biopython] Getting side chain atoms?

[Frederico Moras Ferreira]

That's great! Look forward hearing from you.
Cheers,
Fred

Em 30-05-2012 12:13, João Rodrigues escreveu:
> Dear Frederico and Mark,
>
> I have a few scripts to do exactly what Frederico described, that play 
> with Biopython. I will share them tomorrow and put an example here of 
> how they work. Eventually it will become part of Biopython, in a 
> future release I hope..
>
> Cheers,
>
> João [...] Rodrigues
> http://nmr.chem.uu.nl/~joao <http://nmr.chem.uu.nl/%7Ejoao>
>
>
>
> 2012/5/30 Frederico Moras Ferreira <ferreirafm at usp.br 
> <mailto:ferreirafm at usp.br>>
>
>     Hi Mark,
>     I'm also very interested in overall protein shape analysis. I'm
>     completely new to Biopython and can't help you much. Regarding to
>     your question itself, that's something not trivial. One of the
>     approaches would be to calculate the center of mass of your
>     protein and iteratively calculate the momentum of inertia along
>     three mutually perpendicular axes so as it is maximum in one
>     direction and minimum in another. Sampling the momentum of inertia
>     of the third axis and comparing with the other two will give a
>     good estimation of your protein overall shape.
>     Best of luck,
>     Fred
>
>     Em 30-05-2012 03:04, João Rodrigues escreveu:
>
>         Hi Mark,
>
>         The gyration tensor should give you the means of calculating
>         how oblate or
>         prolate your molecule is.
>
>         Regarding the sidechain, i think you just have to manually do
>         it, but since
>         the backbone atoms are always the same it shouldn't be too hard.
>
>         Cheers,
>
>         João
>         No dia 30 de Mai de 2012 05:10, "Mark Livingstone"<
>         livingstonemark at gmail.com <mailto:livingstonemark at gmail.com>>
>          escreveu:
>
>             Hi Guys,
>
>             I notice on the wiki that it says the mailing list is at
>             biopython at biopython.org <mailto:biopython at biopython.org>,
>             but when I suscribed it said to use
>             biopython at lists.open-bio.org
>             <mailto:biopython at lists.open-bio.org>, so I'm wondering
>             what the difference is?
>
>             What is the simplest way to get a list of the side chain
>             atoms given
>             say a residue number?
>
>             Also, not entirely related to Biopython, but I'm wondering
>             if there is
>             some way to get a sense of the overall shape of a protein?
>             Like is it
>             globular, a big string, a sheet or what? I can see if you
>             looked at
>             the bounding box, that might be a starting point, but does
>             anyone have
>             any other ideas? I habe been looking at it as a geometry
>             type problem
>             but haven't gotten too far yet.
>
>             Thanks in advance,
>
>             MarkL
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