[Biopython] Getting side chain atoms?

[João Rodrigues]

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



2012/5/30 Frederico Moras Ferreira <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>  escreveu:
>>
>>  Hi Guys,
>>>
>>> I notice on the wiki that it says the mailing list is at
>>> biopython at biopython.org, but when I suscribed it said to use
>>> 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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