[Biopython] Getting side chain atoms?

[Frederico Moras Ferreira]

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
>> _______________________________________________
>> Biopython mailing list  -  Biopython at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython
>>
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython