[Biopython] BLOCKS BLOSUM

[George Devaniranjan]

Hi Iddo,
I actaully want to see the fragments being used for the BLOCK in pymol or
VMD but as you can see below
(Is it a alpha helix or a beta sheet..etc)
NIF1_AZOCH  (    120)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
NIF1_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN

I cant find the PDB ID these fragments came from.
The actual calcualtion of the matrix I think I can do.
Thank you,
George






On Tue, Jun 21, 2011 at 2:36 PM, Iddo Friedberg <idoerg at gmail.com> wrote:

> Go here:
>
> http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc232
>
> On Tue, Jun 21, 2011 at 2:01 PM, George Devaniranjan <
> devaniranjan at gmail.com> wrote:
>
>> Hi,
>> This might not be the correct place to ask this question-but some of you
>> may
>> have experience in this.
>> I went to the BLOCKS database and downloaded a text file that contains
>> many
>> BLOCKS but I would like to see the structure of these blocks either in
>> VMD/Pymol
>> Is there a way to find the PDB ID of these blocks?
>>
>> What I want is to use the same BLOCKS info and develop my own BLOSUM like
>> matrix using biopyhton.
>> Thank you and my apologies is this is not directly related to biopython.
>> (example of a block from the downloaded text file is given below)
>> George
>>
>> NIF1_AZOCH  (    120)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
>> NIF1_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
>> NIF1_METTL  (    126)  DLDNLFFDVLGDVVCGGFAMPLRDGLAQEIYIVTSGEMMALYAANN
>> NIF1_RHISO  (    119)  DIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
>> NIF2_AZOCH  (    119)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
>> NIF2_CLOPA  (    115)  DLDFVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
>> NIF2_RHISO  (    119)  DIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
>> NIF3_AZOVI  (    118)  DLDFVFFDDLGDVVCGGFAMPIRDGKAQEVYIVASGEMMAIYAANN
>> NIF3_CLOPA  (    118)  DLDFVFFDVLGDVVCGGFAMPIRDGKAQEVYIVASGEMMAVYAANN
>> NIF4_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
>> NIF5_CLOPA  (    115)  DLDYVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
>> NIF6_CLOPA  (    115)  DLDFVFYDVLGDVVCGGFAMPIREGKAQEIYIVASGEMMALYAANN
>> NIFH_ANASP  (    121)  DLDFVSYDVLGDVVCGGFAMPIREGKAQEIYIVTSGEMMAMYAANN
>> NIFH_AZOBR  (    118)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
>> NIFH_BRAJA  (    119)  NIDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMAMYAANN
>> NIFH_FRASR  (    116)  NLDFVTYDVLGDVVCGGFAMPIRQGKAQEIYIVTSGEMMAMYAANN
>> NIFH_KLEPN  (    118)  DLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANN
>> NIFH_RHILT  (    119)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
>> NIFH_RHOCA  (    119)  DVDYVSYDVLGDVVCGGFAMPIRENKAQEIYIVMSGEMMALYAANN
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>
>
>
> --
> Iddo Friedberg
> http://iddo-friedberg.net/contact.html
>