Re: dimer model

[Stephane Vandevuer <svdevuer@ulb.ac.be>]

Hi,

If you have a dimer as template and want to model a dimer with the same
organisation, you just need to include a "/" character as chain breaker in
the alignment file (between your 2 monomers).

I join an exemple of alignment for a dimer.




On Thu, 12 Jun 2003, Difei Wang wrote:

> Hi, All
> 
> I am wondering if it is possible to model a dimer structure from a dimer
> template.
> I can not find anything in the manual. I tried to model each of them first and
> then
> put them together. However, I am not sure it is good or not for the packing in
> the
> contact region. Thanks for your help.
> 
> Difei
> 
> 

>P1;to_model
sequence:to_model:1:A:218:B:::: 
--RLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAWFPAPEAVPESWLECDLPEADTVVVPSNWQMHGYDAP
IYTNVTYPITVNPPFVPTENPTGCYSLTFNVDESWLQEGQTRIIFDGVNSAFHLWCNGRWVGYGQDSRLPSEFDL
SAFLRAGENRLAVMVLRWSDGSYLEDQDMWRMSGIFRDVSLLHKPTTQISDFHVATRFNDDFSRAVLEAA
/
--RLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAWFPAPEAVPESWLECDLPEADTVVVPSNWQMHGYDAP
IYTNVTYPITVNPPFVPTENPTGCYSLTFNVDESWLQEGQTRIIFDGVNSAFHLWCNGRWVGYGQDSRLPSEFDL
SAFLRAGENRLAVMVLRWSDGSYLEDQDMWRMSGIFRDVSLLHKPTTQISDFHVATRFNDDFSRAVLEAA*

>P1;template
structureX:template:1:A:224:B: : : :
VTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAWFPAPEAVPESWLECDLPEADTVVVPSNWQMHGY
DAPIYTNVTYPITVNPPFVPTENPTGCYSLTFNVDESWLQEGQTRIIFDGVNSAFHLWCNGRWVGYGQDSRLPSE
FDLSAFLRAGENRLAVMVLRWSDGSYLEDQDMWRMSGIFRDVSLLHKPTTQISDFHVATRFNDDFSRAVLEACV
/
VTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAWFPAPEAVPESWLECDLPEADTVVVPSNWQMHGY
DAPIYTNVTYPITVNPPFVPTENPTGCYSLTFNVDESWLQEGQTRIIFDGVNSAFHLWCNGRWVGYGQDSRLPSE
FDLSAFLRAGENRLAVMVLRWSDGSYLEDQDMWRMSGIFRDVSLLHKPTTQISDFHVATRFNDDFSRAVLEACV*