Can anyone tell me how to model Homodimer from target sequence through Modeller? It means A and B chain
If you have a dimer template and model a dimer simply add a "/" sign in your alignment file.
i.e.
{
>P1;template header
Modeling Delimiters
Template sequence of chain A
/
Template sequence of Chain B *
>P1;target header
Modeling Delimiters
Target sequence of chain A
/
Target sequence of Chain B *
}
Thats all.
No its not working see my alignment file its right i place "/" between the chains
>p1;440919431
sequence:440919431:1:a:151:a:polyprotein, partial [dengue virus 3]:dengue virus 3:2.00:-1.00
vstgsqlakrfskgllngqgpmklvmafiaflrflaipptagvlarwgtfkksgaikvlkgfkkeisnmlsi
inkrkktslclmmilpaalafhltsrdgeprmivgknergksllfktasginmctliamdlgemcddtvtyk
cphitev*
/
>p1;440919431
sequence:440919431:1:b:78:b:polyprotein, partial [dengue virus 3]:dengue virus 3:2.00:-1.00
vstgsqlakrfskgllngqgpmklvmafiaflrflaipptagvlarwgtfkksgaikvlkgfkkeisnmlsi
inkrkktslclmmilpaalafhltsrdgeprmivgknergksllfktasginmctliamdlgemcddtvtyk
cphitev*
>p1;seqm1
structurex:seqm1:1:a:78:a: : : :
vstgsqlakrfskgllngqgpmklvmafiaflrflaipptagvlarwgtfkksgaikvlkgfkkeisnmlsi
inkrkk------------------------------------------------------------------
-------*
/
>p1;seqm1
structurex:seqm1:1:b:78:b: : : :
vstgsqlakrfskgllngqgpmklvmafiaflrflaipptagvlarwgtfkksgaikvlkgfkkeisnmlsi
inkrkk------------------------------------------------------------------
-------*
>p1;structure
structurex:structure:1: :151: : : : :
vstgsqlakrfskgllngqgpmklvmafiaflrflaipptagvlarwgtfkksgaikvlkgfkkeisnmlsi
inkrkktslclmmilpaalafhltsrdgeprmivgknergksllfktasginmctliamdlgemcddtvtyk
cphitev*
No dear not that way. See my ans carefully.
>P1
Template Seq of Chain A (No terminaion and no PIR description after )
/
Template Seq of Chain B *
>P1
Target Seq of Chain A (No terminaion and no PIR description
/
Target Seq of Chain B *
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