Dear all
I'm dealing with a little big problem. I need to model a dymer protein. I use as template the A and B chain of a PDB file containing A B C D chains. To create the sequence to be modelled I have pasted twice the monomer sequence.
The program works fine but I get a model with only a chain double sized in respect of th original. In the original pdb A e B chains are not linked and I want a non linked dymer. Ho to do this?
This the alignemet file I have used.
>P1;1JU6 structureX:1JU6:28 :A:313:B :TYMS:Homo Sapiens:-1.00:-1.00 HGELQYLGQIQHILRCGVEKDDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEE LLWFIKGSTNAKELSSKGVKIWDANGSRDFLDSLGFSTREEGDLGPVYGFQWRHFGAEYR DMESDYSGQGVDQLQRVIDTIKTNPDDRRIIMCAWNPRDLPLMALPPCHALCQFYVVNSE LSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKI QLQREPRPFPKLRILRKVEKIDDFKAEDFQIEGYNPHPTIKMEMAVHGELQYLGQIQHIL RCGVEKDDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKEL SSKGVKIWDANGSRDFLDSLGFSTREEGDLGPVYGFQWRHFGAEYRDMESDYSGQGVDQL QRVIDTIKTNPDDRRIIMCAWNPRDLPLMALPPCHALCQFYVVNSELSCQLYQRSGDMGL GVPFNIASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKIQLQREPRPFPKLRI LRKVEKIDDFKAEDFQIEGYNPHPTIKMEMAV * >P1;TYMS_F117L_dym sequence:TYMS_F117L_dym: : : : :::-1.00:-1.00 HGELQYLGQIQHILRCGVEKDDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEE LLWFIKGSTNAKELSSKGVKIWDANGSRDLLDSLGFSTREEGDLGPVYGFQWRHFGAEYR DMESDYSGQGVDQLQRVIDTIKTNPDDRRIIMCAWNPRDLPLMALPPCHALCQFYVVNSE LSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKI QLQREPRPFPKLRILRKVEKIDDFKAEDFQIEGYNPHPTIKMEMAVHGELQYLGQIQHIL RCGVEKDDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKEL SSKGVKIWDANGSRDLLDSLGFSTREEGDLGPVYGFQWRHFGAEYRDMESDYSGQGVDQL QRVIDTIKTNPDDRRIIMCAWNPRDLPLMALPPCHALCQFYVVNSELSCQLYQRSGDMGL GVPFNIASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKIQLQREPRPFPKLRI LRKVEKIDDFKAEDFQIEGYNPHPTIKMEMAV *
Dr. Edoardo Saccenti Fiorgen Foundation c\o CERM Magnetic Nuclear Resonance Research Center Scientific Pole - University of Florence via Luigi Sacconi 6, 50019 Sesto Fiorentino (FI) ITALY Tel: +39 055 4574193 Fax: +39 39 055 4574271 Mob: +39 333 2289912 saccenti@cerm.unifi.it www.cerm.unifi.it
participants (1)
-
Edoardo Saccenti