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