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