Dear Modeler Users!
Recently I've done my chimeric protein based on two different templates in accordance to the http://salilab.org/modeller/9.10/FAQ.html#1
using that script http://salilab.org/modeller/9.10/manual/node21.html
below the alignment of my templates as well as sequence
>P1;1gfl structureX:1gfl:1 ::238 : :::-1.00:-1.00 ASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------*
>P1;3u10 structureN:3u10:470 ::203 : :::-1.00:-1.00 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQGKMFDEDSILGELNGPLREEIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHGVVSVLTKGNKEMKLSDGSYFGEICLLTRGRRTASVRADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVAIDRLDRIGKKNSILL.*
>P1;seq sequence:seq: : : : ::: 0.00: 0.00 ASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYKDSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQGKMFDEDSILGELNGPLREEIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHGVVSVLTKGNKEMKLSDGSYFGEICLLTRGRRTASVRADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVAIDRLDRIGKKNSILLH*
As the result I've obtain model where first template ( beta-can GFP) was in correct form but the conformation of the second protein was differ from the used template ( pdb id 3u10).
Could you tell me why my model was so distorted and how I can improve it further?
Thanks for help
James
2012/8/8, Modeller Caretaker modeller-care@salilab.org: > On 8/8/12 6:27 AM, James Starlight wrote: >> I want to model chimeric protein which consist of two fussed proteins >> ( tail to head fussion C to N termi). It's important that both of that >> proteins have known spatial structures which could be used as the >> templates. > > http://salilab.org/modeller/9.10/FAQ.html#1 > >> Is there any way to use both of the templates to guide such modelling >> ? In the input option I've found only possibility to use one template. > > 'knowns' can be a list of multiple templates. See > http://salilab.org/modeller/9.10/manual/node21.html > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >