[modeller_usage] Fwd: Modelling of Chimeric protein

[James Starlight <>]

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 <>:
> 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
> --
>              http://www.salilab.org/modeller/
> Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
>