Re: [modeller_usage] Fwd: Modelling of Chimeric protein

[flavio seixas <>]

Hi James,

I have 2 suggestions.

1) The alignment file of your second template is set:
> >P1;3u10
> structureN:3u10:470  ::203 : :::-1.00:-1.00

I think the correct must be (first residie to last residue):
> >P1;3u10
> structureN:3u10:203  ::470 : :::-1.00:-1.00


2) Did you put both templates in the same coordinated system? I mean, did you superpose (Secondary Strucuture Match supermpose) both the templates in a way that generated models will reflect the template structure?

Regards

Flavio

--- On Sun, 12/9/12, James Starlight <> wrote:

> From: James Starlight <>
> Subject: [modeller_usage] Fwd:  Modelling of Chimeric protein
> To: "modeller_usage" <>, "Modeller Caretaker" <>
> Date: Sunday, December 9, 2012, 11:25 AM
> 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
> >
> 
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