Re: [modeller_usage] Fwd: Modelling of Chimeric protein

[flavio seixas <>]

Hi James.

Maybe if you post your script, it becomes more easier to help.

But, from your post I can see that the lenght of your target and sequence alignment are not equal. 

See from http://salilab.org/modeller/9.10/manual/node21.html 

that the differences in the lenght are filled with "-"

Maybe you should check this.

Regards,

Flavio


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

> From: James Starlight <>
> Subject: Re: [modeller_usage] Fwd: Modelling of Chimeric protein
> To: "flavio seixas" <>
> Date: Sunday, December 9, 2012, 6:23 PM
> Hi Flavio!
> 
> In the align-multiple.ali file
> structureN:3u10:470  ::203 : :::-1.00:-1.00
> 470 is the number of first residue (in pdb file) and 203 is
> the length
> of the sequence of that protein
> 
> I have superimpose both of the templates and locate them in
> the
> desired location in the initial pdb's templates.
> 
> 
> Is there any string that I should add to my script ?
> ( that example I have used http://salilab.org/modeller/9.10/manual/node21.html )
> 
> Also I've added the string automodel.initial_malign3d= True
> but there were no difference in the output modell
> 
> James
> 
> 2012/12/9, 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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> >> 
> >> https://salilab.org/mailman/listinfo/modeller_usage
> >>
> >
>