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 jmsstarlight@gmail.com wrote:
> From: James Starlight jmsstarlight@gmail.com > Subject: [modeller_usage] Fwd: Modelling of Chimeric protein > To: "modeller_usage" modeller_usage@salilab.org, "Modeller Caretaker" modeller-care@salilab.org > 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 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 > > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mailman/listinfo/modeller_usage >