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 jmsstarlight@gmail.com wrote:
> From: James Starlight jmsstarlight@gmail.com > Subject: Re: [modeller_usage] Fwd: Modelling of Chimeric protein > To: "flavio seixas" oivalf_nix@yahoo.com > 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 oivalf_nix@yahoo.com: > > 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 > >> > > >