Hi James.

Thanks for the return.

Have fun!

Flavio

--- On Wed, 12/12/12, 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: Wednesday, December 12, 2012, 1:58 PM > Thanks Flavio! It works perfect! > > James > > 2012/12/10, flavio seixas oivalf_nix@yahoo.com: > > Hi James! > > > > I am glad to help. > > > > The easier way to include hetatoms to model is to treat > them as BLK, with > > the single letter code "."(dot) > > > > In the alignment file, put "." at the position of your > hetatms, eg: > > > > aaaaaaaa---------.-   (dot refers to > hetatm of the first template) > > --------bbbbbbbbb-.   (dot refers to > hetatm of the second template) > > ccccccccccccccccc..   (model with hetatm > of both templates) > > > > To make your life easier, renumber the templates > sequentially. E.g., > > renumber the first template from 1 to 200 (hetatm is > 401) and the second > > from 201 to 400 (hetatm is 402). > > > > The hetatm of the first and second templates must be > renumbered as they will > > appear in the final model (as alignment above). > > > > Do not forget to put in your script file: > > > > # Read in HETATM records from template PDBs > > env.io.hetatm = True > > > > See http://salilab.org/modeller/manual/node18.html%C2%A0 > for details. > > > > Regards, > > > > Flavio > > > > > > > > > > > > --- On Mon, 12/10/12, 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: Monday, December 10, 2012, 6:33 PM > >> Hi,  Flavio! > >> > >> Thanks for advises! I've used Nedit and exactly the > problem > >> was in the > >> incorrect alignment of y input data. With the > corrections > >> the modeler > >> produced very good models. > >> > >> Could you also tell me about possible options to > include > >> HETATM groups > >> from templates to the model? > >> > >> E.g both of my templates have two HETATM groups; > from GFP > >> protein its > >> chromophore group which is covalently bonded to > the > >> polypeptide chain > >> (like retinal in rhodopsin or HEM in globins) of > that > >> protein. > >> from the second globular domain- its small cyclic > GMP > >> molecule which > >> is the diffusive ligand of that protein. > >> > >> In the final model I'd like to include both of the > groups > >> from both of > >> the templates (chromophore to the GFP part as well > as cGMP > >> to the > >> interior of the second protein). > >> > >> By the way should I define chromophore group as the > part of > >> the first > >> (gfp) as well as 3rd (output fussed chimera) > sequence or > >> there is > >> another way to its inclusion ? > >> > >> Thanks for help again, > >> > >> James > >> > >> 2012/12/10, flavio seixas oivalf_nix@yahoo.com: > >> > Hi James, > >> > > >> > Modeller results are reproducible. I see you > are > >> producing just one model. > >> > Each time you run your script, it will produce > the same > >> model with the same > >> > error. > >> > > >> > Try to run more models and compare them. Try > at least > >> 100. I usually > >> > produces 1000 and select the best by modeller > dope > >> score and procheck > >> > evaluation. > >> > > >> > First of all, try to correct your alignment > file. > >> > > >> > Your alignment file still incorrect (see > attached). I > >> see that in your file, > >> > the sequences are: > >> > > >> > > >> > aaaaaa------* > >> > ----bbbbbbb* > >> > ccccccccccccccc* > >> > > >> > > >> > All sequences must have the same length! > >> > > >> > Maybe this is a problem with your text editor. > Try to > >> use Nedit (for linux). > >> > This editor does not have limits for number of > columns > >> and does not break > >> > the lines. > >> > > >> > I suggest you use Uniprot tab for alignment > >> (www.uniprot.org) > >> > > >> > You can display the alignment in fasta or pir > format. > >> > > >> > regards, > >> > > >> > Flavio > >> > > >> > > >> > > >> > > >> > --- On Mon, 12/10/12, 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: Monday, December 10, 2012, 7:26 AM > >> >> Flavio, > >> >> > >> >> below you could find my script as well as > new > >> alignment > >> >> file. That > >> >> inpud data produces still wrong result in > the > >> conformation > >> >> of second > >> >> template > >> >> > >> >> # Homology modeling with multiple > templates > >> >> from modeller import * > >> >>     # Load standard Modeller classes > >> >> from modeller.automodel import *    # > Load the > >> >> automodel class > >> >> > >> >> log.verbose()    # request verbose > output > >> >> env = environ()  # create a new MODELLER > >> environment to > >> >> build this model in > >> >> > >> >> # directories for input atom files > >> >> env.io.atom_files_directory = ['.', > >> '../atom_files'] > >> >> > >> >> a = automodel(env, > >> >> > >> >> alnfile  = 'align-multiple.ali', # > alignment > >> filename > >> >> > >> >> knowns   = ('1gfl', '3u10'), > >> >>    # codes of the templates > >> >>               sequence = > >> >> 'seq') > >> >>    # code of the target > >> >> automodel.initial_malign3d= True > >> >> a.starting_model= 1 > >> >>      # index of the first model > >> >> a.ending_model  = 1 > >> >>        # index of the last model > >> >> > >> >> > >> >>     # (determines how many models to > calculate) > >> >> a.make() > >> >>               # do the > >> >> actual homology modeling > >> >> > >> >> > >> >> >P1;1gfl > >> >> structureX:1gfl:1    ::238 : > :::-1.00:-1.00 > >> >> > >> > ASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------* > >> >> > >> >> >P1;3u10 > >> >> structureN:3u10:470 :A:671 : > :A::-1.00:-1.00 > >> >> > >> > --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQGKMFDEDSILGELNGPLREEIVNFNCRKLVASM > >> >> > >> > PLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHGVVSVLTKGNKEMKLSDGSYFGEICLLTRGRRTASV > >> >> > RADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVAIDRLDRIGKKNSILL* > >> >> > >> >> >P1;seq > >> >> sequence:seq:     : : > >> >>    : ::: 0.00: 0.00 > >> >> > >> > ASKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYKDSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQGKMFDEDSILGELNGPLREEIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHGVVSVLTKGNKEMKLSDGSYFGEICLLTRGRRTASVRADTYCRLYSLSVDNFNEVLEEYPMMRRAFETVAIDRLDRIGKKNSILLH* > >> >> > >> >> > >> >> by the way do you know any web servers > for > >> produccing such > >> >> multiple > >> >> ali files for modeller input like > >> >> aaaa---- > >> >> ----bbbb > >> >> > >> >> for protein aaaabbbb > >> >> ? > >> >> > >> >>  ( the above file I've done manually) > >> >> > >> >> James > >> >> > >> >> > >> >> 2012/12/9, flavio seixas oivalf_nix@yahoo.com: > >> >> > 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 > >> >> >> >> > >> >> >> > > >> >> >> > >> >> > > >> >> > >> > > >