Re: [modeller_usage] Fwd: Modelling of Chimeric protein
To: James Starlight <>
Subject: Re: [modeller_usage] Fwd: Modelling of Chimeric protein
From: flavio seixas <>
Date: Wed, 12 Dec 2012 17:06:10 -0800 (PST)
Cc: Modeller Usage <>
Hi James.
Thanks for the return.
Have fun!
Flavio
--- On Wed, 12/12/12, James Starlight <> wrote:
> From: James Starlight <>
> Subject: Re: [modeller_usage] Fwd: Modelling of Chimeric protein
> To: "flavio seixas" <>
> Date: Wednesday, December 12, 2012, 1:58 PM
> Thanks Flavio! It works perfect!
>
> James
>
> 2012/12/10, flavio seixas <>:
> > 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 ;
> for details.
> >
> > Regards,
> >
> > Flavio
> >
> >
> >
> >
> >
> > --- On Mon, 12/10/12, James Starlight <>
> wrote:
> >
> >> From: James Starlight <>
> >> Subject: Re: [modeller_usage] Fwd: Modelling of
> Chimeric protein
> >> To: "flavio seixas" <>
> >> 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 <>:
> >> > 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 <>
> >> wrote:
> >> >
> >> >> From: James Starlight <>
> >> >> Subject: Re: [modeller_usage] Fwd:
> Modelling of
> >> Chimeric protein
> >> >> To: "flavio seixas" <>
> >> >> 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 <>:
> >> >> > 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
> >> >> >> >> >
> >> >> >> >>
> >> >> >> >>
> >> >>
> _______________________________________________
> >> >> >> >> modeller_usage mailing
> list
> >> >> >> >>
> >> >> >> >> https://salilab.org/mailman/listinfo/modeller_usage
> >> >> >> >>
> >> >> >> >
> >> >> >>
> >> >> >
> >> >>
> >>
> >
>