Re: [modeller_usage] DOPE and sequence/model length (Modeller Caretaker) - modeller_usage

26 Dec 2010


      On Sat, Dec 25, 2010 at 11:30 PM, modeller_usage-request@salilab.orgwrote:
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> Today's Topics:
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>   1. Re: modified amino acids (Modeller Caretaker)
>   2. DOPE and sequence/model length (Starr Hazard)
>   3. Re: DOPE and sequence/model length (Modeller Caretaker)
>   4. problem in doing difficuly modeling using modeller        9v8
>      (ranu sharma)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 16 Dec 2010 10:09:27 -0800
> From: Modeller Caretaker modeller-care@salilab.org
> Subject: Re: [modeller_usage] modified amino acids
> To: Mike White mwhite@drexelmed.edu
> Cc: ModellerUsage List List modeller_usage@salilab.org
> Message-ID: 4D0A55D7.9050204@salilab.org
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 12/16/10 6:04 AM, Mike White wrote:
> > I am trying to model a small (22 amino acids) peptide with 3
> > disulfide bonds using structures of 6 related peptides with Modeller
> > 9.7. The template peptides have 1-3 modified amino acids
> > (pyroglutamate, hydroxyproline, amidated C-termini) and the peptide
> > to be modeled has an amidated cysteine as the C-terminus.
>
> Modeller cannot build models containing modified amino acids, nor can it
> use structural information from modified amino acids in your templates
> (the only exception is MSE, which Modeller treats as identical to MET).
>
> Your best option in this case is to edit your template PDB file to
> convert the modified amino acids to their unmodified equivalents, build
> models with regular cysteine, and modify the C-terminus of the
> constructed models.
>
> > I tried setting env.io.hetatm= True to see if that made a difference,
> > but then the routine failed with the following track back:
> ...
> > I'm not sure why env.io.hetatm = 'True' causes this error
>
> True and 'True' are two different things. True is a Python boolean;
> 'True' is a string. Only the first will work here.
>
>        Ben Webb, Modeller Caretaker
> --
> modeller-care@salilab.org             http://www.salilab.org/modeller/
> Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 16 Dec 2010 14:51:44 -0500
> From: Starr Hazard hazards@musc.edu
> Subject: [modeller_usage] DOPE and sequence/model length
> To: modeller_usage@salilab.org
> Message-ID: 4D0A6DD0.2000407@musc.edu
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Folks,
>
> I have modeled some dimers of a large protein and a much shorter partner
> (~350aa for X and about 80aa for Y) . There are crystal templates for
> such dimers. The best resolution structures have  different large and
> small proteins. So I have templates with  X'Y' and X''Y''.  X' and X''
> are homologs as are Y' and Y''.  The Y family is quite variable in
> length. When homologs from distant organisms ( eg plant, fungi, fish
> mammal) are aligned there are gaps compared to the mammalian templates.
>
> In mammals X' and X'' are in related but distinct clades. If I model a
> yeast X protein to each mammalian template can I say that the yeast
> protein is better represented by one or the other template based on a
> DOPE score? ( the GA341 scores are not helpful since they are always
> 1.000 for these models)
>
> This is several questions I guess.  1) Are DOPE energies normally
> distributed?
>                                                                Could I
> statistically compare DOPE scores of models made with one template to
> those from another template.
>                                                            2)  I have
> some evidence that longer XY pairs have "better" DOPE scores than
> shorter pairs. Is there a statistical way to control for "length"?
>                                                            3) I was
> just looking at DOPE scores for two models. One with from an alignment
> with gaps and the other from an alignment without  gaps.
>                                                                 The PDB
> model files are different sizes yet the scores are identical. Does DOPE
> ignore regions that are not in the template?
>
> Starr
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 20 Dec 2010 17:01:01 -0800
> From: Modeller Caretaker modeller-care@salilab.org
> Subject: Re: [modeller_usage] DOPE and sequence/model length
> To: Starr Hazard hazards@musc.edu
> Cc: modeller_usage@salilab.org
> Message-ID: 4D0FFC4D.2060005@salilab.org
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 12/16/2010 11:51 AM, Starr Hazard wrote:
> > This is several questions I guess.  1) Are DOPE energies normally
> > distributed? Could I statistically compare DOPE scores of models made
> > with one template to those from another template.
>
> DOPE is a sum of individual energies over all pairs of atoms in your
> final model - it does not include any information from the template or
> modeling process. So you can compare DOPE scores for two models of the
> same sequence, regardless of their source.
>
> > 2)  I have some evidence that longer XY pairs have "better" DOPE
> > scores than shorter pairs. Is there a statistical way to control for
> > "length"?
>
> You can't compare these directly. Use the normalized DOPE score instead,
> which *is* corrected for length (it is a z score).
>
> > 3) I was just looking at DOPE scores for two models. One with from an
> > alignment with gaps and the other from an alignment without  gaps.
> > The PDB model files are different sizes yet the scores are identical.
> > Does DOPE ignore regions that are not in the template?
>
> Yes. See (1) above.
>
>        Ben Webb, Modeller Caretaker
> --
> modeller-care@salilab.org             http://www.salilab.org/modeller/
> Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
>
>
> ------------------------------
>
> Message: 4
> Date: Sun, 26 Dec 2010 13:00:39 +0530
> From: ranu sharma ranusharma09@gmail.com
> Subject: [modeller_usage] problem in doing difficuly modeling using
>        modeller        9v8
> To: modeller_usage@salilab.org
> Message-ID:
>        AANLkTikhoQUvqSQA1GkKauo9=XctiXy2v27mX-LWrtYZ@mail.gmail.com
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello Sir/Madam,
>
> Good Afternoon. I am facing problem while doing Difficult modelling for my
> protein. It is showing the following error.
> I am attaching the .aln file, my .pdb and model.py file for your reference.
> Hope to get a reply from you soon.
>
>
>
>
>
> Thanks & Regards.
>
>
> *ERROR:*
>
> C:\Program Files\Modeller9v8\examples\ranu_basic\C4H>mod9v8 model.py
> 'import site' failed; use -v for traceback
> Traceback (most recent call last):
>  File "model.py", line 9, in ?
>    a.make()
>  File "C:\Program
> Files\Modeller9v8\modlib\modeller\automodel\automodel.py", li
> ne 98, in make
>    self.homcsr(exit_stage)
>  File "C:\Program
> Files\Modeller9v8\modlib\modeller\automodel\automodel.py", li
> ne 424, in homcsr
>    self.check_alignment(aln)
>  File "C:\Program
> Files\Modeller9v8\modlib\modeller\automodel\automodel.py", li
> ne 406, in check_alignment
>    aln.check()
>  File "C:\Program Files\Modeller9v8\modlib\modeller\alignment.py", line
> 200, in
>  check
>    self.check_structure_structure(io=io)
>  File "C:\Program Files\Modeller9v8\modlib\modeller\alignment.py", line
> 209, in
>  check_structure_structure
>    return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
> _modeller.ModellerError: check_a_282E> Unable to read structural
> information
> for
>  alignment sequence:        1  2fdvA This command requires structures.
>
>
>
>
>
>
>
> --
> Ranu Sharma
> Msc Bioinformatics, Pune University
> JRF, National Chemical Laboratory, Pune
>
>
>
> --
> Ranu Sharma
> Msc Bioinformatics, Pune University
> JRF, National Chemical Laboratory, Pune
>
>
>
> --
> Ranu Sharma
> Msc Bioinformatics, Pune University
> JRF, National Chemical Laboratory, Pune
>