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Today's Topics:

  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
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