Thank you for your response. That might be the case but for my purpose, I need the DNA to be fixed (treated as a rigid body) in both the complexes and the modelling to be done irrespective of that. I came across an automodel feature " nonstd_restraints(aln) " (http://salilab.org/modeller/manual/node69.html) but I do not know how to use it - I added a.nonstd_restraints(aln) in the model-ligand.py file but got an error saying that nonstd_restraints() expects 2 arguments, of which 1 is given. 
If someone knows how to use these automodel features, please guide. 


On Wed, Mar 28, 2012 at 9:30 PM, Ashish Runthala <ashishr@bits-pilani.ac.in> wrote:
Dear Sumedha,
You are being confused with the assessment results, but they are correct.  As you have stated, you modelled protein with, without DNA(using as a ligand) and got the RMSD difference between the models as 0.5A' in RMSd, when screened against the selected template.  But this is obvious. The model with 0.1RMSD has probably better localized topology spanned over the 9bases of DNA. Check out the TM-Score of the two models against the template. As you have not provided further details about the protein length, the two models, and the template, it is difficult to precisely conclude something. TM-Score will answer your query the best.

Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA

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Subject: modeller_usage Digest, Vol 11, Issue 35

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Today's Topics:

  1. mutate_selection.py (ARVIND PAL)
  2. Re: mutate_selection.py (Modeller Caretaker)
  3. Re: Regarding protein 3D structure modeling (Modeller Caretaker)
  4. DNA-protein complex modelling discrepancy!! (Sumedha Roy)


----------------------------------------------------------------------

Message: 1
Date: Mon, 26 Mar 2012 12:49:18 +0530
From: ARVIND PAL <arvind.sbt@gmail.com>
To: modeller_usage@salilab.org
Subject: [modeller_usage] mutate_selection.py
Message-ID:
       <CAMw18pPwUrHq13ZNb5Pu_fqe6ms4Nmg6z9cH7igxmM99w6E+TA@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Dear sir
        when i am running the
*mutate_selection.py<http://salilab.org/modeller/9.9/examples/commands/mutate_selection.py>
command i got the error selection contains no atom. what does it means.
        plz help me.
*
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Message: 2
Date: Mon, 26 Mar 2012 10:12:54 -0700
From: Modeller Caretaker <modeller-care@salilab.org>
To: ARVIND PAL <arvind.sbt@gmail.com>
Cc: modeller_usage@salilab.org
Subject: Re: [modeller_usage] mutate_selection.py
Message-ID: <4F70A396.6050703@salilab.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 3/26/12 12:19 AM, ARVIND PAL wrote:
> when i am running the mutate_selection.py command i got the error
> selection contains no atom. what does it means.

Just like it says, you selected no atoms. Obviously you need to select
some atoms in order to mutate them. Check your script carefully - you
may have used the wrong residue numbers or residue types when you made
the selection.

       Ben Webb, Modeller Caretaker
--
modeller-care@salilab.org             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage


------------------------------

Message: 3
Date: Mon, 26 Mar 2012 10:14:39 -0700
From: Modeller Caretaker <modeller-care@salilab.org>
To: vishal Nemaysh <vishal.bioinfotech@gmail.com>,      modeller_usage
       <modeller_usage@salilab.org>
Subject: Re: [modeller_usage] Regarding protein 3D structure modeling
Message-ID: <4F70A3FF.40101@salilab.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 3/26/12 1:30 AM, vishal Nemaysh wrote:
> Regarding this (3D structure prediction) problem sir i will try to find
> out some template for covering the whole query sequence during BLAST.
> but there is no any single template or multiple template are found to
> occupied  this query. so sir plz suggest me some solution...

Modeller is a package for comparative modeling, so if you have no
template, you are out of luck. You either need to try harder to find a
template (BLAST is not that sensitive - you can try other methods that
use profile or HMM information, for example) or settle for only modeling
the part of the sequence for which a template is available.

       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: Wed, 28 Mar 2012 16:02:09 +0530
From: Sumedha Roy <sumedharoy@gmail.com>
To: modeller_usage@salilab.org
Subject: [modeller_usage] DNA-protein complex modelling discrepancy!!
Message-ID:
       <CABFmE0cd-vdsFjaU6441u37SqUDVeEkgNDCH2+jjbp_qJBJ1kw@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hello

I tried modelling a new complex based on a template complex with the same
DNA ligand but a few mutations in the protein. Initially I did the
modelling the usual way and got good detectable RMSD (about 0.6) with the
new mutated PDB (just the new protein, didn't have the DNA) and the
original complex.

However when I tried to do the modelling considering DNA as a ligand
(changed all DNA ATOMs to HETATM and modified alignment file with 9
appended '.'s - as my DNA is 9bp long), the new mutated complex, is nearly
SAME as the template complex with minor changes in coordinates. (0.1 RMSD)

I don't understand that if I am using the same template and mutations, why
is there so much of a difference (nearly 0.5 RMSD) between the two new
complexes (with and without the DNA).
All RMSDs were done by superimposing structures in PyMOL.

Please help, I'm terribly confused!

Regards

--
Sumedha Roy
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--
Sumedha Roy
5th year student,
Biochemical engg & Biotechnology
KTH/IIT Delhi