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Today's Topics:

  1. Re: In what are the initial structures different?
      (Modeller Caretaker)
  2. Re: modeller_usage Digest, Vol 11, Issue 42 (Ashish Runthala)
  3. Re: modeller_usage Digest, Vol 11, Issue 42 (Ashish Runthala)


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Message: 1
Date: Mon, 09 Apr 2012 11:46:02 -0700
From: Modeller Caretaker <modeller-care@salilab.org>
To: BIN ZHANG <zhngbn@gmail.com>
Cc: modeller_usage@salilab.org
Subject: Re: [modeller_usage] In what are the initial structures
    different?
Message-ID: <4F832E6A.5020001@salilab.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 04/08/2012 11:58 PM, BIN ZHANG wrote:
> I have a question about the differences of the initial structure built
> for homology modeling. Can anyone tell me how exactly are these initial
> structures different? Do they differ in the secondary structures in
> uncertain regions? I cannot find this information in the manual.

See http://salilab.org/modeller/9.10/manual/node470.html, in particular
step 3 and substep 3. The initial structures are simply randomized by
calling selection.randomize_xyz().

    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: Tue, 10 Apr 2012 08:33:02 +0530 (IST)
From: Ashish Runthala      <ashishr@bits-pilani.ac.in>
To: modeller usage <modeller_usage@salilab.org>
Subject: Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 42
Message-ID:
    <15240798.16751334026982399.JavaMail.root@mailserver.bits-pilani.ac.in>
   
Content-Type: text/plain; charset=utf-8

Focus on the statement with ALIGN_CODES, as it is inclusive of the PDB_ID and the PDB_CHAIN used in the alignment file.
So it could probably be '2AHNA' or '2AHNB'.



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

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

Message: 2
Date: Mon, 9 Apr 2012 17:21:12 +0530
From: Sumedha Roy <sumedharoy@gmail.com>
To: modeller usage <modeller_usage@salilab.org>
Subject: [modeller_usage] Error in ALIGN_CODES(i)
Message-ID:
    <CABFmE0dNMawUwZgsh07bsRd43+-O3Yrzq6VhfkSQJOTjp=NECA@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hello all,

When I try to model my protein-DNA complex, I get the error:
_modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i)
was not found in the alignment file; ALIGN_CODES(      2) =  2AHN

But I see no mistake either in the alignment or the format. I've attached
both the ALI file and model-ligand.py. Please help!!!

--
Sumedha Roy
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Message: 3
Date: Mon, 09 Apr 2012 11:44:11 -0700
From: Modeller Caretaker <modeller-care@salilab.org>
To: Sumedha Roy <sumedharoy@gmail.com>
Cc: modeller usage <modeller_usage@salilab.org>
Subject: Re: [modeller_usage] Error in ALIGN_CODES(i)
Message-ID: <4F832DFB.1020106@salilab.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 04/09/2012 04:51 AM, Sumedha Roy wrote:
> When I try to model my protein-DNA complex, I get the error:
> _modeller.ModellerError: read_al_373E> Protein specified in
> ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES(
> 2) =  2AHN
>
> But I see no mistake either in the alignment or the format. I've
> attached both the ALI file and model-ligand.py. Please help!!!

Your alignment file is in incorrect format. Each sequence must start
with a >P1; header. Your second sequence starts with >P2; instead.

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


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

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End of modeller_usage Digest, Vol 11, Issue 42
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------------------------------

Message: 3
Date: Tue, 10 Apr 2012 08:30:34 +0530 (IST)
From: Ashish Runthala      <ashishr@bits-pilani.ac.in>
To: modeller usage <modeller_usage@salilab.org>
Subject: Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 42
Message-ID:
    <24731645.16721334026834741.JavaMail.root@mailserver.bits-pilani.ac.in>
   
Content-Type: text/plain; charset=utf-8

Dear  BIN ZHANG,
MODELLER based on your constructed alignment file parsing the reliable template residues mapped against the target ones, constructs and fixes the average alpha carbon backbone (if you choose a single template) or an average backbone topology (for Multiple templates' local aligned chunks). Then it fits in the side chains and backbone atoms to make the model complete. 
However, easy saying but really a vicious circle problem, the alignment could have actually been wrong to incorrectly fit target against parsed template residues.
Regardless of the earlier problems, On increased sampling, MODELLER tries best to satisfy the Lennard Jones and all the energetic equations composing its DOPE energy function. The non-physical local atomic clashes are thus minimized with every such iteration. So only you see, Restraints earlier, now with end of every such iterative step. That in fact, is the trial to leap the energetic landscape, precisely focusing on the probably erroneous regions encompassing the higher local steric clashes.

The story continues until the number of iterations are over.


Ashish


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

Message: 1
Date: Sun, 8 Apr 2012 23:58:13 -0700
From: BIN ZHANG <zhngbn@gmail.com>
To: modeller_usage@salilab.org
Subject: [modeller_usage] In what are the initial structures
    different?
Message-ID: <602A5241-132A-4319-81BA-94C238A459AF@gmail.com>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

Dear All:

I have a question about the differences of the initial structure built 
for homology modeling. Can anyone tell me how exactly are these 
initial structures different? Do they differ in the secondary 
structures in uncertain regions? I cannot find this information in the 
manual.

For example, by using

a = automodel()
a.starting_model = 1
a.ending_model = 50

I can built 50 different homology models starting from different 
initial structures, but I have want to know how these different 
initial structures are constructed.

Thanks very much for help.

Best,
Bin


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

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End of modeller_usage Digest, Vol 11, Issue 43
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