Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 54

4 May 2012

      No, Mary Varughese. Sir just meant that you should parse your sequence mentioned as M in his alignment (with / being the chain delimiter), (M: your target Model residues and not Missing residue)
He simply pointed that You can easily cover up the missing residues of each of chain A and B, through its corresponding coordinate information available in the other chain. So missing residues of A chain you are filling up the gap with B chain, and same way for the other chain.
You should not edit the template files and rather use them as such for target sequence as per the manually curated alignment file as Sir has shown.
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
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Subject: modeller_usage Digest, Vol 11, Issue 54
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Today's Topics:
1. Re: missing residues (Modeller Caretaker)
   2. Re: missing residues (Mary Varughese)
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Message: 1
Date: Thu, 03 May 2012 12:37:34 -0700
From: Modeller Caretaker modeller-care@salilab.org
To: Mary Varughese maryvj1985@gmail.com
Cc: modeller_usage@salilab.org
Subject: Re: [modeller_usage] missing residues
Message-ID: 4FA2DE7E.5060103@salilab.org
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 5/3/12 3:29 AM, Mary Varughese wrote:
> I have a dimer protein with missing residues in both subunits.
>
> I have the target sequence, the original protein pdb with missing gaps
> *(a.pdb* resolution 3.58 Xray structure)and another pdb of the same
> protein with missing residues included (*b.pdb* resolution 3.5 electron
> diffraction)
>
> So i have to add missing residues with b.pdb as the template and rest of
> the protein exact to a.pdb)
Yes, that should be fairly straightforward - simply use both templates 
in modeling, and align the model with a.pdb or b.pdb accordingly. If 
possible, try to overlap the regions a little so that Modeller can 
figure out the conformation of the missing regions.
> Also can i add missing residues in both A and B units simultaneously.
Sure, that's no problem. Your alignment might look something like:
>P1;a
...
AAAAAAAAAA------AAAAAAAAAA/AAAAAAAAAA------AAAAAAAAAA*
 >P1;b
...
--------BBBBBBBBBB--------/--------BBBBBBBBBB--------*
 >P1;model
...
MMMMMMMMMMMMMMMMMMMMMMMMMM/MMMMMMMMMMMMMMMMMMMMMMMMMM*
(This assumes that you've edited b.pdb to only include the regions in 
the alignment above.)
Ben Webb, Modeller Caretaker
-- 
modeller-care@salilab.org             http://www.salilab.org/modeller/
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------------------------------

Message: 2
Date: Fri, 4 May 2012 12:52:13 +0530
From: Mary Varughese maryvj1985@gmail.com
To: modeller_usage@salilab.org
Subject: Re: [modeller_usage] missing residues
Message-ID:
    CAAjRZU0+Ht-HtyqDNn64g-p_5Z5r_Y1QDG3_dqaX+Xn1jhe0xA@mail.gmail.com
Content-Type: text/plain; charset="iso-8859-1"

Sir,

Did you mean that i should edit the template(for missing residues) pdb so
that it contains the co-ordinates of the missing residues only. ; and the
alignment look likes ---------------------mmmmmmmm-------------------*
where m stands for missing residues.?

But what you mean by overlap the regions a little so that modeller can
figure out the conformation of the missing regions?

Thank you very much for your reply

On Thu, May 3, 2012 at 3:59 PM, Mary Varughese maryvj1985@gmail.com wrote:

> hi,
>
> I have a dimer protein with missing residues in both subunits.
>
> I have the target sequence, the original protein pdb with missing gaps *
> (a.pdb* resolution 3.58 Xray structure)and another pdb of the same
> protein with missing residues included (*b.pdb* resolution 3.5 electron
> diffraction)
>
> So i have to add missing residues with b.pdb as the template and rest of
> the protein exact to a.pdb)
>
>   In the given example:
>
>
>  >P1;1qg8structureX:1qg8:   2 :A: 256 :A:undefined:undefined:-1.00:-1.00PKVSVIMTSYNKSDYVAKSISSILSQTFSDFELFIMDDNSNEETLNVIRPFLNDNRVRFYQSDISGVKERTEKTRYAALINQAIEMAEGEYITYATDDNIYMPDRLLKMVRELDTHPEKAVIYSASKTYHLN---DIVKETVRPAAQVTWNAPCAIDHCSVMHRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYIT--------------EFVRNLPPQRNCRELRESLKKLGMG*>P1;1qg8_fillsequence:::::::::PKVSVIMTSYNKSDYVAKSISSILSQTFSDFELFIMDDNSNEETLNVIRPFLNDNRVRFYQSDISGVKERTEKTRYAALINQAIEMAEGEYITYATDDNIYMPDRLLKMVRELDTHPEKAVIYSASKTYHLNENRDIVKETVRPAAQVTWNAPCAIDHCSVMHRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYITDQSIHFQLFELEKNEFVRNLPPQRNCRELRESLKKLGMG*
>
> Here what extra alignment should be added if i have a pdb(*b.pdb*) with
> missing residues included which can be used as a template(same sequence).
>
>   Also can i add missing residues in both A and B units simultaneously.
>
> Thanking you
> --
> Mary Varughese
> Research Scholar
> School of Pure and Applied Physics
> Mahatma Gandhi University
> India
>
>

-- 
Mary Varughese
Research Scholar
School of Pure and Applied Physics
Mahatma Gandhi University
India