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

----- Original Message ----- From: "modeller usage-request" modeller_usage-request@salilab.org To: "modeller usage" modeller_usage@salilab.org Sent: Friday, May 4, 2012 12:52:17 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi 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