In that case, I would split your pdb file in two parts: Nterm to 101 and
99 to Cterm. With the rotate/translate zone option, you can move one
complete domain to have residue 101 of the Nterm domain overlap with
residue 99 of the Cterm domain. In a nex step you will have to delete
residue 101 of the Nterm domain, which was only there as a help for the
superposition, mutate residues 99 and 100 of the Nterm domain to
glycine, renumber the Cterm to start at 101 and combine both pdb files
again. Finally, you will have to regularize the link.
Best, Herman
________________________________
From: CCP4 bulletin board [mailto:[email protected]] On
Behalf Of Qing Chen
Sent: Thursday, January 13, 2011 12:28 PM
To: [email protected]
Subject: Re: [ccp4bb] creat a model with insertion
Let's say I need to insert two G between resi 98 and 99. I tried
in the way as Herman suggest: break the chain in the domain boundary,
add terminal residues at the N-terminus of the 2nd domain. But then
there is no space to accommodate the inserted residues, the two glycerin
backbones overlap with resi 97 and 98. Is there a way to shift the whole
1st domain a bit ?
On Thu, Jan 13, 2011 at 12:16 PM,
<[email protected]> wrote:
use coot: calculate - model/fit/refine - add terminal
residue.
this will add alanines. you can change these to glycines
with the simple mutate option in the same pop up menu.
best,
HErman
________________________________
From: CCP4 bulletin board
[mailto:[email protected]] On Behalf Of Qing Chen
Sent: Thursday, January 13, 2011 11:58 AM
To: [email protected]
Subject: [ccp4bb] creat a model with insertion
Dear all,
I have the wt protein structure that contains
two domains. I want to creat a model with two glycerin inserted between
the two domains.
Which software or webserver could do this?
Pls help.
Qing Chen
