[Chimera-users] Moving a helix, minimizing turns

Thomas Goddard goddard at cgl.ucsf.edu
Tue Nov 24 10:27:53 PST 2009

Hi Haixin,

   As Elaine mentioned, the Tools / Movement / Movement Mouse Mode will 
let you move any selected atoms.  I'd suggest selecting the exact 
residues you want to move (e.g. command "select :123-135") and use the 
"move selection" mode.

   To fix long bonds in the turns connected to the moved helix you could 
try energy minimization, Tools / Structure Editing / Minimize Structure. 
  You would probably select just the turn residues with a "select" 
command ("select :118-122,136-143") and keep all unselected atoms fixed 
in the minimization.  Minimization uses MMTK and can be very slow.  No 
faith should be put in the configuration of a turn you get by doing 
this.  The only purpose is to produce reasonable bond lengths and angles.


-------- Original Message --------
Subject: structure manupulation
From: Haixin Sui
To: 'Tom Goddard'
Date: 11/23/09 5:21 PM

> Tom and Elaine,
> Is there a simple way to manipulate part of a protein structure in 
> Chimera? What I would like to do is the following. Let’s say I have a 
> molecular compose 8 helixes. 7 of them fit in the cryo-EM map perfectly 
> but one short helix is off probably owing to conformational change.   I 
> would like to move the short helix into the density map manually. The 
> difficult part is how to make a smooth transition for loop regions at 
> both ends of the helix. Would you please give me some advice on this? 
> Thanks!
> Haixin

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