[Chimera-users] Moving a helix, minimizing turns
goddard at cgl.ucsf.edu
Tue Nov 24 10:27:53 PST 2009
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?
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