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. Tom -------- 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