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 -- Haixin Sui, Ph.D. Wadsworth Center NYS Dept. of Health Empire State Plaza P.O. Box 509 Albany, NY 12201-0509 (518)474-4235 (office) (518)473-0309 (lab) IMPORTANT NOTICE: This e-mail and any attachments may contain confidential or sensitive information which is, or may be, legally privileged or otherwise protected by law from further disclosure. It is intended only for the addressee. If you received this in error or from someone who was not authorized to send it to you, please do not distribute, copy or use it or any attachments. Please notify the sender immediately by reply e-mail and delete this from your system. Thank you for your cooperation.
Dear Haixin, There is a simple way to manipulate part of a protein structure, but it will not make smooth connections between the moved part and the rest of the structure. Take a look at the "Movement Mouse Mode" tool (under Tools... Movement in the menu). You could either choose "Move helix, strand, or turn" if you can accurately grab the helix you want with the mouse, or select your helix and choose "Move selection." I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Nov 23, 2009, at 5:21 PM, Haixin Sui wrote:
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
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
participants (3)
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Elaine Meng -
Haixin Sui -
Thomas Goddard