Hi, I would like to know if it possible to create fusion proteins by merging two pdb files, or if it is possible in any other way, thanks Bren. _________________________________________________________________ Bing™ brings you maps, menus, and reviews organized in one place. Try it now. http://www.bing.com/search?q=restaurants&form=MLOGEN&publ=WLHMTAG&crea=TXT_M...
Hi Bren, You can create bonds, but only within a single model, so before adding the bond you could use the "combine" command, or in the Model Panel, the "copy/combine" function to combine two models. Then the bond can be added with the "bond" command or the "Build Structure" tool. However, there is nothing in this process to prevent you from creating something completely ridiculous (physically unreasonable). Chimera will not change the relative positions of the structures when you add the bond, so *before* combining the models you would need to generate the desired position of one structure relative to the other. There is a little more detail and some links to the documentation in this previous post: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003255.html
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 http://www.cgl.ucsf.edu/home/meng/index.html On Jul 27, 2009, at 6:06 PM, Brennal Pierre wrote:
Hi, I would like to know if it possible to create fusion proteins by merging two pdb files, or if it is possible in any other way, thanks Bren.
On Jul 28, 2009, at 10:10 AM, Elaine Meng wrote:
Chimera will not change the relative positions of the structures when you add the bond
Just wanted to mentioned that we expect to have a function to bond two fragments with a specified bond length/angle/dihedral by the next release, but we don't have it yet. --Eric
Thanks Elaine for the speedy and thorough response, I will try it as soon as possible. Bren.
From: meng@cgl.ucsf.edu To: brennal1@msn.com Subject: Re: [Chimera-users] fusion proteins Date: Tue, 28 Jul 2009 10:10:28 -0700 CC: chimera-users@cgl.ucsf.edu
Hi Bren, You can create bonds, but only within a single model, so before adding the bond you could use the "combine" command, or in the Model Panel, the "copy/combine" function to combine two models. Then the bond can be added with the "bond" command or the "Build Structure" tool.
However, there is nothing in this process to prevent you from creating something completely ridiculous (physically unreasonable). Chimera will not change the relative positions of the structures when you add the bond, so *before* combining the models you would need to generate the desired position of one structure relative to the other.
There is a little more detail and some links to the documentation in this previous post: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003255.html
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 http://www.cgl.ucsf.edu/home/meng/index.html
On Jul 27, 2009, at 6:06 PM, Brennal Pierre wrote:
Hi, I would like to know if it possible to create fusion proteins by merging two pdb files, or if it is possible in any other way, thanks Bren.
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participants (3)
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Brennal Pierre -
Elaine Meng -
Eric Pettersen