[Chimera-users] Superimposing and joining

Elaine Meng meng at cgl.ucsf.edu
Thu Apr 28 11:02:21 PDT 2011

Hi Elisa,
There are several ways to superimpose structures, discussed here:

For example, if you want Chimera to use the sequences of the structures to figure out which atoms to match, you could use the MatchMaker tool under Tools...Structure Comparison (or command "matchmaker"), or if you want to specify exactly which atoms to pair yourself, you could use the command "match" -- there are links to these in the page mentioned above.

The structures are you are matching should be in separate models (opened from separate input files).  However, after the superpositioning is done, you can combine separate models into one using the "copy/combine" function in the Model Panel (Model Panel is under Tools... Favorites in the menu) or the command "combine".

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Apr 28, 2011, at 7:07 AM, elisa carli wrote:

> Hi,
> I'm trying to model a TM protein using a Fugue approach.
> This method involves to divide a transmembrane protein in fragment (Nter, TM1,LOOP1and so on)
> Each fragments is predicted separatly.
> I'd like to assembly and join fragment, superimposing the backbone of a fragment with that of the
> correspondent segment in the structure of my protein.
> How can I achieve this goal with Chimera?
> regards

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