[Chimera-users] adding group from one structure to another

Elaine Meng meng at cgl.ucsf.edu
Mon Dec 9 09:49:10 PST 2019

> On Dec 7, 2019, at 1:21 PM, simon two <outlook_534E89DC6130A352 at outlook.com> wrote:
> Hello Elaine. Has there been any development of this problem since the 2007 post?
> I’m trying to duplicate a small group in a large molecule and use the copy to substitute it an existing group of very similar size in the same molecule.
> Best wishes    Simon

Hi Simon, 
I guess you mean this … (would have been useful to send the link):


However, I think that was a totally different problem than yours.  That post is about making a multimer by placing copies according to some symmetry or quasisymmetry that is not described in the PDB file.  You are not doing any symmetrical placement.

For your problem, just open the structure with the group  that you plan to add to something else, and delete all the atoms except that group. Next, open the structure to which you want to add the group.  Then….

Approach (A): delete any extra atoms from the second model as needed before adding the new group.  Then use the Join Models tab in the Build Structure tool (in menu under Tools… Structure Editing) to stick the group (first model) onto the second model.   You will need to specify bond length and angles for the join.

Approach (B): superimpose the group in the first model onto the second model in the position that you want it.  That could be done by matching any appropriate overlapping atoms, if any, or positioning by hand by cycles of deactivating (freezing) one model and moving the other with the mouse.  Then save PDB of the group in position “relative to” the other model.  Then manually text-edit the saved PDB into the PDB of the structure you are adding it to.  Requires some familiarity with PDB format files.  
See also superposition methods:

Sending questions to chimera-users at cgl.ucsf.edu rather than to me individually is recommended.
I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

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