Hi Lei,
Matchmaker itself does not change the structure. However, if you save a PDB file after moving any atomic structure (by any method), because of rounding you may get tiny differences comparing the structures before and after.  PDB file format only has 3 digits after the decimal in X,Y,Z coordinates.
Best,
Elaine
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Elaine C. Meng, Ph.D.                      
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 25, 2021, at 10:17 AM, Lei Qian via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
>
> Dear users,
> After aligning protein A to protein B using matchmaker, I found the protein A structure slightly changed compared with its original structure (RMSD: 0.001).
> Could I ask how I can keep protein A structure unchanged after matchmaker (position-change) operation?
> Thanks!
> Lei