Hi Yanhe,
I could not reproduce this problem.  Even if I have the two copies of the same atomic model in exactly the same place before I run the command:

fitmap #2,3 inMap #1 seq 2 res 3.7

... they go to different places.  But if you use "shift false" it will prevent shifting during fitting, so I don't think you want to use that option.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Sep 21, 2022, at 8:17 AM, Yanhe Zhao via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Greeting there developer,
>
> I am using fitmap command of chimerax to fit pdb to map, the command as below:
> fitmap #2,3 inMap #1 seq 2 res 3.7
> #2 and #3 are copy of each other and I manually placed them in different positions in map,
> #2 and #3 come to same position after the command running, I had shift option false, but come to same result.
> I remember it works in chimera.
> Could you please point me out?
>
> Thanks and have a nice day,
> Yanhe