Thank you very much for your answer, but I will find that there is still no overlap in the metal (green atoms). I wonder if I can use the move command to move all the green atoms of the model to the same Cartesian coordinates to achieve the overlap after alignment?

 

Small correction, if the green ones were named M (I accidentally wrote m1 for the first model), it would be something like

align #1:1@m,r1,r2,c2 to #2:1@m,r1,r2,c2


> On Apr 15, 2024, at 9:17 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Hello,
> With "align" you can use whatever atoms you want (not necessarily the whole residue 1), but this requires finding the names of the specific atoms  and including them in the command.
>
> Then it is a process of trial and error to fit just the atoms that you want and then see if the fit is good enough for you. If not then you might try using a different subset of the atoms.
>
> Since you said you want to align the central green atoms, you may want to try only using those green atoms + the two orange atoms coordinating that ion, and at least one other atom (maybe one of the bond partners of the orange atom(s)) from each structure.  You would need to know their names in order to write this command, however. 
>
> I don't know their names in your structure, so this is only an example.  You would have to use the atom names in your structure instead.  If the green ones  were named M and the orange ones R1 and R2 and another bonded to R2 was named C2, something like:
>
> align #1:1@m1,r1,r2,c2 to #2:1@m,r1,r2,c2
>
> You can see atom names by putting the mouse over the atom and waiting for the pop-up balloon, and/or by labeling, e.g.
>
> label #1:1 atoms
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                      
> UCSF Chimera(X) team
> Resource for Biocomputing, Visualization, and Informatics
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>> On Apr 15, 2024, at 4:24 AM, 化工化工 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>>
>> Dear Professor：
>> Hello, I have aligned the atoms #1 of different models with the command "align #1:1 toAtoms #2:1", but I found that the atoms #1 don't overlap very well, which affects the aesthetics of the publication. So, I would like to ask you if there is a way to align the green atoms in the center, thank you very much (see Figure 1)!
>>
>>
>> 化工化工
>> 1366924572@qq.com
>>
>> <图片1.png>
>
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