Hi Arley,
The issue is how the atoms of the two copies are paired.  If the atoms to be matched with one another do not have the same atom names in #0 and #1, then simply saying "rmsd #0 #1" will give a higher value than expected.  To control the order in which they are paired, you may need to list the atoms individually in the command. Here is what it says in the help page for "rmsd":
=-=
If atom order is not specified, for example,

rmsd #1:fad #0:fad
rmsd #2:246,295 #0:195,221

...the atoms within a residue are ordered first by name, and where these are identical, by alternate location identifier, and where these are also identical, by serial number.
=-=
see: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html>

To list the atoms individually in the command would look something like this, pretending my ligand residues are named XXX and YYY :

rmsd #0:XXX@C1,C4,C3,C2,N  #1:YYY@C1,C2,C3,C4,N3

... would pair C1 of XXX with C1 of YYY, C4 with C2, C3 with C3, C2 with C4, and N with N3 to calculate the RMSD.

Or, as also mentioned in the help page, you can select the atoms with the mouse (Shift-Ctrl-click) one by one in the same order first from #0 and then from #1 and then use command

rmsd sel

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 29, 2021, at 7:35 AM, ARLEY REY PAEZ via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
>
> Best regard,
> My name is Arley, I am a postgraduate student at the federal university of Lavras, Brazil.
> I write this message because I have doubts about how to calculate the RMSD between two ligands after docking and redocking. My question is if Chimera works well to perform that calculation, since when for example I have two structures (ligands) that are, visually well superimposed and I calculate the value of RMSD with the use of the rmsd # 0 # 1 command, their value is high when compared With a structure that is not visually superimposed, why does that happen? Is it that chimera is not useful to carry out this task?
> I appreciate you can help me with that concern.
>
> Att;
>
> Arley