Hi Yaikhomba,
Measure rotation is simply telling you how #1 was already moved when it was matched to #2.  It does NOT tell you the transformation between the domains in the after-matched position that would be needed to superimpose those domains.  I tried to explain this in the help, but I know it's confusing:

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation>

If I understand correctly here is how I might try to do it:

(1) superimpose 6gj2 onto 6rfr like you did already
(2) save PDB 6gj2 relative to 6rfr  (in matched position)
(3) close 6gj2
(4) reopen saved version of 6gj2 that is already matched on 6rfr
(5) then superimpose those domains
(6) then measure rotation

E.g. commands something like this:

open 6g2j; open 6rfr
match #1/L,N to #2/5,4 pair ss
save 6g2jnew.pdb #1 rel #2
close #1
open 6g2jnew.pdb
match #1/F to #2/B
measure rotation #1 to #2 coordinate #1 showAxis true showSlabs true

That gives a rotation of about 18 degrees, so maybe it is the measurement you had in mind.  I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                      
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 26, 2021, at 8:41 AM, Y. Mutum via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Hi Elaine and ChimeraX Team
>
> My query relates to measuring rotation between two subunits from homologous models in ChimeraX.
>
> Here, I have first aligned the two models on one of sub-domains of these multi-domain complex. Then, without moving the models, the plan is to calculate the rotation in another domain, between the 2 models, apart from measuring the translational shift.
> So,
>        • Align Chain /L,M (model #1, PDB:6g2j ) and Chains /5,4 (model #2, PDB:6rfr).
>        • Calculate rotation of Chain /F (model #1, PDB:6g2j) and Chain /B (model #2, PDB:6rfr).
> I am using the following commands:
> -- open 6g2j; open 6rfr;
> -- match #1/L,N to #2/5,4 pair ss;
> -- measure rotation #1/F toModel #2/B coordinateSystem #1/F showAxis true showSlabs true;
>
> The log report is:
> Position of 6g2j #1 relative to 6rfr #2 in 6g2j #1 coordinate system:
> Matrix rotation and translation
> 0.80441124 0.40360431 -0.43591986 67.76279700
> 0.18783349 0.52334489 0.83116106 -121.82969657
> 0.56359661 -0.75047565 0.34517410 202.31442783
> Axis -0.83978100 -0.53070022 -0.11456502
> Axis point 0.00000000 87.13355460 206.39866592
> Rotation angle (degrees) 70.33834463
> Shift along axis -15.42901832
>
> Thus, ChimeraX is calculating a rotation of ¬70 degrees, which is clearly the case. The visual inspection suggests, that the rotation should be no more than ~15-20 degrees. I am not sure where I am going wrong.
> Could you please help?
>
> Thanks
> Yaikhomba