[chimerax-users] measuring rotation between two homologous PDB models

[Y. Mutum]

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
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