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: 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