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Hi Elaine and ChimeraX Team</div>
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My query relates to measuring rotation between two subunits from homologous models in ChimeraX.</div>
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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.</div>
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<span style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">So,</span></div>
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<span style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">Align Chain /L,M (model #1, PDB:6g2j ) and Chains /<span style="background-color:rgb(255, 255, 255);display:inline !important">5,4</span> <span style="background-color:rgb(255, 255, 255);display:inline !important">(model
#2, PDB:6rfr).</span></span></li><li style="font-size:12pt;font-family:Calibri, Arial, Helvetica, sans-serif;color:rgb(0, 0, 0)">
<span style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">Calculate rotation of Chain /F <span style="background-color:rgb(255, 255, 255);display:inline !important">(model #1, PDB:6g2j) and Chain /B <span style="background-color:rgb(255, 255, 255);display:inline !important">(model
#2, PDB:6rfr).</span></span></span></li></ul>
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I am using the following commands:</div>
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-- open 6g2j; open 6rfr;</div>
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-- match #1/L,N to #2/5,4 pair ss;</div>
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-- measure rotation #1/F toModel #2/B coordinateSystem #1/F showAxis true showSlabs true;<br>
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The log report is:</div>
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<span style="font-size: 9pt;">Position of 6g2j #1 relative to 6rfr #2 in 6g2j #1 coordinate system:</span>
<div><span style="font-size: 9pt;">Matrix rotation and translation</span></div>
<div><span style="font-size: 9pt;">0.80441124 0.40360431 -0.43591986 67.76279700</span></div>
<div><span style="font-size: 9pt;">0.18783349 0.52334489 0.83116106 -121.82969657</span></div>
<div><span style="font-size: 9pt;">0.56359661 -0.75047565 0.34517410 202.31442783</span></div>
<div><span style="font-size: 9pt;">Axis -0.83978100 -0.53070022 -0.11456502</span></div>
<div><span style="font-size: 9pt;">Axis point 0.00000000 87.13355460 206.39866592</span></div>
<div><span style="font-size: 9pt;">Rotation angle (degrees) 70.33834463</span></div>
<span style="font-size: 9pt;">Shift along axis -15.42901832</span><br>
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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. </div>
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Could you please help?</div>
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Thanks</div>
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Yaikhomba</div>
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