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Hi,</div>
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I am trying to implement a python script that takes a rotation matrix and a translation vector from Chimeras' fitmap output, and applies those rotations and translations to particle 2D projections from electron micrographs. I have successfully applied the reverse
rotation, getting 3D reconstructions that are almost aligned, except for the translation. I am having problems interpreting the values of the translation vector (4th column from fitmap output matrix). According to information I found online the units of this
vector are angstroms, but the length of the translation vector output by fitmap would put my density near the edge of the particle box. My interpretation of the tranlation vector is the following: original_position + trans_vec = new_position.</div>
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For example, I have two densities (box size 264^3, angpix correctly set to 1.15Å), both near the center of the box, fitmap aligns them with what is clearly a small translation after rotation, yet I get the following fitmap output, with a translation vector
of length >180Å:</div>
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<span>> fitmap #1 #0 search 50<br>
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<div>Found 34 unique fits from 50 random placements having fraction of points inside contour >= 0.100 (50 of 50).<br>
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<div>Correlations and times found:<br>
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<div>0.9847 (1), 0.9722 (5), 0.9523 (3), 0.9044 (2), 0.8574 (2), 0.8567 (2), 0.8534 (1), 0.8503 (2), 0.849 (2), 0.832 (2), 0.8317 (2), 0.8274 (1), 0.8225 (3), 0.8205 (1), 0.8184 (1), 0.8062 (1), 0.8058 (1), 0.8043 (2), 0.8017 (1), 0.8007 (1), 0.7977 (1), 0.7809
(1), 0.78 (1), 0.7761 (1), 0.7566 (1), 0.7557 (1), 0.7555 (1), 0.7467 (1), 0.7431 (1), 0.7145 (1), 0.7062 (1), 0.6922 (1), 0.6049 (1), 0.6015 (1)<br>
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<div>Best fit found:<br>
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<div>Fit map run_it025_class003.mrc in map run_it025_class002.mrc using 70798 points<br>
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<div> correlation = 0.9847, correlation about mean = 0.6976, overlap = 38.71<br>
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<div> steps = 448, shift = 52.7, angle = 48.4 degrees<br>
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<div>Position of run_it025_class003.mrc (#1) relative to run_it025_class002.mrc (#0) coordinates:<br>
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<div> Matrix rotation and translation<br>
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<div> 0.98449497 -0.14831781 0.09365615 <span style="color: rgb(200, 38, 19);"><b>14.82575334</b></span><br>
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<div> 0.15479139 0.48339849 -0.86160636 <span style="color: rgb(200, 38, 19);">
<b>179.12850738</b></span><br>
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<div> 0.08251833 0.86274430 0.49886170 <span style="color: rgb(200, 38, 19);">
<b>-54.91381047</b></span><br>
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<div> Axis 0.98487954 0.00636148 0.17312375<br>
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<div> Axis point 0.00000000 137.68459847 125.30174028<br>
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<div> Rotation angle (degrees) 61.09376942<br>
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<span> Shift along axis 6.23421857</span><br>
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<span>Disallowing fitmap shift outputs an even larger translation, which I find odd:</span></div>
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<span>> fitmap #1 #0 search 50 shift false<br>
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<div>Found 35 unique fits from 50 random placements having fraction of points inside contour >= 0.100 (35 of 50).<br>
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<div>Correlations and times found:<br>
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<div>0.8342 (1), 0.8038 (1), 0.7294 (1), 0.699 (1), 0.6862 (1), 0.685 (1), 0.6602 (1), 0.6548 (1), 0.6403 (1), 0.6318 (1), 0.629 (1), 0.6281 (1), 0.6145 (1), 0.6072 (1), 0.601 (1), 0.582 (1), 0.5695 (1), 0.5682 (1), 0.5529 (1), 0.544 (1), 0.5386 (1), 0.5317
(1), 0.5225 (1), 0.5152 (1), 0.5049 (1), 0.4984 (1), 0.4933 (1), 0.4718 (1), 0.4715 (1), 0.4698 (1), 0.4515 (1), 0.44 (1), 0.4243 (1), 0.4102 (1), 0.3598 (1)<br>
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<div>Best fit found:<br>
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<div>Fit map run_it025_class003.mrc in map run_it025_class002.mrc using 70798 points<br>
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<div> correlation = 0.8342, correlation about mean = 0.1402, overlap = 24.51<br>
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<div> steps = 224, shift = 3.75e-13, angle = 59.1 degrees<br>
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<div>Position of run_it025_class003.mrc (#1) relative to run_it025_class002.mrc (#0) coordinates:<br>
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<div> Matrix rotation and translation<br>
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<div> -0.99670235 -0.06634245 -0.04672373 <span style="color: rgb(200, 38, 19);">
<b>320.71861709</b></span><br>
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<div> -0.08010133 0.71238040 0.69720724 <span style="color: rgb(200, 38, 19);">
<b>-47.18870041</b></span><br>
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<div> -0.01296937 0.69865073 -0.71534534 <span style="color: rgb(200, 38, 19);">
<b>162.45334925</b></span><br>
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<div> Axis 0.03956990 -0.92529900 -0.37716838<br>
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<div> Axis point 158.55880471 0.00000000 92.42576286<br>
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<div> Rotation angle (degrees) 178.95488392<br>
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<span> Shift along axis -4.91780500</span><br>
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I am clearly missing something, how should I interpret the translation vector output by fitmap?</div>
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Thank you for your help,</div>
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Benjamin</div>
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