# [Chimera-users] Interpretation of fitmap translation vector

Benjamin Basanta bbasanta at scripps.edu
Tue Jul 21 10:31:17 PDT 2020

```Hi,

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.

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:

> fitmap #1 #0 search 50
Found 34 unique fits from 50 random placements having fraction of points inside contour >= 0.100 (50 of 50).
Correlations and times found:
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)
Best fit found:
Fit map run_it025_class003.mrc in map run_it025_class002.mrc using 70798 points
correlation = 0.9847, correlation about mean = 0.6976, overlap = 38.71
steps = 448, shift = 52.7, angle = 48.4 degrees
Position of run_it025_class003.mrc (#1) relative to run_it025_class002.mrc (#0) coordinates:
Matrix rotation and translation
0.98449497  -0.14831781   0.09365615  14.82575334
0.15479139   0.48339849  -0.86160636 179.12850738
0.08251833   0.86274430   0.49886170 -54.91381047
Axis   0.98487954   0.00636148   0.17312375
Axis point   0.00000000 137.68459847 125.30174028
Rotation angle (degrees)  61.09376942
Shift along axis   6.23421857

Disallowing fitmap shift outputs an even larger translation, which I find odd:

> fitmap #1 #0 search 50 shift false
Found 35 unique fits from 50 random placements having fraction of points inside contour >= 0.100 (35 of 50).
Correlations and times found:
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)
Best fit found:
Fit map run_it025_class003.mrc in map run_it025_class002.mrc using 70798 points
correlation = 0.8342, correlation about mean = 0.1402, overlap = 24.51
steps = 224, shift = 3.75e-13, angle = 59.1 degrees
Position of run_it025_class003.mrc (#1) relative to run_it025_class002.mrc (#0) coordinates:
Matrix rotation and translation
-0.99670235  -0.06634245  -0.04672373 320.71861709
-0.08010133   0.71238040   0.69720724 -47.18870041
-0.01296937   0.69865073  -0.71534534 162.45334925
Axis   0.03956990  -0.92529900  -0.37716838
Axis point 158.55880471   0.00000000  92.42576286
Rotation angle (degrees) 178.95488392
Shift along axis  -4.91780500

I am clearly missing something, how should I interpret the translation vector output by fitmap?