corrected_micrographs.star file entry 4, 5 and 6.

[fbonnet08]

Hi,

I have a question about the following relion keys:

_rlnAccumMotionTotal #4
_rlnAccumMotionEarly #5
_rlnAccumMotionLate #6

After the motion corr has been calculated using MotionCor2_v1.3.1-Cuda102 within Relion-3.1.0, in the corrected_micrographs.star star file we get entries such as:

MotionCorr/job016/Micrographs/FoilHole_18180471_Data_18181927_18181929_20200618_233150_fractions.mrc MotionCorr/job016/Micrographs/FoilHole_18180471_Data_18181927_18181929_20200618_233150_fractions.star 1 36.612271 8.74079
8 27.871472

for example.

which corresponds to
_rlnMicrographName #1
_rlnMicrographMetadata #2
_rlnOpticsGroup #3
_rlnAccumMotionTotal #4
_rlnAccumMotionEarly #5
_rlnAccumMotionLate #6

About #4, 5 and 6. Are these calculated inside relion following a parsing of the MotionCor2_v1.3.1-Cuda102 or a straight parsing?

If a straight parsing which file is being parsed?

If calculated within relion how are these calculated and from which input data log file coming from MotionCor2_v1.3.1-Cuda102?

Frederic.

[biochem-fan]

The trajectory is read from the standard output of UCSF MotionCor2, which is redirected to *.out.
The values are under Full-frame alignment shift.

Then shifts are integrated before/after 4e/A2 (or the value specified in --dose_motionstats_cutoff).

[fbonnet08]

Ok Thanks,
I see the values under Full-frame alignment shift

for the
_rlnAccumMotionTotal #4
_rlnAccumMotionEarly #5
_rlnAccumMotionLate #6
I get 36.612271 8.740798 27.871472 in the

In the .out for the Full-frame alignment shift I get the following

Full-frame alignment shift
...... Frame ( 1) shift: 0.000 0.000
...... Frame ( 2) shift: 2.660 -4.750
...... Frame ( 3) shift: 2.820 -6.760
...... Frame ( 4) shift: 3.340 -7.930
...... Frame ( 5) shift: 1.950 -8.090
...... Frame ( 6) shift: 1.980 -7.810
...... Frame ( 7) shift: 1.350 -8.110
...... Frame ( 8) shift: 0.810 -8.580
...... Frame ( 9) shift: 0.620 -8.280
...... Frame ( 10) shift: -0.020 -7.540
...... Frame ( 11) shift: -0.390 -7.470
...... Frame ( 12) shift: 0.330 -7.000
...... Frame ( 13) shift: -0.390 -7.550
...... Frame ( 14) shift: 0.000 -7.160
...... Frame ( 15) shift: -0.350 -7.120
...... Frame ( 16) shift: -0.590 -7.250
...... Frame ( 17) shift: -0.750 -7.430
...... Frame ( 18) shift: -0.390 -6.960
...... Frame ( 19) shift: -0.780 -6.350
...... Frame ( 20) shift: 0.000 -7.440
...... Frame ( 21) shift: -0.520 -7.410
...... Frame ( 22) shift: -0.070 -6.880
...... Frame ( 23) shift: -0.210 -6.920
...... Frame ( 24) shift: 0.610 -6.200
...... Frame ( 25) shift: -0.330 -6.700
...... Frame ( 26) shift: -0.280 -6.830
...... Frame ( 27) shift: -0.390 -6.480
...... Frame ( 28) shift: -0.460 -6.970
...... Frame ( 29) shift: -0.040 -6.750
...... Frame ( 30) shift: 0.140 -6.690
...... Frame ( 31) shift: -0.120 -6.800
...... Frame ( 32) shift: -0.090 -6.330
...... Frame ( 33) shift: -0.140 -6.300
...... Frame ( 34) shift: -0.270 -6.450
...... Frame ( 35) shift: 0.230 -5.590
...... Frame ( 36) shift: 0.230 -6.360
...... Frame ( 37) shift: 0.230 -6.590
...... Frame ( 38) shift: -0.170 -5.490
...... Frame ( 39) shift: 0.100 -5.740
...... Frame ( 40) shift: -0.430 -6.240
...... Frame ( 41) shift: -0.370 -6.000
...... Frame ( 42) shift: -0.790 -5.880
...... Frame ( 43) shift: -0.550 -5.370
...... Frame ( 44) shift: -0.860 -5.820
...... Frame ( 45) shift: -0.320 -5.680
...... Frame ( 46) shift: 0.180 -5.370
...... Frame ( 47) shift: -0.340 -5.260
...... Frame ( 48) shift: 0.290 -4.530
...... Frame ( 49) shift: -0.080 -5.340
...... Frame ( 50) shift: -0.470 -4.700
...... Frame ( 51) shift: -1.150 -4.850

Sorry, but how do you get 36.612271 8.740798 27.871472 ?

Frederic.

[biochem-fan]

Shift from frame 1 to 0 is sqrt((2.660 - 0.000)^ 2 + (-4.750 - 0.000)^2),
Shift from frame 2 to 1 is sqrt((2.820 - 2.660)^ 2 + (-6.760 + 4.750)^2)
and so on.

Add these shifts until 4 e/A2. That is Early. Add the others to get Late. Add both to get Total.

[fbonnet08]

I can see how the file:
Micrographs/FoilHole_18180471_Data_18181927_18181929_20200618_233150_fractions.star

is constructed.

If I understand this correctly:

shift 0 [1--->0]= sqrt((2.660 - 0.000)^ 2 + (-4.750 - 0.000)^2) = 5,444088537
shift 1 [2--->1]= sqrt((2.820 - 2.660)^ 2 + (-6.760 + 4.750)^2) = 2,016358103
....
shift i [i+1--->i]= sqrt((x_i - x_(i-1))^ 2 + (y_i - y_(i-1))^2) = s_i
....
shift 50 [51--->50]= sqrt((-1.150 - -0.470)^ 2 + (-4.850 - -4.700)^2) = 0,696347614

Sum_{i=0}^{50} (s_i) = Total

But I do not understand exactly what you mean numerically but understand what you roughly mean.
Add these shifts until 4 e/A2. That is Early.
Add the others to get Late.
Add both to get Total.

[biochem-fan]

If this is 1e/A2/frame, shift 0 to 4 becomes early motion. Shift 4 to the end becomes late motion.