Table 4 CPU hours for combinations of voxel and angle spacing settings.

From: VESPER: global and local cryo-EM map alignment using local density vectors

 

Voxel Spacing (Ã…)

 

3

7

10

DOT score

   

Comp. Vector

8.09 (0.020)

1.21 (0.0029)

0.76 (0.0019)

Angle 10°

5643.2 (13.8)

158.9 (0.388)

44.5 (0.109)

Angle 30°

250.8 (0.612)

18.94 (0.0462)

8.42 (0.0205)

Angle 60°

129.9 (0.317)

13.39 (0.0327)

7.12 (0.0174)

Angle 90°

120.4 (0.294)

12.80 (0.0312)

6.93 (0.0169)

CC

G. kernel

7.42 (0.0181)

1.15 (0.0028)

0.74 (0.0018)

Angle 10°

2962.9 (7.227)

96.1 (0.234)

24.61 (0.060)

Angle 30°

197.5 (0.482)

14.6 (0.0355)

7.15 (0.0174)

Angle 60°

98.0 (0.239)

11.5 (0.0280)

6.49 (0.0158)

Angle 90°

93.3 (0.227)

11.2 (0.0274)

2.82 (0.0069)

  1. For each voxel spacing and angle spacing combination, the average CPU hours by VESPER on global map search for three query maps, EMD-3661, EMD-8724, and EMD-1203, against the global map dataset of 410 maps. The upper half of the table shows times for using the DOT score while the latter half shows the times for using CC. Comp. Vector in the DOT score category shows the computational time needed for computing vector representation of the 410 maps. G. kernel in the CC category shows the time needed for applying the Gaussian kernel (Eq. (2)) to the 410 maps. The values shown are an average for processing the 410 maps and 410 comparisons. The times for preparing one file or comparing a pair of maps are shown in parentheses.
  2. gmfit took 72.7 CPU hours for computing the Gaussian mixture models and search by gmfit took 0.09 CPU hours. Fitmap took 14.7 CPU hours. 3DZD took 0.2 CPU hours, among which the 3DZD computation took almost all the time. We used Intel Xeon E5 processor@2.60 GHz with 128 GB memory on the Halstead cluster computer at Purdue to measure the times.
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