The extraction box size calculation is critical for both accurate and efficient processing of your data. If an extraction box size is too large, computational time is increased. If too small, CTF signal is cut off and CTF correction is not done properly, resulting in a loss of expected resolution.
There are a few ways to determine the appropriate box size. The easiest to understand would be from the Jiang lab. In brief estimate your maximum particle diameter, add 150A. Account for the A/pix, and then select a good box size that is divisible for 2 and 4 for binning, and has low prime factors like 2, 3, 5, and 7. We do not need to select 150A, in fact we could do variations (pad by 20% of longest axis for example) and determine what would be the best through trial and error. I generally will do 120-140% of the predicted longest diameter of the particle and go from there. For this example we’ll stick with padding by 150A.
Lets deal with an example of a particle that is 100A long and during collection had an A/pix of 0.8.
Particle Size=100 A
Buffer size to add = 150 A
100 + 150 = 250 A new particle size.
We convert this value to pixels by dividing by the A/pix.
250 / 0.8 = 312.5
We can’t select such a box size. We will then select from a list of “Good Box Sizes”.
Good box sizes: 16, 20, 24, 28, 32, 36, 40, 48, 56, 60, 64, 72, 80, 84, 96, 100, 108, 112, 120, 128, 140, 144, 160, 168, 180, 192, 196, 200, 216, 224, 240, 252, 256, 280, 288, 300, 320, 324, 336, 360, 384, 392, 400, 420, 432, 448, 480, 500, 504, 512, 540, 560, 576, 588, 600, 640, 648, 672, 700, 720, 756, 768, 784, 800, 840, 864, 896, 900, 960, 972, 980, 1000, 1008, 1024, 1080, 1120, 1152, 1176, 1200, 1260, 1280, 1296, 1344, 1372, 1400, 1440, 1500, 1512, 1536, 1568, 1600, 1620, 1680, 1728, 1764, 1792, 1800, 1920, 1944, 1960, 2000
From this list we can either choose 300 or 320.