Sensible Box sizes
Optimal box sizes in terms of processing times. This information has been taken directly from the eman2 website, https://blake.bcm.edu/emanwiki/EMAN2/BoxSize
Particle Box Size
List of good box sizes: :
16, 24, 32, 36, 40, 44, 48, 52, 56, 60, 64, 72, 84, 96, 100, 104, 112, 120, 128, 132, 140, 168, 180, 192, 196, 208, 216, 220, 224, 240, 256, 260, 288, 300, 320, 352, 360, 384, 416, 440, 448, 480, 512, 540, 560, 576, 588, 600, 630, 640, 648, 672, 686, 700, 720, 750, 756, 768, 784, 800, 810, 840, 864, 882, 896, 900, 960, 972, 980, 1000, 1008, 1024
for traditional single particle analysis. If you were to pick a size not on this list, moving up to the next number on the list would make your refinement FASTER, sometimes MUCH faster. For example, refinements would take almost 2x longer with a box size of 134 as compared to 136
These sizes are less well tested, but also probably good: 1050, 1080, 1120, 1134, 1152, 1176, 1200, 1250, 1260, 1280, 1296, 1344, 1350, 1372, 1400, 1440, 1458, 1470, 1500, 1512, 1536, 1568, 1600, 1620, 1680, 1728, 1750, 1764, 1792, 1800, 1890, 1920, 1944, 1960, 2000, 2016, 2048, 2058, 2100, 2160, 2240, 2250, 2268, 2304, 2352, 2400, 2430, 2450, 2500, 2520, 2560, 2592, 2646, 2688, 2700, 2744, 2800, 2880, 2916, 2940, 3000, 3024, 3072, 3136, 3150, 3200, 3240, 3360, 3402, 3430, 3456, 3500, 3528, 3584, 3600, 3750, 3780, 3840, 3888, 3920, 4000, 4032, 4050, 4096
What box size should i go for?
Really difficult to say. It is important to go for a box that has a reasonable amount of background information to minimise information loss, as based on this formula from the JMB 2003 paper:
B = A + (2 * L *(dFoc / D))
A = particle diameter
L = wavelength, 0.02 A @ 300 kV
D = Target res.
A ballpark could be around 2 x particle size, but obviously depends on how much info you suspect that you will get from your data-if it is a negative stain collection, for instance, a massive box size really is not going to be helpful!